Starting phenix.real_space_refine (version: dev) on Fri Feb 24 00:33:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6l_33023/02_2023/7x6l_33023.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6l_33023/02_2023/7x6l_33023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6l_33023/02_2023/7x6l_33023.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6l_33023/02_2023/7x6l_33023.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6l_33023/02_2023/7x6l_33023.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6l_33023/02_2023/7x6l_33023.pdb" } resolution = 3.7 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= 0.002 sd= 0.033 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 Process input model Symmetric amino acids flipped Residue "I PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 72": "NH1" <-> "NH2" Residue "I PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 21486 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "K" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "A" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2461 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 299} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 164} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "J" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "C" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2461 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 299} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 164} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1719 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 218} Chain: "L" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1635 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "D" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2461 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 299} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1347 Classifications: {'peptide': 165} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 164} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 12.03, per 1000 atoms: 0.56 Number of scatterers: 21486 At special positions: 0 Unit cell: (175.294, 175.294, 142.344, 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 102 16.00 O 4257 8.00 N 3705 7.00 C 13422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 102 " - pdb=" SG CYS I 107 " distance=2.03 Simple disulfide: pdb=" SG CYS I 157 " - pdb=" SG CYS I 213 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 102 " - pdb=" SG CYS G 107 " distance=2.03 Simple disulfide: pdb=" SG CYS G 157 " - pdb=" SG CYS G 213 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS E 137 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 107 " distance=2.03 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 213 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 277 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 76 " distance=2.03 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 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: 8.10 Conformation dependent library (CDL) restraints added in 3.2 seconds 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 63 sheets defined 15.1% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'I' and resid 204 through 206 No H-bonds generated for 'chain 'I' and resid 204 through 206' Processing helix chain 'K' and resid 121 through 126 removed outlier: 3.600A pdb=" N LYS K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 189 removed outlier: 3.710A pdb=" N GLU K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS K 189 " --> pdb=" O ASP K 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.505A pdb=" N GLY A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.987A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.578A pdb=" N LEU A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 109 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 113 " --> pdb=" O ARG A 109 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.690A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 54 removed outlier: 4.041A pdb=" N GLN B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 51 " --> pdb=" O GLN B 47 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 124 removed outlier: 3.791A pdb=" N GLU B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 162 through 171 removed outlier: 3.610A pdb=" N ALA B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'J' and resid 121 through 126 removed outlier: 3.511A pdb=" N LEU J 125 " --> pdb=" O SER J 121 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS J 126 " --> pdb=" O ASP J 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 121 through 126' Processing helix chain 'J' and resid 183 through 189 removed outlier: 3.722A pdb=" N GLU J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS J 189 " --> pdb=" O ASP J 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.985A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.615A pdb=" N LEU C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 109 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.692A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 54 removed outlier: 4.043A pdb=" N GLN E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS E 51 " --> pdb=" O GLN E 47 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 124 removed outlier: 3.650A pdb=" N GLU E 81 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E 83 " --> pdb=" O ASP E 79 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA E 101 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 154 removed outlier: 3.501A pdb=" N ILE E 152 " --> pdb=" O CYS E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 171 removed outlier: 3.624A pdb=" N ALA E 166 " --> pdb=" O TYR E 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN E 168 " --> pdb=" O