Starting phenix.real_space_refine on Mon Mar 18 17:40:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/03_2024/7x6o_33024.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/03_2024/7x6o_33024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/03_2024/7x6o_33024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/03_2024/7x6o_33024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/03_2024/7x6o_33024.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6o_33024/03_2024/7x6o_33024.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 13581 2.51 5 N 3678 2.21 5 O 4254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 67": "NH1" <-> "NH2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 67": "NH1" <-> "NH2" 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 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 24": "NH1" <-> "NH2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 49": "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 98": "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 "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J ARG 72": "NH1" <-> "NH2" Residue "J PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "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 98": "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" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21609 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain breaks: 1 Chain: "B" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1335 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "C" 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: "D" 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: "E" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain breaks: 1 Chain: "G" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1335 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} 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: "F" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2514 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 301} Chain breaks: 1 Chain: "H" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1335 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 1, 'TRANS': 163} Chain: "J" 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} Time building chain proxies: 11.30, per 1000 atoms: 0.52 Number of scatterers: 21609 At special positions: 0 Unit cell: (185.838, 176.612, 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 96 16.00 O 4254 8.00 N 3678 7.00 C 13581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 285 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 107 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 285 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 146 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 313 " distance=2.03 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 148 " distance=2.03 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 F 52 " - pdb=" SG CYS F 285 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 100 " - pdb=" SG CYS F 146 " distance=2.03 Simple disulfide: pdb=" SG CYS F 289 " - pdb=" SG CYS F 313 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 148 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 102 " - pdb=" SG CYS J 107 " distance=2.03 Simple disulfide: pdb=" SG CYS J 157 " - pdb=" SG CYS J 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 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: 6.82 Conformation dependent library (CDL) restraints added in 4.3 seconds 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5142 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 60 sheets defined 15.6% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.610A pdb=" N LEU A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.830A pdb=" N GLU A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 removed outlier: 3.675A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 removed outlier: 3.510A pdb=" N GLN A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 53 removed outlier: 3.541A pdb=" N ILE B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 124 removed outlier: 3.941A pdb=" N LEU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 96 " --> pdb=" O TRP B 92 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.620A pdb=" N VAL B 152 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS B 153 " --> pdb=" O MET B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 167 removed outlier: 3.799A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 166 " --> pdb=" O TYR B 162 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.767A pdb=" N THR C 91 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.963A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.643A pdb=" N LEU D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 121 through 126' Processing helix chain 'D' and resid 183 through 187 removed outlier: 3.818A pdb=" N GLU D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 183 through 187' Processing helix chain 'D' and resid 212 through 214 No H-bonds generated for 'chain 'D' and resid 212 through 214' Processing helix chain 'E' and resid 66 through 72 removed outlier: 3.606A pdb=" N LEU E 72 " --> pdb=" O ALA E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 78 removed outlier: 3.777A pdb=" N GLU E 78 " --> pdb=" O PRO E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 115 removed outlier: 3.667A pdb=" N LEU E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 removed outlier: 3.540A pdb=" N GLN E 199 " --> pdb=" O THR E 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 53 Processing helix chain 'G' and resid 74 through 124 removed outlier: 3.790A pdb=" N LEU G 80 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 87 " --> pdb=" O LYS G 83 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA G 96 " --> pdb=" O TRP G 92 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU G 97 " --> pdb=" O THR G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 155 removed outlier: 3.643A pdb=" N VAL G 152 " --> pdb=" O CYS G 148 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS G 153 " --> pdb=" O MET G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 167 removed outlier: 3.628A pdb=" N TYR G 162 " --> pdb=" O ASP G 158 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU G 165 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA G 166 " --> pdb=" O TYR G 162 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS G 167 " --> pdb=" O SER G 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.788A pdb=" N THR I 91 " --> pdb=" O ASP I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'K' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 126 removed outlier: 3.671A pdb=" N LEU K 125 " --> pdb=" O SER K 121 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 121 through 126' Processing helix chain 'K' and resid 183 through 189 removed outlier: 3.799A pdb=" N GLU K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS K 188 " --> pdb=" O ALA K 184 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS K 189 " --> pdb=" O ASP K 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 183 through 189' Processing helix chain 'K' and resid 212 through 214 No H-bonds generated for 'chain 'K' and resid 212 through 214' Processing helix chain 'F' and resid 66 through 72 removed outlier: 3.623A pdb=" N LEU F 72 " --> pdb=" O ALA F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 78 removed outlier: 3.729A pdb=" N GLU F 78 " --> pdb=" O PRO F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 115 removed outlier: 3.669A pdb=" N LEU F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 202 removed outlier: 3.532A pdb=" N GLN F 199 " --> pdb=" O THR F 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 53 Processing helix chain 'H' and resid 74 through 124 removed outlier: 3.804A pdb=" N LEU H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY H 87 " --> pdb=" O LYS H 83 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA H 96 " --> pdb=" O TRP H 92 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU H 97 " --> pdb=" O THR H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 155 removed outlier: 3.648A pdb=" N VAL H 152 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS H 153 " --> pdb=" O MET H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 167 removed outlier: 3.773A pdb=" N TYR H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU H 164 " --> pdb=" O PRO H 160 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLU H 165 " --> pdb=" O LYS H 161 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA H 166 " --> pdb=" O TYR H 162 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.791A pdb=" N THR J 91 " --> pdb=" O ASP J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 175 No H-bonds generated for 'chain 'J' and resid 173 through 175' Processing helix chain 'J' and resid 204 through 206 No H-bonds generated for 'chain 'J' and resid 204 through 206' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.965A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.623A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 3.583A 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 187 removed outlier: 3.804A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 