Starting phenix.real_space_refine on Sun Mar 17 23:36:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0f_9763/03_2024/6j0f_9763.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0f_9763/03_2024/6j0f_9763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0f_9763/03_2024/6j0f_9763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0f_9763/03_2024/6j0f_9763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0f_9763/03_2024/6j0f_9763.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0f_9763/03_2024/6j0f_9763.pdb" } resolution = 3.8 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= 0.024 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 78 5.16 5 C 12192 2.51 5 N 3222 2.21 5 O 3822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A ASP 15": "OD1" <-> "OD2" Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 29": "NH1" <-> "NH2" Residue "A ASP 31": "OD1" <-> "OD2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A ASP 41": "OD1" <-> "OD2" Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A ASP 54": "OD1" <-> "OD2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B ASP 235": "OD1" <-> "OD2" Residue "B ASP 259": "OD1" <-> "OD2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "C ASP 9": "OD1" <-> "OD2" Residue "C ASP 15": "OD1" <-> "OD2" Residue "C TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C ASP 31": "OD1" <-> "OD2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 281": "NH1" <-> "NH2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "D ASP 9": "OD1" <-> "OD2" Residue "D ASP 15": "OD1" <-> "OD2" Residue "D TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D ASP 31": "OD1" <-> "OD2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D ASP 41": "OD1" <-> "OD2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D ASP 215": "OD1" <-> "OD2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "D ASP 259": "OD1" <-> "OD2" Residue "D PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 281": "NH1" <-> "NH2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "E ASP 9": "OD1" <-> "OD2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E GLU 34": "OE1" <-> "OE2" Residue "E ASP 41": "OD1" <-> "OD2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E ASP 54": "OD1" <-> "OD2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E GLU 188": "OE1" <-> "OE2" Residue "E ASP 215": "OD1" <-> "OD2" Residue "E ASP 235": "OD1" <-> "OD2" Residue "E ASP 259": "OD1" <-> "OD2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 281": "NH1" <-> "NH2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "F ASP 9": "OD1" <-> "OD2" Residue "F ASP 15": "OD1" <-> "OD2" Residue "F TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 29": "NH1" <-> "NH2" Residue "F ASP 31": "OD1" <-> "OD2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F ASP 41": "OD1" <-> "OD2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F ARG 63": "NH1" <-> "NH2" Residue "F TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "F GLU 188": "OE1" <-> "OE2" Residue "F ASP 215": "OD1" <-> "OD2" Residue "F ASP 235": "OD1" <-> "OD2" Residue "F ASP 259": "OD1" <-> "OD2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 281": "NH1" <-> "NH2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "a TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 18": "NH1" <-> "NH2" Residue "a PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 25": "OD1" <-> "OD2" Residue "a ASP 37": "OD1" <-> "OD2" Residue "a TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 41": "OD1" <-> "OD2" Residue "a ARG 46": "NH1" <-> "NH2" Residue "a PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 67": "NH1" <-> "NH2" Residue "a GLU 76": "OE1" <-> "OE2" Residue "a PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 93": "OD1" <-> "OD2" Residue "a ASP 131": "OD1" <-> "OD2" Residue "a GLU 136": "OE1" <-> "OE2" Residue "a ARG 143": "NH1" <-> "NH2" Residue "b TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 18": "NH1" <-> "NH2" Residue "b PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 25": "OD1" <-> "OD2" Residue "b ASP 37": "OD1" <-> "OD2" Residue "b TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 41": "OD1" <-> "OD2" Residue "b ARG 46": "NH1" <-> "NH2" Residue "b PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b GLU 76": "OE1" <-> "OE2" Residue "b PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 93": "OD1" <-> "OD2" Residue "b ASP 131": "OD1" <-> "OD2" Residue "b GLU 136": "OE1" <-> "OE2" Residue "b ARG 143": "NH1" <-> "NH2" Residue "c TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 18": "NH1" <-> "NH2" Residue "c PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 25": "OD1" <-> "OD2" Residue "c ASP 37": "OD1" <-> "OD2" Residue "c TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 41": "OD1" <-> "OD2" Residue "c ARG 46": "NH1" <-> "NH2" Residue "c PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 67": "NH1" <-> "NH2" Residue "c GLU 76": "OE1" <-> "OE2" Residue "c PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 93": "OD1" <-> "OD2" Residue "c ASP 131": "OD1" <-> "OD2" Residue "c GLU 136": "OE1" <-> "OE2" Residue "c ARG 143": "NH1" <-> "NH2" Residue "d TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 18": "NH1" <-> "NH2" Residue "d PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 25": "OD1" <-> "OD2" Residue "d ASP 37": "OD1" <-> "OD2" Residue "d TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 41": "OD1" <-> "OD2" Residue "d ARG 46": "NH1" <-> "NH2" Residue "d PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 67": "NH1" <-> "NH2" Residue "d GLU 76": "OE1" <-> "OE2" Residue "d PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 93": "OD1" <-> "OD2" Residue "d ASP 131": "OD1" <-> "OD2" Residue "d GLU 136": "OE1" <-> "OE2" Residue "d ARG 143": "NH1" <-> "NH2" Residue "e TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 18": "NH1" <-> "NH2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 25": "OD1" <-> "OD2" Residue "e ASP 37": "OD1" <-> "OD2" Residue "e TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 41": "OD1" <-> "OD2" Residue "e ARG 46": "NH1" <-> "NH2" Residue "e PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 67": "NH1" <-> "NH2" Residue "e GLU 76": "OE1" <-> "OE2" Residue "e PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 93": "OD1" <-> "OD2" Residue "e ASP 131": "OD1" <-> "OD2" Residue "e GLU 136": "OE1" <-> "OE2" Residue "e ARG 143": "NH1" <-> "NH2" Residue "f TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 18": "NH1" <-> "NH2" Residue "f PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 25": "OD1" <-> "OD2" Residue "f ASP 37": "OD1" <-> "OD2" Residue "f TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 41": "OD1" <-> "OD2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 67": "NH1" <-> "NH2" Residue "f GLU 76": "OE1" <-> "OE2" Residue "f PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 93": "OD1" <-> "OD2" Residue "f ASP 131": "OD1" <-> "OD2" Residue "f GLU 136": "OE1" <-> "OE2" Residue "f ARG 143": "NH1" <-> "NH2" 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: 19314 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2122 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 3 Chain: "B" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2122 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 3 Chain: "C" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2122 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 3 Chain: "D" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2122 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 3 Chain: "E" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2122 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 3 Chain: "F" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2122 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 3 Chain: "a" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1097 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "b" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1097 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "c" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1097 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "d" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1097 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "e" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1097 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "f" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1097 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} Time building chain proxies: 9.59, per 1000 atoms: 0.50 Number of scatterers: 19314 At special positions: 0 Unit cell: (153.577, 167.029, 103.132, 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 78 16.00 O 3822 8.00 N 3222 7.00 C 12192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.37 Conformation dependent library (CDL) restraints added in 3.8 seconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 36 sheets defined 21.4% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 removed outlier: 3.608A pdb=" N ALA A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.561A pdb=" N GLN A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.521A pdb=" N ASN A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 214 through 220 removed outlier: 4.050A pdb=" N VAL A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 4.296A pdb=" N GLU A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 19 removed outlier: 3.608A pdb=" N ALA B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 removed outlier: 3.561A pdb=" N GLN B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 152 removed outlier: 3.522A pdb=" N ASN B 147 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 211 Processing helix chain 'B' and resid 214 through 220 removed outlier: 4.051A pdb=" N VAL B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 267 removed outlier: 4.295A pdb=" N GLU B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 19 removed outlier: 3.608A pdb=" N ALA C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP C 15 " --> pdb=" O ASN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 120 removed outlier: 3.560A pdb=" N GLN C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 118 " --> pdb=" O GLN C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 152 removed outlier: 3.521A pdb=" N ASN C 147 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 151 " --> pdb=" O ASN C 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 211 Processing helix chain 'C' and resid 214 through 220 removed outlier: 4.050A pdb=" N VAL C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 267 removed outlier: 4.296A pdb=" N GLU C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL C 266 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 19 removed outlier: 3.608A pdb=" N ALA D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP D 15 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 removed outlier: 3.561A pdb=" N GLN D 110 " --> pdb=" O ASN D 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 118 " --> pdb=" O GLN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 152 removed outlier: 3.521A pdb=" N ASN D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 211 Processing helix chain 'D' and resid 214 through 220 removed outlier: 4.051A pdb=" N VAL D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 220 " --> pdb=" O ASN D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 267 removed outlier: 4.297A pdb=" N GLU D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG D 264 " --> pdb=" O ASN D 260 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL D 266 " --> pdb=" O PHE D 262 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 19 removed outlier: 3.608A pdb=" N ALA E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP E 15 " --> pdb=" O ASN E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 120 removed outlier: 3.561A pdb=" N GLN E 110 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA E 118 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 