ASP E 164 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE E 171 " --> pdb=" O LEU E 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.515A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 121 through 126' Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.709A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 73 through 80 removed outlier: 3.984A pdb=" N ASP D 77 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL D 78 " --> pdb=" O HIS D 75 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN D 80 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 116 removed outlier: 3.653A pdb=" N LEU D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG D 109 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.684A pdb=" N GLN D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 54 removed outlier: 4.012A pdb=" N GLN F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS F 51 " --> pdb=" O GLN F 47 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG F 54 " --> pdb=" O GLY F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 124 removed outlier: 3.760A pdb=" N GLU F 81 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA F 101 " --> pdb=" O GLU F 97 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 162 through 171 removed outlier: 3.612A pdb=" N ALA F 166 " --> pdb=" O TYR F 162 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASN F 168 " --> pdb=" O ASP F 164 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.518A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N CYS I 22 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU I 79 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.678A pdb=" N THR I 124 " --> pdb=" O TYR I 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR I 94 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL I 126 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA I 92 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N MET I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 97 through 98 removed outlier: 3.899A pdb=" N VAL I 119 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 137 through 140 removed outlier: 3.999A pdb=" N VAL I 201 " --> pdb=" O ALA I 153 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU I 155 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 197 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR I 193 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 137 through 140 removed outlier: 3.999A pdb=" N VAL I 201 " --> pdb=" O ALA I 153 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU I 155 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 197 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR I 193 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 168 through 171 removed outlier: 3.678A pdb=" N THR I 168 " --> pdb=" O ASN I 216 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN I 216 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR I 211 " --> pdb=" O VAL I 228 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS I 226 " --> pdb=" O CYS I 213 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL I 215 " --> pdb=" O VAL I 224 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR I 222 " --> pdb=" O HIS I 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 7 removed outlier: 3.961A pdb=" N CYS K 23 " --> pdb=" O PHE K 71 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.209A pdb=" N VAL K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 114 through 118 removed outlier: 3.747A pdb=" N ASN K 137 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL K 133 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA K 130 " --> pdb=" O LEU K 181 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL K 132 " --> pdb=" O LEU K 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 145 through 150 removed outlier: 3.783A pdb=" N LYS K 149 " --> pdb=" O ALA K 193 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS K 207 " --> pdb=" O CYS K 194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.546A pdb=" N GLY B 33 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY B 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 16 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B 25 " --> pdb=" O CYS A 14 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 14 " --> pdb=" O ARG B 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 24 through 26 removed outlier: 3.825A pdb=" N THR A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 34 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AB5, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.583A pdb=" N GLN A 44 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.726A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 58 through 61 removed outlier: 5.692A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 136 through 141 removed outlier: 5.197A pdb=" N CYS A 139 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY A 144 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.735A pdb=" N GLY A 181 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 235 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A 180 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 229 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.735A pdb=" N GLY A 181 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.646A pdb=" N LEU A 164 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 247 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 166 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 245 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 281 through 282 removed outlier: 3.579A pdb=" N ILE A 282 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 302 " --> pdb=" O ILE A 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.517A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS G 22 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU G 79 " --> pdb=" O CYS G 22 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.510A pdb=" N GLY G 10 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR G 124 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR G 94 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 126 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA G 92 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL G 93 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N MET G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TYR G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 97 through 98 removed outlier: 3.915A pdb=" N VAL G 119 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 137 through 140 removed outlier: 4.015A pdb=" N VAL G 201 " --> pdb=" O ALA G 153 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU G 155 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER G 197 " --> pdb=" O CYS G 157 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP G 161 " --> pdb=" O TYR G 193 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR G 193 " --> pdb=" O ASP G 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 198 " --> pdb=" O HIS G 181 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 137 through 140 removed outlier: 4.015A pdb=" N VAL G 201 " --> pdb=" O ALA G 153 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU G 155 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER G 197 " --> pdb=" O CYS G 157 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP G 161 " --> pdb=" O TYR G 193 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR G 193 " --> pdb=" O ASP G 161 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 168 through 171 removed outlier: 3.662A pdb=" N THR G 168 " --> pdb=" O ASN G 216 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN G 216 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR G 211 " --> pdb=" O VAL G 228 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 226 " --> pdb=" O CYS G 213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL G 215 " --> pdb=" O VAL G 224 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR G 222 " --> pdb=" O HIS G 217 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 6 through 7 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.228A pdb=" N VAL J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 114 through 118 removed outlier: 3.714A pdb=" N ASN J 137 " --> pdb=" O SER J 114 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL J 133 " --> pdb=" O PHE J 118 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 130 " --> pdb=" O LEU J 181 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL J 132 " --> pdb=" O LEU J 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 145 through 150 removed outlier: 3.799A pdb=" N LYS J 149 " --> pdb=" O ALA J 193 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR J 192 " --> pdb=" O PHE J 209 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS J 207 " --> pdb=" O CYS J 194 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 31 through 35 removed outlier: 3.545A pdb=" N GLY E 33 " --> pdb=" O HIS E 26 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY E 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY C 16 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG E 25 " --> pdb=" O CYS C 14 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS C 14 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.832A pdb=" N THR C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C 34 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AD8, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.544A pdb=" N GLN C 44 " --> pdb=" O PHE C 294 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.712A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 58 through 61 removed outlier: 5.706A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 136 through 141 removed outlier: 5.217A pdb=" N CYS C 139 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY C 144 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.755A pdb=" N GLY C 181 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR C 235 " --> pdb=" O TYR C 178 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP C 180 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 229 " --> pdb=" O HIS C 184 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.755A pdb=" N GLY C 181 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.691A pdb=" N VAL C 166 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 245 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 281 through 282 removed outlier: 3.656A pdb=" N ILE C 282 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 302 " --> pdb=" O ILE C 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.521A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.685A pdb=" N THR H 124 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR H 94 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL H 126 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA H 92 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 97 through 98 removed outlier: 3.923A pdb=" N VAL H 119 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 137 through 140 removed outlier: 4.012A pdb=" N VAL H 201 " --> pdb=" O ALA H 153 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU H 155 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H 197 " --> pdb=" O CYS H 157 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP H 161 " --> pdb=" O TYR H 193 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 137 through 140 removed outlier: 4.012A pdb=" N VAL H 201 " --> pdb=" O ALA H 153 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU H 155 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H 