183 through 187' Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 36 removed outlier: 3.509A pdb=" N GLY B 33 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS A 14 " --> pdb=" O HIS B 25 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 139 " --> pdb=" O LYS B 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 7.453A pdb=" N LEU A 51 " --> pdb=" O CYS A 285 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THR A 287 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LYS A 53 " --> pdb=" O THR A 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 60 through 61 removed outlier: 7.699A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.514A pdb=" N ALA A 266 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LEU A 186 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.514A pdb=" N ALA A 266 " --> pdb=" O GLU A 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 171 through 176 removed outlier: 3.514A pdb=" N ALA A 254 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A 175 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 211 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 294 through 296 removed outlier: 3.651A pdb=" N THR A 291 " --> pdb=" O GLY A 294 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 296 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS A 289 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR B 64 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.878A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.928A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR C 127 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 12 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.928A pdb=" N GLY C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR C 127 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 12 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 97 " --> pdb=" O ASN C 35 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG C 98 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N GLY C 116 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 137 through 140 removed outlier: 3.641A pdb=" N SER C 197 " --> pdb=" O CYS C 157 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR C 193 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 198 " --> pdb=" O HIS C 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 137 through 140 removed outlier: 3.641A pdb=" N SER C 197 " --> pdb=" O CYS C 157 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TYR C 193 " --> pdb=" O ASP C 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 167 through 171 removed outlier: 3.746A pdb=" N TYR C 211 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.513A pdb=" N SER D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.454A pdb=" N VAL D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR D 49 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 118 removed outlier: 3.639A pdb=" N ASN D 137 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN D 138 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 145 through 150 removed outlier: 3.641A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 149 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR D 192 " --> pdb=" O PHE D 209 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 207 " --> pdb=" O CYS D 194 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 32 through 36 removed outlier: 3.528A pdb=" N GLY G 33 " --> pdb=" O HIS G 26 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS E 14 " --> pdb=" O HIS G 25 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU G 139 " --> pdb=" O LYS G 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AC5, first strand: chain 'E' and resid 39 through 40 Processing sheet with id=AC6, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC7, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.559A pdb=" N LEU E 51 " --> pdb=" O HIS E 283 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N CYS E 285 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 60 through 61 removed outlier: 7.683A pdb=" N LEU E 60 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.586A pdb=" N ALA E 266 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU E 186 " --> pdb=" O PRO E 261 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 122 through 124 removed outlier: 3.586A pdb=" N ALA E 266 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 171 through 176 removed outlier: 3.619A pdb=" N TYR E 175 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 211 " --> pdb=" O LYS E 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 294 through 296 removed outlier: 3.531A pdb=" N THR E 291 " --> pdb=" O GLY E 294 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 296 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS E 289 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 310 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR G 64 " --> pdb=" O GLY E 311 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.868A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.842A pdb=" N GLY I 10 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR I 127 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 12 " --> pdb=" O THR I 127 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N MET I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.842A pdb=" N GLY I 10 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR I 127 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 12 " --> pdb=" O THR I 127 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA I 97 " --> pdb=" O ASN I 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG I 98 " --> pdb=" O ASP I 118 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY I 116 " --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 137 through 140 removed outlier: 3.609A pdb=" N SER I 197 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR I 193 " --> pdb=" O ASP I 161 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL I 198 " --> pdb=" O HIS I 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 137 through 140 removed outlier: 3.609A pdb=" N SER I 197 " --> pdb=" O CYS I 157 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR I 193 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 167 through 171 removed outlier: 3.793A pdb=" N TYR I 211 " --> pdb=" O VAL I 228 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.637A pdb=" N SER K 65 " --> pdb=" O THR K 72 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.535A pdb=" N VAL K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR K 49 " --> pdb=" O ARG K 53 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG K 53 " --> pdb=" O TYR K 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 114 through 118 removed outlier: 3.642A pdb=" N ASN K 137 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL K 133 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN K 138 " --> pdb=" O TYR K 173 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 145 through 150 removed outlier: 3.607A pdb=" N LYS K 145 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS K 149 " --> pdb=" O ALA K 193 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR K 192 " --> pdb=" O PHE K 209 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS K 207 " --> pdb=" O CYS K 194 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL K 205 " --> pdb=" O VAL K 196 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 32 through 36 removed outlier: 3.534A pdb=" N GLY H 33 " --> pdb=" O HIS H 26 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS F 14 " --> pdb=" O HIS H 25 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU H 139 " --> pdb=" O LYS H 131 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 25 through 26 Processing sheet with id=AE7, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AE8, first strand: chain 'F' and resid 43 through 44 removed outlier: 3.535A pdb=" N GLU F 44 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 51 through 54 removed outlier: 7.479A pdb=" N LEU F 51 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR F 287 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LYS F 53 " --> pdb=" O THR F 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 60 through 61 removed outlier: 7.689A pdb=" N LEU F 60 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 122 through 124 removed outlier: 3.545A pdb=" N ALA F 266 " --> pdb=" O GLU F 122 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU F 186 " --> pdb=" O PRO F 261 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 122 through 124 removed outlier: 3.545A pdb=" N ALA F 266 " --> pdb=" O GLU F 122 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 171 through 176 removed outlier: 3.507A pdb=" N ALA F 254 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR F 175 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 211 " --> pdb=" O LYS F 218 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 294 through 296 removed outlier: 3.638A pdb=" N THR F 291 " --> pdb=" O GLY F 294 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE F 296 " --> pdb=" O CYS F 289 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS F 289 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 310 " --> pdb=" O GLN F 290 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR H 64 " --> pdb=" O GLY F 311 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.840A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER J 25 " --> pdb=" O GLN J 3 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.885A pdb=" N GLY J 10 " --> pdb=" O THR J 125 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR J 127 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL J 12 " --> pdb=" O THR J 127 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR J 124 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N MET J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.885A pdb=" N GLY J 10 " --> pdb=" O THR J 125 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR J 127 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL J 12 " --> pdb=" O THR J 127 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR J 124 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA J 97 " --> pdb=" O ASN J 35 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG J 98 " --> pdb=" O ASP J 118 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLY J 116 " --> pdb=" O ARG J 100 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 137 through 140 removed outlier: 3.642A pdb=" N SER J 197 " --> pdb=" O CYS J 157 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR J 193 " --> pdb=" O ASP J 161 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL J 198 " --> pdb=" O HIS J 181 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 137 through 140 removed outlier: 3.642A pdb=" N SER J 197 " --> pdb=" O CYS J 157 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR J 193 " --> pdb=" O ASP J 161 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 167 through 171 removed outlier: 3.745A pdb=" N TYR J 211 " --> pdb=" O VAL J 228 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.548A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.499A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR L 49 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.655A pdb=" N ASN L 137 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN L 138 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 145 through 150 removed outlier: 3.645A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS L 149 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 1950 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: 8.04 Time building geometry restraints manager: 7.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7002 1.34 - 1.46: 5243 1.46 - 1.58: 9730 1.58 - 1.70: 0 1.70 - 1.81: 123 Bond restraints: 22098 Sorted by residual: bond pdb=" N SER A 299 " pdb=" CA SER A 299 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.34e+00 bond pdb=" N SER E 299 " pdb=" CA SER E 299 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.24e+00 bond pdb=" N SER F 299 " pdb=" CA SER F 299 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.90e-02 2.77e+03 4.22e+00 bond pdb=" C THR F 298 " pdb=" N SER F 299 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.40e-02 5.10e+03 2.84e+00 bond pdb=" C THR E 298 " pdb=" N SER E 299 " ideal model delta sigma weight residual 1.329 1.352 -0.023 1.40e-02 5.10e+03 2.66e+00 ... (remaining 22093 not shown) Histogram of bond angle deviations from ideal: 100.64 - 107.54: 816 107.54 - 114.44: 12757 114.44 - 121.34: 9880 121.34 - 128.24: 6361 128.24 - 135.14: 177 Bond angle restraints: 29991 Sorted by residual: angle pdb=" C THR E 298 " pdb=" N SER E 299 " pdb=" CA SER E 299 " ideal model delta sigma weight residual 121.70 135.14 -13.44 1.80e+00 3.09e-01 5.57e+01 angle pdb=" C THR F 298 " pdb=" N SER F 299 " pdb=" CA SER F 299 " ideal model delta sigma weight residual 121.70 135.10 -13.40 1.80e+00 3.09e-01 5.54e+01 angle pdb=" C THR A 298 " pdb=" N SER A 299 " pdb=" CA SER A 299 " ideal model delta sigma weight residual 121.70 134.87 -13.17 1.80e+00 3.09e-01 5.36e+01 angle pdb=" N VAL G 66 " pdb=" CA VAL G 66 " pdb=" C VAL G 66 " ideal model delta sigma weight residual 111.81 108.61 3.20 8.60e-01 1.35e+00 1.38e+01 angle pdb=" N VAL B 66 " pdb=" CA VAL B 66 " pdb=" C VAL B 66 " ideal model delta sigma weight residual 111.81 108.73 3.08 8.60e-01 1.35e+00 1.28e+01 ... (remaining 29986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.70: 12644 14.70 - 29.41: 414 29.41 - 44.11: 135 44.11 - 58.82: 16 58.82 - 73.52: 3 Dihedral angle restraints: 13212 sinusoidal: 5163 harmonic: 8049 Sorted by residual: dihedral pdb=" CA HIS G 72 " pdb=" C HIS G 72 " pdb=" N LEU G 73 " pdb=" CA LEU G 73 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA HIS B 72 " pdb=" C HIS B 72 " pdb=" N LEU B 73 " pdb=" CA LEU B 73 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA HIS H 72 " pdb=" C HIS H 72 " pdb=" N LEU H 73 " pdb=" CA LEU H 73 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 13209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2504 0.041 - 0.081: 504 0.081 - 0.122: 286 0.122 - 0.162: 18 0.162 - 0.203: 3 Chirality restraints: 3315 Sorted by residual: chirality pdb=" CA SER F 299 " pdb=" N SER F 299 " pdb=" C SER F 299 " pdb=" CB SER F 299 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA SER E 299 " pdb=" N SER E 299 " pdb=" C SER E 299 " pdb=" CB SER E 299 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA SER A 299 " pdb=" N SER A 299 " pdb=" C SER A 299 " pdb=" CB SER A 299 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.74e-01 ... (remaining 3312 not shown) Planarity restraints: 3864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN K 79 " -0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO K 80 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 80 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 80 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO L 80 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 79 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO D 80 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 80 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 80 " -0.026 5.00e-02 4.00e+02 ... (remaining 3861 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 5723 2.81 - 3.33: 16250 3.33 - 3.85: 36637 3.85 - 4.38: 39644 4.38 - 4.90: 70741 Nonbonded interactions: 168995 Sorted by model distance: nonbonded pdb=" OG1 THR E 287 " pdb=" O ILE E 296 " model vdw 2.283 2.440 nonbonded pdb=" O LEU B 89 " pdb=" OG1 THR B 93 " model vdw 2.311 2.440 nonbonded pdb=" O CYS A 52 " pdb=" OH TYR A 88 " model vdw 2.312 2.440 nonbonded pdb=" O LEU H 89 " pdb=" OG1 THR H 93 " model vdw 2.314 2.440 nonbonded pdb=" O LEU G 89 " pdb=" OG1 THR G 93 " model vdw 2.319 2.440 ... (remaining 168990 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 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.530 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: 0.000 Extract box with map and model: 3.090 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 56.730 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5249 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 0.040 22098 Z= 0.136 Angle : 0.487 13.437 29991 Z= 0.280 Chirality : 0.042 0.203 3315 Planarity : 0.005 0.049 3864 Dihedral : 8.088 73.519 7980 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.82 % Allowed : 3.31 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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: 2757 helix: -4.02 (0.11), residues: 300 sheet: -1.37 (0.17), residues: 822 loop : -2.03 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 86 HIS 0.005 0.000 HIS H 72 PHE 0.013 0.001 PHE A 154 TYR 0.009 0.001 TYR F 88 ARG 0.002 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 527 time to evaluate : 2.180 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: A 42 LEU cc_start: 0.7396 (mp) cc_final: 0.7109 (mt) REVERT: A 90 VAL cc_start: 0.5771 (t) cc_final: 0.5550 (t) REVERT: A 108 TYR cc_start: 0.7161 (t80) cc_final: 0.6655 (t80) REVERT: A 133 TRP cc_start: 0.5698 (m-90) cc_final: 0.5073 (m-90) REVERT: A 170 LYS cc_start: 0.7683 (tttt) cc_final: 0.7269 (mmtt) REVERT: A 175 TYR cc_start: 0.6765 (t80) cc_final: 0.6497 (t80) REVERT: A 231 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7693 (ttt-90) REVERT: A 233 GLN cc_start: 0.6637 (mm-40) cc_final: 0.6344 (mm-40) REVERT: A 293 LYS cc_start: 0.7106 (mttt) cc_final: 0.6827 (mttt) REVERT: B 81 ASN cc_start: 0.7457 (t0) cc_final: 0.7245 (t0) REVERT: B 103 GLU cc_start: 0.6434 (mm-30) cc_final: 0.6223 (mm-30) REVERT: B 110 TYR cc_start: 0.7094 (t80) cc_final: 0.6747 (t80) REVERT: B 149 MET cc_start: 0.5695 (mmt) cc_final: 0.5389 (mmm) REVERT: B 150 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7023 (mm-30) REVERT: B 152 VAL cc_start: 0.6773 (t) cc_final: 0.6451 (m) REVERT: B 153 LYS cc_start: 0.6736 (ttpt) cc_final: 0.6419 (ttpt) REVERT: C 25 SER cc_start: 0.6975 (p) cc_final: 0.6768 (m) REVERT: C 36 TRP cc_start: 0.5129 (m100) cc_final: 0.4845 (m100) REVERT: C 67 ARG cc_start: 0.6312 (mtm180) cc_final: 0.6073 (mtm180) REVERT: D 4 MET cc_start: 0.5388 (mmm) cc_final: 0.4729 (mmm) REVERT: D 36 TYR cc_start: 0.4375 (m-80) cc_final: 0.4130 (m-80) REVERT: D 82 ASP cc_start: 0.6356 (m-30) cc_final: 0.5142 (m-30) REVERT: E 217 SER cc_start: 0.6550 (m) cc_final: 0.5919 (p) REVERT: E 231 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7390 (mtp-110) REVERT: E 249 LYS cc_start: 0.6322 (ttpt) cc_final: 0.5878 (ttmm) REVERT: E 267 MET cc_start: 0.5526 (ppp) cc_final: 0.5188 (ppp) REVERT: G 40 SER cc_start: 0.8776 (m) cc_final: 0.8373 (p) REVERT: G 53 ASN cc_start: 0.7116 (m-40) cc_final: 0.6803 (m-40) REVERT: G 81 ASN cc_start: 0.7269 (t0) cc_final: 0.7035 (t0) REVERT: G 131 LYS cc_start: 0.7249 (tttt) cc_final: 0.7049 (tttt) REVERT: I 67 ARG cc_start: 0.6780 (mtm180) cc_final: 0.6365 (mtm180) REVERT: I 115 TYR cc_start: 0.6761 (m-80) cc_final: 0.6165 (m-80) REVERT: I 163 PHE cc_start: 0.5121 (t80) cc_final: 0.4845 (t80) REVERT: K 4 MET cc_start: 0.5849 (mmm) cc_final: 0.4715 (ttt) REVERT: K 5 THR cc_start: 0.6528 (m) cc_final: 0.6320 (t) REVERT: K 37 GLN cc_start: 0.7607 (tt0) cc_final: 0.7041 (tt0) REVERT: K 63 SER cc_start: 0.7054 (t) cc_final: 0.6827 (t) REVERT: K 82 ASP cc_start: 0.6077 (m-30) cc_final: 0.4199 (m-30) REVERT: F 108 TYR cc_start: 0.6935 (t80) cc_final: 0.6696 (t80) REVERT: F 170 LYS cc_start: 0.7852 (tttt) cc_final: 0.7424 (mptt) REVERT: F 179 LYS cc_start: 0.7009 (mmtt) cc_final: 0.6677 (mttp) REVERT: F 191 HIS cc_start: 0.5112 (m-70) cc_final: 0.4739 (m-70) REVERT: F 312 LYS cc_start: 0.7113 (mttt) cc_final: 0.6665 (mmtt) REVERT: F 321 LYS cc_start: 0.7114 (pttt) cc_final: 0.6903 (tppt) REVERT: F 322 LEU cc_start: 0.8057 (mt) cc_final: 0.7789 (mt) REVERT: F 323 ARG cc_start: 0.7212 (ttm-80) cc_final: 0.6997 (ttt90) REVERT: H 131 LYS cc_start: 0.7329 (tttt) cc_final: 0.7017 (tttt) REVERT: H 149 MET cc_start: 0.5754 (mmt) cc_final: 0.5504 (mmp) REVERT: L 4 MET cc_start: 0.5946 (mmm) cc_final: 0.5184 (tpp) REVERT: L 37 GLN cc_start: 0.7502 (tt0) cc_final: 0.6756 (tt0) REVERT: L 82 ASP cc_start: 0.6256 (m-30) cc_final: 0.6044 (m-30) REVERT: L 97 THR cc_start: 0.7518 (m) cc_final: 0.7203 (p) outliers start: 44 outliers final: 10 residues processed: 560 average time/residue: 0.3163 time to fit residues: 273.6378 Evaluate side-chains 442 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 432 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 139 optimal weight: 0.0040 chunk 110 optimal weight: 2.9990 chunk 213 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 159 optimal weight: 40.0000 chunk 247 optimal weight: 20.0000 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN B 25 HIS B 50 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN C 56 ASN G 25 HIS G 42 GLN G 62 GLN G 114 ASN ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN H 25 HIS H 81 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 ASN ** J 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5607 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22098 Z= 0.298 Angle : 0.668 9.948 29991 Z= 0.354 Chirality : 0.047 0.260 3315 Planarity : 0.005 0.063 3864 Dihedral : 4.382 55.276 3020 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.32 % Allowed : 8.07 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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: -1.91 (0.15), residues: 2757 helix: -1.72 (0.23), residues: 294 sheet: -0.98 (0.17), residues: 822 loop : -1.31 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 14 HIS 0.007 0.001 HIS F 61 PHE 0.031 0.002 PHE B 88 TYR 0.023 0.002 TYR H 94 ARG 0.011 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 487 time to evaluate : 2.358 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: A 42 LEU cc_start: 0.7659 (mp) cc_final: 0.7374 (mt) REVERT: A 170 LYS cc_start: 0.7874 (tttt) cc_final: 0.7441 (mmtt) REVERT: A 175 TYR cc_start: 0.6738 (t80) cc_final: 0.6430 (t80) REVERT: A 234 GLU cc_start: 0.4426 (pm20) cc_final: 0.4186 (pm20) REVERT: A 293 LYS cc_start: 0.7120 (mttt) cc_final: 0.6875 (mttt) REVERT: A 321 LYS cc_start: 0.7267 (tptt) cc_final: 0.6760 (tptt) REVERT: A 323 ARG cc_start: 0.7722 (ttm-80) cc_final: 0.7016 (mtt90) REVERT: B 97 GLU cc_start: 0.7236 (tp30) cc_final: 0.6879 (tp30) REVERT: B 102 LEU cc_start: 0.7021 (mt) cc_final: 0.6611 (mt) REVERT: B 103 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6726 (mm-30) REVERT: B 110 TYR cc_start: 0.7187 (t80) cc_final: 0.6937 (t80) REVERT: B 131 LYS cc_start: 0.7296 (tttt) cc_final: 0.6902 (tttt) REVERT: B 140 PHE cc_start: 0.5564 (m-80) cc_final: 0.5191 (m-80) REVERT: B 149 MET cc_start: 0.5716 (mmt) cc_final: 0.5305 (mmm) REVERT: C 27 PHE cc_start: 0.6345 (p90) cc_final: 0.6021 (p90) REVERT: C 67 ARG cc_start: 0.6790 (mtm180) cc_final: 0.6474 (mtm180) REVERT: D 4 MET cc_start: 0.4295 (mmm) cc_final: 0.3782 (ttt) REVERT: D 6 GLN cc_start: 0.6098 (mp10) cc_final: 0.5776 (mp10) REVERT: D 81 GLU cc_start: 0.6735 (pm20) cc_final: 0.6436 (pm20) REVERT: D 82 ASP cc_start: 0.6675 (m-30) cc_final: 0.5623 (m-30) REVERT: E 112 ARG cc_start: 0.6915 (mtp85) cc_final: 0.6657 (mtp85) REVERT: E 122 GLU cc_start: 0.7117 (tt0) cc_final: 0.6852 (tt0) REVERT: E 217 SER cc_start: 0.7638 (m) cc_final: 0.7097 (p) REVERT: E 318 LYS cc_start: 0.7487 (mtmt) cc_final: 0.7124 (pttm) REVERT: G 41 THR cc_start: 0.8366 (m) cc_final: 0.7949 (p) REVERT: I 29 PHE cc_start: 0.6582 (t80) cc_final: 0.6215 (t80) REVERT: I 67 ARG cc_start: 0.7084 (mtm180) cc_final: 0.6662 (mtm180) REVERT: I 112 TYR cc_start: 0.6239 (m-80) cc_final: 0.5511 (m-10) REVERT: I 163 PHE cc_start: 0.5253 (t80) cc_final: 0.4880 (t80) REVERT: K 4 MET cc_start: 0.4552 (mmm) cc_final: 0.4040 (ttt) REVERT: K 37 GLN cc_start: 0.7161 (tt0) cc_final: 0.6609 (tt0) REVERT: K 53 ARG cc_start: 0.6618 (mtp85) cc_final: 0.6352 (mtp85) REVERT: K 82 ASP cc_start: 0.5941 (m-30) cc_final: 0.5652 (m-30) REVERT: F 70 TRP cc_start: 0.6673 (t60) cc_final: 0.6329 (t60) REVERT: F 106 ILE cc_start: 0.7182 (mt) cc_final: 0.6968 (mp) REVERT: F 170 LYS cc_start: 0.8037 (tttt) cc_final: 0.7667 (tttt) REVERT: F 179 LYS cc_start: 0.7319 (mmtt) cc_final: 0.6910 (mttt) REVERT: F 191 HIS cc_start: 0.5426 (m-70) cc_final: 0.4731 (m-70) REVERT: F 321 LYS cc_start: 0.7567 (pttt) cc_final: 0.7350 (tppt) REVERT: F 322 LEU cc_start: 0.8246 (mt) cc_final: 0.7945 (mt) REVERT: F 323 ARG cc_start: 0.7276 (ttm-80) cc_final: 0.7007 (ttm-80) REVERT: H 89 LEU cc_start: 0.6802 (tp) cc_final: 0.6398 (tt) REVERT: H 92 TRP cc_start: 0.5083 (m-10) cc_final: 0.3876 (m-90) REVERT: H 103 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6251 (mm-30) REVERT: J 163 PHE cc_start: 0.5467 (t80) cc_final: 0.5230 (t80) REVERT: L 4 MET cc_start: 0.5321 (mmm) cc_final: 0.4814 (ttm) REVERT: L 37 GLN cc_start: 0.7409 (tt0) cc_final: 0.6500 (tt0) REVERT: L 82 ASP cc_start: 0.6317 (m-30) cc_final: 0.4574 (m-30) REVERT: L 94 PHE cc_start: 0.6756 (p90) cc_final: 0.6422 (p90) REVERT: L 97 THR cc_start: 0.7272 (m) cc_final: 0.6948 (p) outliers start: 56 outliers final: 33 residues processed: 521 average time/residue: 0.3458 time to fit residues: 271.3766 Evaluate side-chains 482 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 449 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 172 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 206 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 221 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN B 50 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN G 42 GLN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5654 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22098 Z= 0.227 Angle : 0.604 10.345 29991 Z= 0.316 Chirality : 0.045 0.215 3315 Planarity : 0.004 0.042 3864 Dihedral : 4.006 29.596 3008 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.40 % Allowed : 10.52 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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: -1.35 (0.15), residues: 2757 helix: -1.04 (0.26), residues: 312 sheet: -0.54 (0.18), residues: 807 loop : -1.02 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 14 HIS 0.006 0.001 HIS B 72 PHE 0.040 0.002 PHE C 29 TYR 0.030 0.002 TYR J 115 ARG 0.006 0.000 ARG F 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 468 time to evaluate : 2.301 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: A 42 LEU cc_start: 0.7718 (mp) cc_final: 0.7503 (mt) REVERT: A 123 ARG cc_start: 0.7338 (ttm170) cc_final: 0.7106 (ttm110) REVERT: A 170 LYS cc_start: 0.7866 (tttt) cc_final: 0.7433 (mmtt) REVERT: A 175 TYR cc_start: 0.6692 (t80) cc_final: 0.6428 (t80) REVERT: A 293 LYS cc_start: 0.7176 (mttt) cc_final: 0.6901 (mttt) REVERT: A 312 LYS cc_start: 0.7386 (mttt) cc_final: 0.7014 (mttt) REVERT: A 321 LYS cc_start: 0.7388 (tptt) cc_final: 0.7090 (tptt) REVERT: A 329 ARG cc_start: 0.5870 (ttt90) cc_final: 0.5504 (ptt90) REVERT: B 42 GLN cc_start: 0.7244 (tp40) cc_final: 0.6996 (tp-100) REVERT: B 102 LEU cc_start: 0.7165 (mt) cc_final: 0.6804 (mt) REVERT: B 103 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6760 (mm-30) REVERT: B 110 TYR cc_start: 0.7162 (t80) cc_final: 0.6953 (t80) REVERT: B 114 ASN cc_start: 0.7027 (m-40) cc_final: 0.6632 (m110) REVERT: B 131 LYS cc_start: 0.7245 (tttt) cc_final: 0.6833 (tttt) REVERT: B 140 PHE cc_start: 0.5684 (m-80) cc_final: 0.5256 (m-80) REVERT: B 149 MET cc_start: 0.5475 (mmt) cc_final: 0.4873 (mmm) REVERT: C 72 ARG cc_start: 0.5470 (ptm160) cc_final: 0.5195 (ptm160) REVERT: D 81 GLU cc_start: 0.6737 (pm20) cc_final: 0.6426 (pm20) REVERT: D 82 ASP cc_start: 0.6732 (m-30) cc_final: 0.5647 (m-30) REVERT: E 122 GLU