197 " --> pdb=" O CYS H 157 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP H 161 " --> pdb=" O TYR H 193 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 168 through 171 removed outlier: 3.689A pdb=" N THR H 168 " --> pdb=" O ASN H 216 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN H 216 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR H 211 " --> pdb=" O VAL H 228 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS H 226 " --> pdb=" O CYS H 213 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 215 " --> pdb=" O VAL H 224 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR H 222 " --> pdb=" O HIS H 217 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 6 through 7 removed outlier: 3.886A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.218A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.708A pdb=" N ASN L 137 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA L 130 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL L 132 " --> pdb=" O LEU L 179 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 145 through 150 removed outlier: 3.790A pdb=" N LYS L 149 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 31 through 35 removed outlier: 3.589A pdb=" N GLY F 33 " --> pdb=" O HIS F 26 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY F 23 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY D 16 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG F 25 " --> pdb=" O CYS D 14 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS D 14 " --> pdb=" O ARG F 25 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 24 through 26 removed outlier: 3.832A pdb=" N THR D 24 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 34 " --> pdb=" O VAL D 26 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AG2, first strand: chain 'D' and resid 43 through 44 removed outlier: 3.564A pdb=" N GLN D 44 " --> pdb=" O PHE D 294 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 51 through 54 removed outlier: 5.710A pdb=" N ILE D 51 " --> pdb=" O ASP D 275 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N CYS D 277 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN D 53 " --> pdb=" O CYS D 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'D' and resid 58 through 61 removed outlier: 5.700A pdb=" N PHE D 87 " --> pdb=" O MET D 268 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 136 through 141 removed outlier: 5.177A pdb=" N CYS D 139 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY D 144 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.788A pdb=" N GLY D 181 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE D 179 " --> pdb=" O PRO D 254 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 235 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TRP D 180 " --> pdb=" O TYR D 233 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 229 " --> pdb=" O HIS D 184 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 151 through 153 removed outlier: 3.788A pdb=" N GLY D 181 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE D 179 " --> pdb=" O PRO D 254 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 166 through 169 removed outlier: 3.693A pdb=" N VAL D 166 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE D 245 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 281 through 282 removed outlier: 3.553A pdb=" N ILE D 282 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR D 302 " --> pdb=" O ILE D 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 653 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.05 Time building geometry restraints manager: 8.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3618 1.32 - 1.44: 6018 1.44 - 1.57: 12174 1.57 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 21945 Sorted by residual: bond pdb=" C PRO A 324 " pdb=" O PRO A 324 " ideal model delta sigma weight residual 1.235 1.194 0.041 1.30e-02 5.92e+03 9.96e+00 bond pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 1.469 1.442 0.026 1.28e-02 6.10e+03 4.19e+00 bond pdb=" CA PRO A 324 " pdb=" C PRO A 324 " ideal model delta sigma weight residual 1.520 1.498 0.021 1.42e-02 4.96e+03 2.26e+00 bond pdb=" C LYS H 218 " pdb=" N PRO H 219 " ideal model delta sigma weight residual 1.337 1.352 -0.016 1.06e-02 8.90e+03 2.23e+00 bond pdb=" CA PRO A 324 " pdb=" CB PRO A 324 " ideal model delta sigma weight residual 1.533 1.513 0.020 1.42e-02 4.96e+03 2.05e+00 ... (remaining 21940 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.73: 474 105.73 - 112.79: 11742 112.79 - 119.85: 6865 119.85 - 126.91: 10416 126.91 - 133.98: 293 Bond angle restraints: 29790 Sorted by residual: angle pdb=" C SER J 67 " pdb=" CA SER J 67 " pdb=" CB SER J 67 " ideal model delta sigma weight residual 116.54 110.06 6.48 1.46e+00 4.69e-01 1.97e+01 angle pdb=" C PRO A 324 " pdb=" N GLU A 325 " pdb=" CA GLU A 325 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C VAL A 323 " pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 119.84 116.15 3.69 1.25e+00 6.40e-01 8.70e+00 angle pdb=" CA SER J 67 " pdb=" C SER J 67 " pdb=" N GLY J 68 " ideal model delta sigma weight residual 118.57 116.17 2.40 8.80e-01 1.29e+00 7.41e+00 angle pdb=" CA LYS H 218 " pdb=" C LYS H 218 " pdb=" N PRO H 219 " ideal model delta sigma weight residual 118.44 122.36 -3.92 1.59e+00 3.96e-01 6.08e+00 ... (remaining 29785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 12808 17.48 - 34.96: 305 34.96 - 52.44: 41 52.44 - 69.93: 7 69.93 - 87.41: 3 Dihedral angle restraints: 13164 sinusoidal: 5175 harmonic: 7989 Sorted by residual: dihedral pdb=" CA PRO A 324 " pdb=" C PRO A 324 " pdb=" N GLU A 325 " pdb=" CA GLU A 325 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" N CYS D 76 " pdb=" CA CYS D 76 " pdb=" CB CYS D 76 " pdb=" SG CYS D 