cc_start: 0.7124 (tt0) cc_final: 0.6845 (tt0) REVERT: E 231 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7468 (mtp-110) REVERT: E 315 LYS cc_start: 0.3870 (mttt) cc_final: 0.3627 (mttt) REVERT: G 82 LYS cc_start: 0.8578 (tttm) cc_final: 0.8350 (pttt) REVERT: G 103 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6976 (mm-30) REVERT: I 29 PHE cc_start: 0.6762 (t80) cc_final: 0.6334 (t80) REVERT: I 112 TYR cc_start: 0.6063 (m-80) cc_final: 0.5725 (m-10) REVERT: K 6 GLN cc_start: 0.6261 (mp10) cc_final: 0.5263 (mp10) REVERT: F 106 ILE cc_start: 0.7118 (mt) cc_final: 0.6870 (mp) REVERT: F 170 LYS cc_start: 0.8026 (tttt) cc_final: 0.7683 (tttt) REVERT: F 179 LYS cc_start: 0.7379 (mmtt) cc_final: 0.6985 (mttt) REVERT: F 191 HIS cc_start: 0.5602 (m-70) cc_final: 0.5000 (m-70) REVERT: F 233 GLN cc_start: 0.7409 (mm-40) cc_final: 0.7173 (mm-40) REVERT: F 319 SER cc_start: 0.8408 (OUTLIER) cc_final: 0.7996 (m) REVERT: F 322 LEU cc_start: 0.8191 (mt) cc_final: 0.7844 (mt) REVERT: H 91 ILE cc_start: 0.7268 (tp) cc_final: 0.6874 (tt) REVERT: H 103 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6369 (mm-30) REVERT: H 118 LEU cc_start: 0.8202 (mm) cc_final: 0.7840 (mm) REVERT: H 131 LYS cc_start: 0.7232 (tttt) cc_final: 0.6955 (tttt) REVERT: J 72 ARG cc_start: 0.5812 (ttm170) cc_final: 0.4890 (ttm-80) REVERT: J 163 PHE cc_start: 0.5539 (t80) cc_final: 0.5234 (t80) REVERT: L 37 GLN cc_start: 0.7383 (tt0) cc_final: 0.6429 (tt0) REVERT: L 81 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6140 (pm20) REVERT: L 94 PHE cc_start: 0.6912 (p90) cc_final: 0.6601 (p90) REVERT: L 97 THR cc_start: 0.7216 (m) cc_final: 0.6871 (p) outliers start: 58 outliers final: 35 residues processed: 502 average time/residue: 0.3445 time to fit residues: 261.3209 Evaluate side-chains 489 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 452 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 30.0000 chunk 186 optimal weight: 0.0470 chunk 128 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 249 optimal weight: 2.9990 chunk 263 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 290 GLN B 50 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN E 290 GLN ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 ASN ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN F 290 GLN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22098 Z= 0.222 Angle : 0.602 12.631 29991 Z= 0.311 Chirality : 0.044 0.208 3315 Planarity : 0.004 0.040 3864 Dihedral : 4.059 25.125 3005 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.57 % Allowed : 12.34 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % 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: -1.04 (0.15), residues: 2757 helix: -0.80 (0.26), residues: 315 sheet: -0.27 (0.18), residues: 822 loop : -0.86 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 14 HIS 0.007 0.001 HIS B 72 PHE 0.038 0.002 PHE C 29 TYR 0.028 0.002 TYR A 108 ARG 0.007 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 461 time to evaluate : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7769 (mp) cc_final: 0.7537 (mt) REVERT: A 121 PHE cc_start: 0.6183 (t80) cc_final: 0.5799 (t80) REVERT: A 123 ARG cc_start: 0.7295 (ttm170) cc_final: 0.7077 (ttm110) REVERT: A 170 LYS cc_start: 0.7861 (tttt) cc_final: 0.7433 (mmtt) REVERT: A 175 TYR cc_start: 0.6657 (t80) cc_final: 0.6391 (t80) REVERT: A 234 GLU cc_start: 0.4712 (pm20) cc_final: 0.4465 (pm20) REVERT: A 293 LYS cc_start: 0.7404 (mttt) cc_final: 0.7091 (mttt) REVERT: A 321 LYS cc_start: 0.7510 (tptt) cc_final: 0.7240 (tptt) REVERT: B 42 GLN cc_start: 0.7316 (tp40) cc_final: 0.7115 (tp-100) REVERT: B 60 ASN cc_start: 0.7392 (t0) cc_final: 0.7119 (p0) REVERT: B 103 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6909 (mm-30) REVERT: B 114 ASN cc_start: 0.6922 (m-40) cc_final: 0.6335 (m110) REVERT: B 131 LYS cc_start: 0.7266 (tttt) cc_final: 0.6839 (tttt) REVERT: B 140 PHE cc_start: 0.5722 (m-80) cc_final: 0.5288 (m-80) REVERT: B 149 MET cc_start: 0.5550 (mmt) cc_final: 0.4930 (mmm) REVERT: D 81 GLU cc_start: 0.6777 (pm20) cc_final: 0.6447 (pm20) REVERT: D 82 ASP cc_start: 0.6857 (m-30) cc_final: 0.5767 (m-30) REVERT: E 40 VAL cc_start: 0.8222 (t) cc_final: 0.8011 (t) REVERT: E 122 GLU cc_start: 0.7185 (tt0) cc_final: 0.6915 (tt0) REVERT: E 231 ARG cc_start: 0.8080 (mtt-85) cc_final: 0.7460 (mtp-110) REVERT: E 267 MET cc_start: 0.6010 (ppp) cc_final: 0.5088 (ppp) REVERT: E 315 LYS cc_start: 0.3950 (mttt) cc_final: 0.3732 (mttt) REVERT: G 68 LYS cc_start: 0.8278 (mmtt) cc_final: 0.8060 (mmmt) REVERT: G 103 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7040 (mm-30) REVERT: G 149 MET cc_start: 0.5872 (mmp) cc_final: 0.5555 (mmm) REVERT: I 29 PHE cc_start: 0.6786 (t80) cc_final: 0.6433 (t80) REVERT: K 36 TYR cc_start: 0.5163 (m-80) cc_final: 0.4421 (m-80) REVERT: F 70 TRP cc_start: 0.6626 (t60) cc_final: 0.6162 (t60) REVERT: F 106 ILE cc_start: 0.7195 (mt) cc_final: 0.6972 (mp) REVERT: F 166 ASN cc_start: 0.6027 (m-40) cc_final: 0.5817 (t0) REVERT: F 170 LYS cc_start: 0.8021 (tttt) cc_final: 0.7750 (mptt) REVERT: F 176 ILE cc_start: 0.7807 (mt) cc_final: 0.7581 (mp) REVERT: F 179 LYS cc_start: 0.7414 (mmtt) cc_final: 0.7030 (mttp) REVERT: F 191 HIS cc_start: 0.5471 (m-70) cc_final: 0.4896 (m-70) REVERT: F 230 VAL cc_start: 0.7702 (t) cc_final: 0.7331 (p) REVERT: F 276 ILE cc_start: 0.5520 (OUTLIER) cc_final: 0.5317 (mt) REVERT: F 312 LYS cc_start: 0.7055 (mttt) cc_final: 0.6680 (mmtt) REVERT: F 319 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8147 (m) REVERT: F 323 ARG cc_start: 0.7576 (ttm-80) cc_final: 0.7242 (ttt90) REVERT: H 91 ILE cc_start: 0.7109 (tp) cc_final: 0.6805 (tt) REVERT: H 103 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6416 (mm-30) REVERT: H 131 LYS cc_start: 0.7328 (tttt) cc_final: 0.6984 (tttt) REVERT: H 149 MET cc_start: 0.5950 (mmt) cc_final: 0.5535 (mmp) REVERT: H 153 LYS cc_start: 0.7758 (ttpt) cc_final: 0.7517 (ttpt) REVERT: J 72 ARG cc_start: 0.5898 (ttm170) cc_final: 0.4750 (ttm-80) REVERT: J 163 PHE cc_start: 0.5741 (t80) cc_final: 0.5429 (t80) REVERT: J 227 LYS cc_start: 0.5564 (tppt) cc_final: 0.5356 (tppt) REVERT: L 94 PHE cc_start: 0.6849 (p90) cc_final: 0.6387 (p90) REVERT: L 97 THR cc_start: 0.7139 (m) cc_final: 0.6899 (p) outliers start: 62 outliers final: 44 residues processed: 490 average time/residue: 0.3569 time to fit residues: 265.4833 Evaluate side-chains 488 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 442 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 22 TYR Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 121 LYS Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 0.1980 chunk 149 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 196 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 225 optimal weight: 0.6980 chunk 182 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 236 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5665 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22098 Z= 0.173 Angle : 0.570 10.360 29991 Z= 0.295 Chirality : 0.043 0.194 3315 Planarity : 0.004 0.063 3864 Dihedral : 3.972 25.482 3005 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.40 % Allowed : 13.21 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.16), residues: 2757 helix: -0.62 (0.27), residues: 315 sheet: 0.08 (0.18), residues: 801 loop : -0.74 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 14 HIS 0.007 0.001 HIS B 72 PHE 0.039 0.002 PHE C 29 TYR 0.027 0.001 TYR A 88 ARG 0.006 0.000 ARG E 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 443 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7446 (mt) REVERT: A 121 PHE cc_start: 0.6146 (t80) cc_final: 0.5825 (t80) REVERT: A 123 ARG cc_start: 0.7261 (ttm170) cc_final: 0.7008 (ttm110) REVERT: A 170 LYS cc_start: 0.7787 (tttt) cc_final: 0.7384 (mmtt) REVERT: A 175 TYR cc_start: 0.6677 (t80) cc_final: 0.6403 (t80) REVERT: A 191 HIS cc_start: 0.5220 (m-70) cc_final: 0.4998 (m-70) REVERT: A 231 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7763 (ttt-90) REVERT: A 234 GLU cc_start: 0.4622 (pm20) cc_final: 0.4417 (pm20) REVERT: A 237 MET cc_start: 0.5422 (ttm) cc_final: 0.5169 (ttm) REVERT: A 293 LYS cc_start: 0.7221 (mttt) cc_final: 0.6932 (mttt) REVERT: B 81 ASN cc_start: 0.7860 (t0) cc_final: 0.7608 (t0) REVERT: B 82 LYS cc_start: 0.8605 (pttt) cc_final: 0.8237 (pttt) REVERT: B 103 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6962 (mm-30) REVERT: B 131 LYS cc_start: 0.7249 (tttt) cc_final: 0.6808 (tttt) REVERT: B 140 PHE cc_start: 0.5768 (m-80) cc_final: 0.5320 (m-80) REVERT: B 149 MET cc_start: 0.5608 (mmt) cc_final: 0.4960 (mmm) REVERT: C 122 GLN cc_start: 0.5950 (mm-40) cc_final: 0.5731 (mm-40) REVERT: D 81 GLU cc_start: 0.6773 (pm20) cc_final: 0.6428 (pm20) REVERT: D 82 ASP cc_start: 0.6792 (m-30) cc_final: 0.5798 (m-30) REVERT: E 122 GLU cc_start: 0.7153 (tt0) cc_final: 0.6836 (tt0) REVERT: E 176 ILE cc_start: 0.7649 (mt) cc_final: 0.7370 (mp) REVERT: E 231 ARG cc_start: 0.8095 (mtt-85) cc_final: 0.7450 (mtp-110) REVERT: G 17 MET cc_start: 0.6454 (ttp) cc_final: 0.6152 (ttp) REVERT: G 68 LYS cc_start: 0.8265 (mmtt) cc_final: 0.8014 (mmmt) REVERT: G 88 PHE cc_start: 0.6384 (m-80) cc_final: 0.5114 (m-80) REVERT: G 103 