76 " ideal model delta sinusoidal sigma weight residual 60.00 1.20 58.80 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N CYS A 76 " pdb=" CA CYS A 76 " pdb=" CB CYS A 76 " pdb=" SG CYS A 76 " ideal model delta sinusoidal sigma weight residual 60.00 1.32 58.68 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 13161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2701 0.048 - 0.096: 394 0.096 - 0.144: 210 0.144 - 0.191: 3 0.191 - 0.239: 1 Chirality restraints: 3309 Sorted by residual: chirality pdb=" CA PRO A 324 " pdb=" N PRO A 324 " pdb=" C PRO A 324 " pdb=" CB PRO A 324 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA LYS G 218 " pdb=" N LYS G 218 " pdb=" C LYS G 218 " pdb=" CB LYS G 218 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA LYS I 218 " pdb=" N LYS I 218 " pdb=" C LYS I 218 " pdb=" CB LYS I 218 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 3306 not shown) Planarity restraints: 3876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 323 " 0.086 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO A 324 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 323 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C VAL A 323 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 323 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO A 324 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 238 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 239 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 239 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 239 " -0.021 5.00e-02 4.00e+02 ... (remaining 3873 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6063 2.81 - 3.33: 15982 3.33 - 3.86: 36058 3.86 - 4.38: 39232 4.38 - 4.90: 69614 Nonbonded interactions: 166949 Sorted by model distance: nonbonded pdb=" OG1 THR A 283 " pdb=" O GLY A 286 " model vdw 2.291 2.440 nonbonded pdb=" OG1 THR D 283 " pdb=" O GLY D 286 " model vdw 2.292 2.440 nonbonded pdb=" OG1 THR C 283 " pdb=" O GLY C 286 " model vdw 2.294 2.440 nonbonded pdb=" O GLU E 103 " pdb=" OG1 THR E 107 " model vdw 2.309 2.440 nonbonded pdb=" O GLU B 103 " pdb=" OG1 THR B 107 " model vdw 2.310 2.440 ... (remaining 166944 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 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } 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 102 5.16 5 C 13422 2.51 5 N 3705 2.21 5 O 4257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.590 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: 0.010 Extract box with map and model: 4.440 Check model and map are aligned: 0.320 Process input model: 54.010 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.200 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5634 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 : 0.002 0.041 21945 Z= 0.131 Angle : 0.446 7.459 29790 Z= 0.261 Chirality : 0.041 0.239 3309 Planarity : 0.005 0.133 3876 Dihedral : 7.433 87.406 7953 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.92 % Favored : 97.89 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.13), residues: 2754 helix: -4.45 (0.08), residues: 303 sheet: -1.05 (0.17), residues: 807 loop : -2.13 (0.13), residues: 1644 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 694 time to evaluate : 2.560 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 14 residues processed: 730 average time/residue: 0.3633 time to fit residues: 400.2839 Evaluate side-chains 577 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 563 time to evaluate : 2.535 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.1931 time to fit residues: 8.8227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 211 optimal weight: 0.0020 chunk 81 optimal weight: 0.4980 chunk 128 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 245 optimal weight: 2.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN I 181 HIS ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN K 90 GLN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 GLN A 53 ASN A 56 HIS A 250 ASN A 290 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN G 33 ASN G 56 ASN ** G 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN ** J 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN C 250 ASN C 285 ASN ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 HIS ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN H 106 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN L 160 GLN D 56 HIS D 285 ASN ** F 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 HIS ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 21945 Z= 0.226 Angle : 0.633 12.941 29790 Z= 0.325 Chirality : 0.045 0.185 3309 Planarity : 0.005 0.072 3876 Dihedral : 3.548 19.416 3000 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.14 % Favored : 97.75 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.15), residues: 2754 helix: -2.01 (0.22), residues: 351 sheet: -0.63 (0.18), residues: 801 loop : -1.58 (0.14), residues: 1602 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 617 time to evaluate : 2.477 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 outliers start: 58 outliers final: 37 residues processed: 639 average time/residue: 0.3653 time to fit residues: 347.8814 Evaluate side-chains 608 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 571 time to evaluate : 2.436 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 2 residues processed: 37 average time/residue: 0.2249 time to fit residues: 18.1335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 197 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN A 250 ASN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 160 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN L 166 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.145 21945 Z= 0.505 Angle : 0.868 12.339 29790 Z= 0.468 Chirality : 0.051 0.305 3309 Planarity : 0.007 0.065 3876 Dihedral : 5.379 33.017 3000 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.90 % Rotamer Outliers : 3.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.83 % Twisted General : 0.04 % 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: -1.97 (0.15), residues: 2754 helix: -1.14 (0.24), residues: 378 sheet: -0.66 (0.17), residues: 870 loop : -1.76 (0.15), residues: 1506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 631 time to evaluate : 2.417 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 outliers start: 94 outliers final: 64 residues processed: 671 average time/residue: 0.3513 time to fit residues: 354.9698 Evaluate side-chains 653 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 589 time to evaluate : 2.451 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 2 residues processed: 64 average time/residue: 0.2080 time to fit residues: 28.0620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 242 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 127 optimal weight: 0.0170 chunk 27 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 260 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 233 optimal weight: 0.0270 chunk 70 optimal weight: 0.9980 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN G 106 ASN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6119 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 21945 Z= 0.210 Angle : 0.638 11.047 29790 Z= 0.330 Chirality : 0.045 0.268 3309 Planarity : 0.005 0.052 3876 Dihedral : 4.507 26.680 3000 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.49 % Favored : 96.41 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.15), residues: 2754 helix: -0.36 (0.26), residues: 372 sheet: -0.63 (0.17), residues: 804 loop : -1.54 (0.15), residues: 1578 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 606 time to evaluate : 2.679 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 outliers start: 48 outliers final: 32 residues processed: 623 average time/residue: 0.3719 time to fit residues: 346.1756 Evaluate side-chains 612 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 580 time to evaluate : 2.490 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 2 residues processed: 32 average time/residue: 0.2584 time to fit residues: 19.1388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 217 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 65 optimal weight: 0.0470 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 GLN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 GLN C 44 GLN ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS E 168 ASN H 188 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.096 21945 Z= 0.322 Angle : 0.706 11.051 29790 Z= 0.368 Chirality : 0.047 0.299 3309 Planarity : 0.005 0.068 3876 Dihedral : 4.897 27.861 3000 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.34 % Favored : 94.55 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.15), residues: 2754 helix: -0.64 (0.25), residues: 378 sheet: -0.52 (0.18), residues: 783 loop : -1.65 (0.14), residues: 1593 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 599 time to evaluate : 2.675 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 outliers start: 63 outliers final: 37 residues processed: 625 average time/residue: 0.3699 time to fit residues: 346.9617 Evaluate side-chains 615 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 578 time to evaluate : 2.476 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 2 residues processed: 37 average time/residue: 0.2590 time to fit residues: 19.9109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 87 optimal weight: 4.9990 chunk 235 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 ASN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 ASN H 188 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.103 21945 Z= 0.343 Angle : 0.733 11.543 29790 Z= 0.381 Chirality : 0.047 0.271 3309 Planarity : 0.005 0.062 3876 Dihedral : 5.136 28.480 3000 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.88 % Favored : 94.01 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.15), residues: 2754 helix: -0.70 (0.25), residues: 369 sheet: -0.51 (0.17), residues: 801 loop : -1.73 (0.14), residues: 1584 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 587 time to evaluate : 2.457 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 outliers start: 61 outliers final: 32 residues processed: 610 average time/residue: 0.3593 time to fit residues: 327.0726 Evaluate side-chains 605 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 573 time to evaluate : 2.516 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 2 residues processed: 32 average time/residue: 0.2079 time to fit residues: 15.7483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 251 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 190 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 219 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 260 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN A 81 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN F 106 HIS F 146 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 21945 Z= 0.221 Angle : 0.683 14.268 29790 Z= 0.348 Chirality : 0.046 0.306 3309 Planarity : 0.004 0.054 3876 Dihedral : 4.790 24.829 3000 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.99 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.15), residues: 2754 helix: -0.41 (0.25), residues: 363 sheet: -0.48 (0.17), residues: 864 loop : -1.64 (0.15), residues: 1527 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 577 time to evaluate : 2.502 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 outliers start: 34 outliers final: 22 residues processed: 592 average