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7156 (mm-30) REVERT: G 149 MET cc_start: 0.6003 (mmp) cc_final: 0.5770 (mmm) REVERT: I 29 PHE cc_start: 0.6788 (t80) cc_final: 0.6410 (t80) REVERT: K 4 MET cc_start: 0.5053 (ttm) cc_final: 0.4520 (ttt) REVERT: K 27 GLN cc_start: 0.5286 (mp10) cc_final: 0.4807 (mp10) REVERT: K 36 TYR cc_start: 0.4856 (m-80) cc_final: 0.4181 (m-80) REVERT: K 53 ARG cc_start: 0.6707 (mtp85) cc_final: 0.6495 (mtp85) REVERT: F 70 TRP cc_start: 0.6636 (t60) cc_final: 0.6233 (t60) REVERT: F 106 ILE cc_start: 0.7316 (mt) cc_final: 0.7082 (mp) REVERT: F 160 TRP cc_start: 0.6444 (OUTLIER) cc_final: 0.6223 (m100) REVERT: F 170 LYS cc_start: 0.8006 (tttt) cc_final: 0.7737 (mptt) REVERT: F 179 LYS cc_start: 0.7384 (mmtt) cc_final: 0.7010 (mttp) REVERT: F 191 HIS cc_start: 0.5528 (m-70) cc_final: 0.4959 (m-70) REVERT: F 230 VAL cc_start: 0.7796 (t) cc_final: 0.7336 (p) REVERT: F 312 LYS cc_start: 0.7057 (mttt) cc_final: 0.6660 (mmtt) REVERT: F 323 ARG cc_start: 0.7515 (ttm-80) cc_final: 0.7262 (ttt90) REVERT: H 91 ILE cc_start: 0.7078 (tp) cc_final: 0.6810 (tt) REVERT: H 103 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6576 (mm-30) REVERT: H 131 LYS cc_start: 0.7307 (tttt) cc_final: 0.6969 (tttt) REVERT: H 149 MET cc_start: 0.5912 (mmt) cc_final: 0.5626 (mmp) REVERT: H 153 LYS cc_start: 0.7764 (ttpt) cc_final: 0.7523 (ttpt) REVERT: J 163 PHE cc_start: 0.5751 (t80) cc_final: 0.5425 (t80) REVERT: L 37 GLN cc_start: 0.7293 (tt0) cc_final: 0.6428 (tt0) REVERT: L 94 PHE cc_start: 0.7038 (p90) cc_final: 0.6602 (p90) REVERT: L 97 THR cc_start: 0.7105 (m) cc_final: 0.6865 (p) outliers start: 58 outliers final: 41 residues processed: 473 average time/residue: 0.3451 time to fit residues: 247.7809 Evaluate side-chains 473 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 429 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 154 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 chunk 264 optimal weight: 0.0040 chunk 219 optimal weight: 0.0170 chunk 122 optimal weight: 6.9990 chunk 21 optimal weight: 0.0970 chunk 87 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.2232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 ASN ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5740 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22098 Z= 0.235 Angle : 0.608 10.162 29991 Z= 0.319 Chirality : 0.044 0.196 3315 Planarity : 0.004 0.052 3864 Dihedral : 4.193 26.769 3005 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.02 % Allowed : 13.50 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.16), residues: 2757 helix: -0.66 (0.28), residues: 306 sheet: 0.14 (0.18), residues: 810 loop : -0.65 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 14 HIS 0.008 0.001 HIS B 72 PHE 0.032 0.002 PHE C 29 TYR 0.029 0.002 TYR E 88 ARG 0.006 0.000 ARG E 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 437 time to evaluate : 2.334 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: A 42 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7503 (mt) REVERT: A 121 PHE cc_start: 0.6315 (t80) cc_final: 0.5846 (t80) REVERT: A 123 ARG cc_start: 0.7273 (ttm170) cc_final: 0.7043 (ttm110) REVERT: A 170 LYS cc_start: 0.7866 (tttt) cc_final: 0.7448 (mmtt) REVERT: A 175 TYR cc_start: 0.6694 (t80) cc_final: 0.6431 (t80) REVERT: A 231 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7616 (ttt-90) REVERT: A 293 LYS cc_start: 0.7496 (mttt) cc_final: 0.7161 (mttt) REVERT: A 312 LYS cc_start: 0.7418 (mttt) cc_final: 0.6887 (mptt) REVERT: A 321 LYS cc_start: 0.7614 (tptt) cc_final: 0.7308 (tptt) REVERT: B 42 GLN cc_start: 0.7460 (tp40) cc_final: 0.7201 (tp-100) REVERT: B 82 LYS cc_start: 0.8688 (pttt) cc_final: 0.8264 (pttt) REVERT: B 97 GLU cc_start: 0.7544 (tp30) cc_final: 0.7265 (tp30) REVERT: B 131 LYS cc_start: 0.7314 (tttt) cc_final: 0.6875 (tttt) REVERT: B 140 PHE cc_start: 0.5816 (m-80) cc_final: 0.5490 (m-80) REVERT: B 149 MET cc_start: 0.5649 (mmt) cc_final: 0.4948 (mmm) REVERT: D 81 GLU cc_start: 0.6832 (pm20) cc_final: 0.6480 (pm20) REVERT: D 82 ASP cc_start: 0.7059 (m-30) cc_final: 0.6008 (m-30) REVERT: E 15 ILE cc_start: 0.6114 (tt) cc_final: 0.5814 (pt) REVERT: E 122 GLU cc_start: 0.7205 (tt0) cc_final: 0.6948 (tt0) REVERT: E 231 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7593 (mtp-110) REVERT: E 267 MET cc_start: 0.6807 (ppp) cc_final: 0.5939 (ppp) REVERT: G 17 MET cc_start: 0.6549 (ttp) cc_final: 0.6233 (ttp) REVERT: G 68 LYS cc_start: 0.8327 (mmtt) cc_final: 0.7994 (mmmt) REVERT: G 95 ASN cc_start: 0.8484 (t0) cc_final: 0.8252 (t0) REVERT: G 103 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7282 (mm-30) REVERT: G 121 LYS cc_start: 0.8149 (tttt) cc_final: 0.7830 (tmtt) REVERT: G 149 MET cc_start: 0.6095 (mmp) cc_final: 0.5830 (mmm) REVERT: I 29 PHE cc_start: 0.6840 (t80) cc_final: 0.6471 (t80) REVERT: I 112 TYR cc_start: 0.5674 (m-10) cc_final: 0.5396 (m-10) REVERT: F 106 ILE cc_start: 0.7473 (mt) cc_final: 0.7187 (mp) REVERT: F 160 TRP cc_start: 0.6585 (OUTLIER) cc_final: 0.6364 (m100) REVERT: F 170 LYS cc_start: 0.8041 (tttt) cc_final: 0.7760 (mptt) REVERT: F 179 LYS cc_start: 0.7450 (mmtt) cc_final: 0.7061 (mttp) REVERT: F 191 HIS cc_start: 0.5611 (m-70) cc_final: 0.5011 (m-70) REVERT: F 230 VAL cc_start: 0.7799 (t) cc_final: 0.7416 (p) REVERT: F 322 LEU cc_start: 0.8103 (mt) cc_final: 0.7805 (mt) REVERT: H 103 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6699 (mm-30) REVERT: H 131 LYS cc_start: 0.7403 (tttt) cc_final: 0.7042 (tttt) REVERT: H 149 MET cc_start: 0.5979 (mmt) cc_final: 0.5628 (mmp) REVERT: H 153 LYS cc_start: 0.7754 (ttpt) cc_final: 0.7470 (ttpt) REVERT: J 163 PHE cc_start: 0.5846 (t80) cc_final: 0.5508 (t80) REVERT: L 94 PHE cc_start: 0.6984 (p90) cc_final: 0.6727 (p90) REVERT: L 97 THR cc_start: 0.7170 (m) cc_final: 0.6907 (p) outliers start: 73 outliers final: 45 residues processed: 485 average time/residue: 0.3337 time to fit residues: 246.1805 Evaluate side-chains 479 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 431 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain G residue 14 TRP Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 263 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN E 233 GLN ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN F 74 ASN ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 ASN J 217 HIS L 55 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 22098 Z= 0.354 Angle : 0.716 10.356 29991 Z= 0.377 Chirality : 0.048 0.379 3315 Planarity : 0.005 0.049 3864 Dihedral : 4.882 25.394 3003 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.15 % Allowed : 13.83 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.16), residues: 2757 helix: -1.06 (0.27), residues: 318 sheet: -0.10 (0.18), residues: 885 loop : -0.77 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP H 14 HIS 0.010 0.002 HIS H 72 PHE 0.030 0.002 PHE C 29 TYR 0.032 0.002 TYR E 88 ARG 0.005 0.001 ARG E 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 469 time to evaluate : 2.277 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: A 42 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7560 (mt) REVERT: A 123 ARG cc_start: 0.7353 (ttm170) cc_final: 0.6957 (ttm170) REVERT: A 170 LYS cc_start: 0.7828 (tttt) cc_final: 0.7527 (mmtt) REVERT: A 175 TYR cc_start: 0.6746 (t80) cc_final: 0.6503 (t80) REVERT: A 234 GLU cc_start: 0.5464 (pm20) cc_final: 0.5222 (pm20) REVERT: A 293 LYS cc_start: 0.7739 (mttt) cc_final: 0.7417 (mttt) REVERT: A 312 LYS cc_start: 0.7381 (mttt) cc_final: 0.6836 (mptt) REVERT: A 315 LYS cc_start: 0.4055 (mttt) cc_final: 0.3744 (mttt) REVERT: B 68 LYS cc_start: 0.8408 (mmmt) cc_final: 0.8107 (mmmt) REVERT: B 82 LYS cc_start: 0.8512 (pttt) cc_final: 0.8127 (pttt) REVERT: B 92 TRP cc_start: 0.5851 (m-10) cc_final: 0.5139 (m-90) REVERT: B 131 LYS cc_start: 0.7471 (tttt) cc_final: 0.6978 (tttt) REVERT: B 140 PHE cc_start: 0.5919 (m-80) cc_final: 0.5622 (m-80) REVERT: B 149 MET cc_start: 0.5872 (mmt) cc_final: 0.5296 (mmm) REVERT: B 158 ASP cc_start: 0.6942 (t0) cc_final: 0.6446 (t0) REVERT: C 36 TRP cc_start: 0.6451 (m100) cc_final: 0.5629 (m100) REVERT: C 70 ILE cc_start: 0.5131 (OUTLIER) cc_final: 0.4813 (tp) REVERT: D 53 ARG cc_start: 0.6911 (mtp85) cc_final: 0.6664 (mtp85) REVERT: D 81 GLU cc_start: 0.7033 (pm20) cc_final: 0.6758 (pm20) REVERT: E 38 HIS cc_start: 0.6646 (m170) cc_final: 0.6369 (m170) REVERT: E 121 PHE cc_start: 0.6434 (t80) cc_final: 0.5756 (t80) REVERT: E 173 LYS cc_start: 0.8073 (tppt) cc_final: 0.7553 (tppt) REVERT: E 177 ASN cc_start: 0.7671 (t0) cc_final: 0.7122 (t0) REVERT: E 231 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7649 (mtp-110) REVERT: E 323 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.7376 (mtp85) REVERT: G 17 MET cc_start: 0.6790 (ttp) cc_final: 0.6450 (ttp) REVERT: G 58 LYS cc_start: 0.7921 (mmtm) cc_final: 0.7710 (mmtp) REVERT: G 68 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7882 (mmmt) REVERT: G 86 ASP cc_start: 0.7647 (m-30) cc_final: 0.7413 (m-30) REVERT: G 88 PHE cc_start: 0.6467 (m-80) cc_final: 0.5145 (m-80) REVERT: G 95 ASN cc_start: 0.8583 (t0) cc_final: 0.8313 (t0) REVERT: G 103 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7339 (mm-30) REVERT: G 121 LYS cc_start: 0.8261 (tttt) cc_final: 