time/residue: 0.3640 time to fit residues: 320.3098 Evaluate side-chains 590 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 568 time to evaluate : 2.473 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 2 residues processed: 22 average time/residue: 0.2520 time to fit residues: 12.7851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 160 optimal weight: 0.9980 chunk 103 optimal weight: 0.2980 chunk 155 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 0.0060 chunk 50 optimal weight: 0.4980 chunk 165 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 204 optimal weight: 0.9980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN F 106 HIS F 146 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 21945 Z= 0.191 Angle : 0.682 15.247 29790 Z= 0.345 Chirality : 0.046 0.290 3309 Planarity : 0.004 0.079 3876 Dihedral : 4.608 25.241 3000 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.50 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 2754 helix: -0.25 (0.26), residues: 366 sheet: -0.33 (0.17), residues: 861 loop : -1.65 (0.15), residues: 1527 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 575 time to evaluate : 2.490 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 outliers start: 27 outliers final: 20 residues processed: 584 average time/residue: 0.3828 time to fit residues: 337.7554 Evaluate side-chains 579 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 559 time to evaluate : 2.544 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 20 average time/residue: 0.2443 time to fit residues: 12.5132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 236 optimal weight: 9.9990 chunk 249 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 242 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 190 optimal weight: 0.0670 chunk 74 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 229 optimal weight: 0.9990 chunk 241 optimal weight: 5.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 GLN ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 GLN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.6711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.109 21945 Z= 0.382 Angle : 0.800 12.195 29790 Z= 0.418 Chirality : 0.049 0.296 3309 Planarity : 0.005 0.072 3876 Dihedral : 5.313 31.515 3000 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.61 % Favored : 93.28 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.83 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.15), residues: 2754 helix: -0.74 (0.25), residues: 363 sheet: -0.27 (0.17), residues: 861 loop : -1.83 (0.15), residues: 1530 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 572 time to evaluate : 2.560 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 outliers start: 32 outliers final: 23 residues processed: 583 average time/residue: 0.3594 time to fit residues: 314.2812 Evaluate side-chains 583 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 560 time to evaluate : 2.503 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 2 residues processed: 23 average time/residue: 0.1970 time to fit residues: 12.2996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 159 optimal weight: 0.4980 chunk 256 optimal weight: 8.9990 chunk 156 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 268 optimal weight: 0.6980 chunk 247 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 HIS A 81 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 166 GLN C 80 GLN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 21945 Z= 0.233 Angle : 0.735 17.654 29790 Z= 0.374 Chirality : 0.047 0.292 3309 Planarity : 0.005 0.063 3876 Dihedral : 4.976 25.227 3000 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.50 % Favored : 95.39 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.15), residues: 2754 helix: -0.56 (0.26), residues: 363 sheet: -0.32 (0.17), residues: 879 loop : -1.79 (0.15), residues: 1512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5508 Ramachandran restraints generated. 2754 Oldfield, 0 Emsley, 2754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 558 time to evaluate : 2.484 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 outliers start: 14 outliers final: 7 residues processed: 561 average time/residue: 0.3714 time to fit residues: 310.2501 Evaluate side-chains 550 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 543 time to evaluate : 2.702 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.3023 time to fit residues: 7.2916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 170 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 214 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** I 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 HIS ** L 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN F 106 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.168300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.142012 restraints weight = 36105.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.147617 restraints weight = 17918.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.151238 restraints weight = 10295.431| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.6937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.093 21945 Z= 0.312 Angle : 0.777 15.918 29790 Z= 0.400 Chirality : 0.049 0.393 3309 Planarity : 0.005 0.068 3876 Dihedral : 5.276 28.363 3000 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.83 % Favored : 93.06 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.15), residues: 2754 helix: -0.71 (0.25), residues: 363 sheet: -0.33 (0.18), residues: 867 loop : -1.83 (0.15), residues: 1524 =============================================================================== Job complete usr+sys time: 5842.67 seconds wall clock time: 105 minutes 55.26 seconds (6355.26 seconds total)