0.7889 (tmtt) REVERT: G 149 MET cc_start: 0.6075 (mmp) cc_final: 0.5840 (mmm) REVERT: I 29 PHE cc_start: 0.6971 (t80) cc_final: 0.6354 (t80) REVERT: I 112 TYR cc_start: 0.5926 (m-10) cc_final: 0.5543 (m-10) REVERT: K 78 LEU cc_start: 0.6874 (tp) cc_final: 0.6469 (mp) REVERT: F 106 ILE cc_start: 0.7741 (mt) cc_final: 0.7436 (mt) REVERT: F 121 PHE cc_start: 0.6502 (t80) cc_final: 0.5920 (t80) REVERT: F 160 TRP cc_start: 0.6723 (OUTLIER) cc_final: 0.6450 (m100) REVERT: F 170 LYS cc_start: 0.8140 (tttt) cc_final: 0.7779 (mptt) REVERT: F 179 LYS cc_start: 0.7530 (mmtt) cc_final: 0.7147 (mttp) REVERT: F 191 HIS cc_start: 0.5376 (m-70) cc_final: 0.4826 (m-70) REVERT: F 230 VAL cc_start: 0.7930 (t) cc_final: 0.7610 (p) REVERT: F 312 LYS cc_start: 0.7099 (mttt) cc_final: 0.6743 (mmtm) REVERT: F 318 LYS cc_start: 0.7628 (mtmt) cc_final: 0.7375 (mmmm) REVERT: F 319 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8209 (p) REVERT: F 322 LEU cc_start: 0.8159 (mt) cc_final: 0.7838 (mt) REVERT: H 51 LYS cc_start: 0.7738 (ttmt) cc_final: 0.7431 (ttmt) REVERT: H 103 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6431 (mm-30) REVERT: H 131 LYS cc_start: 0.7510 (tttt) cc_final: 0.7171 (tttt) REVERT: H 158 ASP cc_start: 0.7222 (t0) cc_final: 0.6528 (t70) REVERT: J 163 PHE cc_start: 0.5989 (t80) cc_final: 0.5722 (t80) REVERT: L 94 PHE cc_start: 0.7026 (p90) cc_final: 0.6651 (p90) REVERT: L 97 THR cc_start: 0.7362 (m) cc_final: 0.6945 (p) outliers start: 76 outliers final: 60 residues processed: 511 average time/residue: 0.3241 time to fit residues: 251.8955 Evaluate side-chains 511 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 447 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 160 TRP Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 249 LYS Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 14 TRP Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 79 optimal weight: 0.3980 chunk 51 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 179 optimal weight: 10.0000 chunk 130 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 206 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN B 62 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN H 79 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 ASN ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22098 Z= 0.187 Angle : 0.620 10.360 29991 Z= 0.321 Chirality : 0.045 0.192 3315 Planarity : 0.004 0.048 3864 Dihedral : 4.393 25.332 3003 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.57 % Allowed : 15.53 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2757 helix: -0.81 (0.28), residues: 321 sheet: 0.26 (0.19), residues: 804 loop : -0.73 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP G 92 HIS 0.008 0.001 HIS B 72 PHE 0.041 0.002 PHE F 154 TYR 0.032 0.002 TYR F 17 ARG 0.006 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 452 time to evaluate : 2.282 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: A 42 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7393 (mt) REVERT: A 88 TYR cc_start: 0.6477 (p90) cc_final: 0.6160 (p90) REVERT: A 123 ARG cc_start: 0.7264 (ttm170) cc_final: 0.6831 (ttm110) REVERT: A 170 LYS cc_start: 0.7705 (tttt) cc_final: 0.7381 (mmtt) REVERT: A 171 LEU cc_start: 0.7549 (mt) cc_final: 0.7196 (tp) REVERT: A 175 TYR cc_start: 0.6677 (t80) cc_final: 0.6411 (t80) REVERT: A 231 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7235 (ttt-90) REVERT: A 293 LYS cc_start: 0.7493 (mttt) cc_final: 0.7214 (mttt) REVERT: A 312 LYS cc_start: 0.7243 (mttt) cc_final: 0.6885 (mptt) REVERT: A 318 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7015 (ttmt) REVERT: B 92 TRP cc_start: 0.5642 (m-10) cc_final: 0.5115 (m-90) REVERT: B 131 LYS cc_start: 0.7424 (tttt) cc_final: 0.6911 (tttt) REVERT: B 140 PHE cc_start: 0.5970 (m-80) cc_final: 0.5610 (m-80) REVERT: B 149 MET cc_start: 0.5804 (mmt) cc_final: 0.5186 (mmm) REVERT: B 158 ASP cc_start: 0.6906 (t0) cc_final: 0.6393 (t0) REVERT: C 20 LEU cc_start: 0.4566 (OUTLIER) cc_final: 0.4346 (mm) REVERT: C 36 TRP cc_start: 0.6406 (m100) cc_final: 0.5577 (m100) REVERT: C 70 ILE cc_start: 0.4760 (OUTLIER) cc_final: 0.4463 (tp) REVERT: C 114 PHE cc_start: 0.8021 (m-80) cc_final: 0.7782 (m-80) REVERT: D 81 GLU cc_start: 0.6999 (pm20) cc_final: 0.6665 (pm20) REVERT: D 82 ASP cc_start: 0.7267 (m-30) cc_final: 0.6227 (m-30) REVERT: E 38 HIS cc_start: 0.6292 (m170) cc_final: 0.6007 (m170) REVERT: E 121 PHE cc_start: 0.6319 (t80) cc_final: 0.5663 (t80) REVERT: E 170 LYS cc_start: 0.7995 (ttpp) cc_final: 0.7790 (ttpp) REVERT: E 173 LYS cc_start: 0.8057 (tppt) cc_final: 0.7472 (tppt) REVERT: E 231 ARG cc_start: 0.8180 (mtt-85) cc_final: 0.7680 (mtp-110) REVERT: E 267 MET cc_start: 0.6743 (ppp) cc_final: 0.5412 (ppp) REVERT: E 268 GLU cc_start: 0.7449 (mp0) cc_final: 0.7244 (mp0) REVERT: E 323 ARG cc_start: 0.7688 (ttm-80) cc_final: 0.7369 (mmm160) REVERT: G 17 MET cc_start: 0.6591 (ttp) cc_final: 0.6243 (ttp) REVERT: G 68 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7886 (mmmt) REVERT: G 88 PHE cc_start: 0.6408 (m-80) cc_final: 0.5549 (m-80) REVERT: G 95 ASN cc_start: 0.8458 (t0) cc_final: 0.8255 (t0) REVERT: G 121 LYS cc_start: 0.8030 (tttt) cc_final: 0.7726 (tmtt) REVERT: I 29 PHE cc_start: 0.6966 (t80) cc_final: 0.6564 (t80) REVERT: I 112 TYR cc_start: 0.5559 (m-10) cc_final: 0.5233 (m-10) REVERT: K 78 LEU cc_start: 0.6983 (tp) cc_final: 0.6515 (mp) REVERT: F 106 ILE cc_start: 0.7625 (mt) cc_final: 0.7351 (mt) REVERT: F 160 TRP cc_start: 0.6532 (OUTLIER) cc_final: 0.6324 (m100) REVERT: F 179 LYS cc_start: 0.7433 (mmtt) cc_final: 0.7082 (mttp) REVERT: F 191 HIS cc_start: 0.5465 (m-70) cc_final: 0.4898 (m-70) REVERT: F 230 VAL cc_start: 0.7928 (t) cc_final: 0.7604 (p) REVERT: F 319 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8191 (p) REVERT: F 321 LYS cc_start: 0.7776 (tptt) cc_final: 0.7415 (tppt) REVERT: F 322 LEU cc_start: 0.8115 (mt) cc_final: 0.7751 (mt) REVERT: H 88 PHE cc_start: 0.6484 (m-80) cc_final: 0.4441 (m-10) REVERT: H 103 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6517 (mm-30) REVERT: H 131 LYS cc_start: 0.7449 (tttt) cc_final: 0.7144 (tttt) REVERT: H 158 ASP cc_start: 0.7203 (t0) cc_final: 0.6622 (t70) REVERT: J 163 PHE cc_start: 0.6236 (t80) cc_final: 0.6015 (t80) REVERT: L 94 PHE cc_start: 0.7125 (p90) cc_final: 0.6802 (p90) REVERT: L 97 THR cc_start: 0.7210 (m) cc_final: 0.6930 (p) outliers start: 62 outliers final: 43 residues processed: 489 average time/residue: 0.3360 time to fit residues: 247.6720 Evaluate side-chains 489 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 439 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain G residue 14 TRP Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 160 TRP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 1.9990 chunk 252 optimal weight: 0.9980 chunk 229 optimal weight: 0.0670 chunk 245 optimal weight: 30.0000 chunk 147 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5789 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22098 Z= 0.224 Angle : 0.640 10.551 29991 Z= 0.331 Chirality : 0.045 0.209 3315 Planarity : 0.004 0.046 3864 Dihedral : 4.458 24.987 3003 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.61 % Allowed : 16.36 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2757 helix: -0.83 (0.28), residues: 321 sheet: 0.35 (0.19), residues: 804 loop : -0.72 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP G 92 HIS 0.008 0.001 HIS H 72 PHE 0.036 0.002 PHE F 154 TYR 0.033 0.002 TYR F 17 ARG 0.004 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 445 time to evaluate : 2.278 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: A 42 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7418 (mt) REVERT: A 88 TYR cc_start: 0.6552 (p90) cc_final: 0.6112 (p90) REVERT: A 123 ARG cc_start: 0.7222 (ttm170) cc_final: 0.6803 (ttm110) REVERT: A 170 LYS cc_start: 0.7662 (tttt) cc_final: 0.7318 (mmtt) REVERT: A 171 LEU cc_start: 0.7589 (mt) cc_final: 0.7230 (tp) REVERT: A 175 TYR cc_start: 0.6733 (t80) cc_final: 0.6414 (t80) REVERT: A 231 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7593 (ttt-90) REVERT: A 293 LYS cc_start: 0.7579 (mttt) cc_final: 0.7279 (mttt) REVERT: A 305 ILE cc_start: 0.8064 (mt) cc_final: 0.7574 (mm) REVERT: A 312 LYS cc_start: 0.7300 (mttt) cc_final: 0.6790 (mptt) REVERT: A 318 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7093 (ttmt) REVERT: A 321 LYS cc_start: 0.7483 (tptt) cc_final: 0.7192 (tptt) REVERT: B 82 LYS cc_start: 0.8419 (pttt) cc_final: 0.8090 (pttt) REVERT: B 92 TRP cc_start: 0.5732 (m-10) cc_final: 0.4978 (m-90) REVERT: B 131 LYS cc_start: 0.7468 (tttt) cc_final: 0.6957 (tttt) REVERT: B 140 PHE cc_start: 0.6002 (m-80) cc_final: 0.5646 (m-80) REVERT: B 149 MET cc_start: 0.5867 (mmt) cc_final: 0.5223 (mmm) REVERT: B 158 ASP cc_start: 0.6958 (t0) cc_final: 0.6470 (t0) REVERT: C 36 TRP cc_start: 0.6413 (m100) cc_final: 0.5605 (m100) REVERT: C 70 ILE cc_start: 0.4688 (OUTLIER) cc_final: 0.4380 (tp) REVERT: C 114 PHE cc_start: 0.7986 (m-80) cc_final: 0.7767 (m-80) REVERT: D 33 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.6042 (mp) REVERT: D 81 GLU cc_start: 0.6980 (pm20) cc_final: 0.6641 (pm20) REVERT: D 82 ASP cc_start: 0.7321 (m-30) cc_final: 0.6179 (m-30) REVERT: E 38 HIS cc_start: 0.6379 (m170) cc_final: 0.6067 (m170) REVERT: E 121 PHE cc_start: 0.6320 (t80) cc_final: 0.5647 (t80) REVERT: E 173 LYS cc_start: 0.8055 (tppt) cc_final: 0.7464 (tppt) REVERT: E 231 ARG cc_start: 0.8192 (mtt-85) cc_final: 0.7701 (mtp-110) REVERT: E 267 MET cc_start: 0.6727 (ppp) cc_final: 0.5691 (ppp) REVERT: E 323 ARG cc_start: 0.7674 (ttm-80) cc_final: 0.7440 (mtp85) REVERT: G 17 MET cc_start: 0.6646 (ttp) cc_final: 0.6313 (ttp) REVERT: G 86 ASP cc_start: 0.7526 (m-30) cc_final: 0.7267 (m-30) REVERT: G 88 PHE cc_start: 0.6500 (m-80) cc_final: 0.5531 (m-80) REVERT: G 121 LYS cc_start: 0.8075 (tttt) cc_final: 0.7746 (tmtt) REVERT: G 149 MET cc_start: 0.5752 (mmm) cc_final: 0.5227 (mmm) REVERT: I 29 PHE cc_start: 0.6944 (t80) cc_final: 0.6612 (t80) REVERT: I 112 TYR cc_start: 0.5547 (m-10) cc_final: 0.5236 (m-10) REVERT: K 78 LEU cc_start: 0.6998 (tp) cc_final: 0.6535 (mp) REVERT: F 106 ILE cc_start: 0.7630 (mt) cc_final: 0.7359 (mt) REVERT: F 179 LYS cc_start: 0.7196 (mmtt) cc_final: 0.6869 (mttp) REVERT: F 230 VAL cc_start: 0.7959 (t) cc_final: 0.7649 (p) REVERT: F 319 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8190 (p) REVERT: F 321 LYS cc_start: 0.7802 (tptt) cc_final: 0.7250 (tppt) REVERT: F 322 LEU cc_start: 0.8140 (mt) cc_final: 0.7744 (mt) REVERT: H 68 LYS cc_start: 0.8685 (mmtt) cc_final: 0.7843 (mmmt) REVERT: H 103 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6630 (mm-30) REVERT: H 131 LYS cc_start: 0.7447 (tttt) cc_final: 0.7170 (tttt) REVERT: H 158 ASP cc_start: 0.7224 (t0) cc_final: 0.6634 (t70) REVERT: J 163 PHE cc_start: 0.6230 (t80) cc_final: 0.5990 (t80) REVERT: L 72 THR cc_start: 0.7672 (m) cc_final: 0.7429 (t) REVERT: L 94 PHE cc_start: 0.7151 (p90) cc_final: 0.6826 (p90) outliers start: 63 outliers final: 45 residues processed: 482 average time/residue: 0.3429 time to fit residues: 249.9754 Evaluate side-chains 492 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 441 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 94 PHE Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 3.9990 chunk 259 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 chunk 271 optimal weight: 30.0000 chunk 250 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** E 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5967 moved from start: 0.6116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 22098 Z= 0.495 Angle : 0.858 11.400 29991 Z= 0.452 Chirality : 0.053 0.322 3315 Planarity : 0.005 0.058 3864 Dihedral : 5.637 40.860 3003 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.77 % Allowed : 16.15 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % 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: -1.20 (0.16), residues: 2757 helix: -1.51 (0.26), residues: 315 sheet: -0.10 (0.18), residues: 846 loop : -1.01 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP H 14 HIS 0.013 0.003 HIS F 190 PHE 0.049 0.003 PHE G 140 TYR 0.056 0.003 TYR F 17 ARG 0.008 0.001 ARG E 323 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5514 Ramachandran restraints generated. 2757 Oldfield, 0 Emsley, 2757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 452 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7504 (mt) REVERT: A 123 ARG cc_start: 0.7339 (ttm170) cc_final: 0.6914 (ttm110) REVERT: A 161 LEU cc_start: 0.6996 (mp) cc_final: 0.6717 (mp) REVERT: A 170 LYS cc_start: 0.7957 (tttt) cc_final: 0.7648 (mmtt) REVERT: A 175 TYR cc_start: 0.6796 (t80) cc_final: 0.6504 (t80) REVERT: A 176 ILE cc_start: 0.7757 (mt) cc_final: 0.7544 (mp) REVERT: A 234 GLU cc_start: 0.5203 (pm20) cc_final: 0.4942 (pm20) REVERT: A 293 LYS cc_start: 0.7895 (mttt) cc_final: 0.7487 (mttt) REVERT: A 312 LYS cc_start: 0.7371 (mttt) cc_final: 0.6830 (mptt) REVERT: A 318 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7510 (ttmt) REVERT: B 89 LEU cc_start: 0.7455 (tt) cc_final: 0.7145 (tp) REVERT: B 92 TRP cc_start: 0.5381 (m-10) cc_final: 0.4424 (m-90) REVERT: B 131 LYS cc_start: 0.7731 (tttt) cc_final: 0.7191 (tttt) REVERT: B 140 PHE cc_start: 0.6204 (m-80) cc_final: 0.5925 (m-80) REVERT: B 149 MET cc_start: 0.6119 (mmt) cc_final: 0.5424 (mmm) REVERT: B 158 ASP cc_start: 0.7294 (t0) cc_final: 0.6689 (t0) REVERT: C 12 VAL cc_start: 0.8051 (t) cc_final: 0.7518 (p) REVERT: C 36 TRP cc_start: 0.6556 (m100) cc_final: 0.5762 (m100) REVERT: C 70 ILE cc_start: 0.5303 (OUTLIER) cc_final: 0.4981 (tp) REVERT: D 33 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6184 (mp) REVERT: D 53 ARG cc_start: 0.7032 (mtp85) cc_final: 0.6590 (mtp85) REVERT: D 61 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7043 (ttp-110) REVERT: D 81 GLU cc_start: 0.7109 (pm20) cc_final: 0.6808 (pm20) REVERT: E 38 HIS cc_start: 0.6992 (m170) cc_final: 0.6763 (m-70) REVERT: E 121 PHE cc_start: 0.6649 (t80) cc_final: 0.5943 (t80) REVERT: E 170 LYS cc_start: 0.8017 (ttpp) cc_final: 0.7771 (ttpp) REVERT: E 231 ARG cc_start: 0.8209 (mtt-85) cc_final: 0.7671 (mtp-110) REVERT: E 267 MET cc_start: 0.6506 (ppp) cc_final: 0.5553 (ppp) REVERT: E 312 LYS cc_start: 0.7854 (mttt) cc_final: 0.7478 (mttt) REVERT: G 17 MET cc_start: 0.6788 (ttp) cc_final: 0.6202 (ttp) REVERT: G 86 ASP cc_start: 0.7755 (m-30) cc_final: 0.7555 (m-30) REVERT: G 92 TRP cc_start: 0.6270 (m-90) cc_final: 0.5388 (m-90) REVERT: G 149 MET cc_start: 0.6404 (mmm) cc_final: 0.5913 (mmm) REVERT: G 158 ASP cc_start: 0.7320 (t0) cc_final: 0.6736 (t0) REVERT: I 112 TYR cc_start: 0.5951 (m-10) cc_final: 0.5618 (m-10) REVERT: I 114 PHE cc_start: 0.7848 (m-80) cc_final: 0.7140 (m-80) REVERT: K 53 ARG cc_start: 0.6972 (mtp85) cc_final: 0.6727 (mtp85) REVERT: K 78 LEU cc_start: 0.6927 (tp) cc_final: 0.6474 (mp) REVERT: F 43 LEU cc_start: 0.7157 (tp) cc_final: 0.6921 (tp) REVERT: F 106 ILE cc_start: 0.7858 (mt) cc_final: 0.7520 (mt) REVERT: F 113 GLU cc_start: 0.5370 (tm-30) cc_final: 0.5085 (tm-30) REVERT: F 179 LYS cc_start: 0.7638 (mmtt) cc_final: 0.7164 (mttp) REVERT: F 191 HIS cc_start: 0.5503 (m-70) cc_final: 0.4889 (m-70) REVERT: F 230 VAL cc_start: 0.8065 (t) cc_final: 0.7785 (p) REVERT: F 296 ILE cc_start: 0.8065 (mt) cc_final: 0.7531 (tt) REVERT: F 312 LYS cc_start: 0.7088 (mttt) cc_final: 0.6775 (mmtm) REVERT: F 319 SER cc_start: 0.8694 (OUTLIER) cc_final: 0.8172 (p) REVERT: F 322 LEU cc_start: 0.8225 (mt) cc_final: 0.7718 (mt) REVERT: F 323 ARG cc_start: 0.7681 (ttt90) cc_final: 0.7369 (ttm-80) REVERT: H 68 LYS cc_start: 0.8766 (mmtt) cc_final: 0.7884 (mmmt) REVERT: H 76 ARG cc_start: 0.5936 (ttp80) cc_final: 0.5498 (ttp80) REVERT: H 103 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6802 (mm-30) REVERT: H 119 TYR cc_start: 0.7564 (m-80) cc_final: 0.6468 (t80) REVERT: H 131 LYS cc_start: 0.7274 (tttt) cc_final: 0.7032 (tttt) REVERT: H 149 MET cc_start: 0.6176 (mmt) cc_final: 0.5638 (mmm) REVERT: H 156 THR cc_start: 0.8737 (m) cc_final: 0.8390 (p) REVERT: H 158 ASP cc_start: 0.7422 (t0) cc_final: 0.6833 (t0) REVERT: J 163 PHE cc_start: 0.6394 (t80) cc_final: 0.6130 (t80) REVERT: L 37 GLN cc_start: 0.7644 (tt0) cc_final: 0.7422 (tt0) REVERT: L 72 THR cc_start: 0.8007 (m) cc_final: 0.7648 (t) REVERT: L 94 PHE cc_start: 0.7217 (p90) cc_final: 0.6956 (p90) REVERT: L 97 THR cc_start: 0.7532 (m) cc_final: 0.6977 (p) outliers start: 67 outliers final: 52 residues processed: 492 average time/residue: 0.3525 time to fit residues: 260.6639 Evaluate side-chains 497 residues out of total 2415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 439 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 14 TRP Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 61 ARG Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 259 VAL Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain I residue 106 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 319 SER Chi-restraints excluded: chain H residue 14 TRP Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 163 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 99 ASP Chi-restraints excluded: chain J residue 106 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 7.9990 chunk 230 optimal weight: 0.0980 chunk 66 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 222 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.218104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.183317 restraints weight = 33748.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.188948 restraints weight = 17585.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.192422 restraints weight = 10543.896| |-----------------------------------------------------------------------------| r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22098 Z= 0.220 Angle : 0.708 14.116 29991 Z= 0.362 Chirality : 0.048 0.309 3315 Planarity : 0.004 0.047 3864 Dihedral : 5.078 39.242 3003 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.15 % Allowed : 17.47 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.16), residues: 2757 helix: -1.51 (0.26), residues: 327 sheet: 0.17 (0.19), residues: 807 loop : -0.88 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP G 92 HIS 0.010 0.001 HIS H 72 PHE 0.040 0.002 PHE F 154 TYR 0.042 0.002 TYR A 17 ARG 0.006 0.000 ARG D 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5284.59 seconds wall clock time: 96 minutes 31.64 seconds (5791.64 seconds total)