152 removed outlier: 3.522A pdb=" N ASN E 147 " --> pdb=" O ASN E 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU E 152 " --> pdb=" O PHE E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 211 Processing helix chain 'E' and resid 214 through 220 removed outlier: 4.050A pdb=" N VAL E 219 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 220 " --> pdb=" O ASN E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 267 removed outlier: 4.296A pdb=" N GLU E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL E 266 " --> pdb=" O PHE E 262 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 19 removed outlier: 3.609A pdb=" N ALA F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP F 15 " --> pdb=" O ASN F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 120 removed outlier: 3.562A pdb=" N GLN F 110 " --> pdb=" O ASN F 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA F 118 " --> pdb=" O GLN F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 152 removed outlier: 3.521A pdb=" N ASN F 147 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU F 152 " --> pdb=" O PHE F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 211 Processing helix chain 'F' and resid 214 through 220 removed outlier: 4.050A pdb=" N VAL F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F 220 " --> pdb=" O ASN F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 267 removed outlier: 4.296A pdb=" N GLU F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG F 264 " --> pdb=" O ASN F 260 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 82 Processing helix chain 'b' and resid 76 through 82 Processing helix chain 'c' and resid 76 through 82 Processing helix chain 'd' and resid 76 through 82 Processing helix chain 'e' and resid 76 through 82 Processing helix chain 'f' and resid 76 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.796A pdb=" N ALA A 27 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE A 46 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG A 29 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU A 48 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN A 82 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 51 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS A 80 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR A 162 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 132 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.550A pdb=" N ARG A 71 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 230 removed outlier: 3.619A pdb=" N SER A 247 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 243 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 241 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE A 242 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A 285 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 244 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 287 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.796A pdb=" N ALA B 27 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE B 46 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG B 29 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 48 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASN B 82 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE B 51 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS B 80 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR B 162 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 132 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.550A pdb=" N ARG B 71 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 223 through 230 removed outlier: 3.619A pdb=" N SER B 247 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 243 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 241 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE B 242 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE B 285 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 244 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 287 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 27 through 29 removed outlier: 6.795A pdb=" N ALA C 27 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE C 46 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG C 29 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU C 48 " --> pdb=" O ARG C 29 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN C 82 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE C 51 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS C 80 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR C 162 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 132 " --> pdb=" O THR C 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.550A pdb=" N ARG C 71 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 223 through 230 removed outlier: 3.619A pdb=" N SER C 247 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 243 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 241 " --> pdb=" O GLU C 230 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE C 242 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE C 285 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 244 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 287 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 27 through 29 removed outlier: 6.796A pdb=" N ALA D 27 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE D 46 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG D 29 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU D 48 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN D 82 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE D 51 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS D 80 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR D 162 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR D 132 " --> pdb=" O THR D 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 65 through 66 removed outlier: 3.549A pdb=" N ARG D 71 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 223 through 230 removed outlier: 3.619A pdb=" N SER D 247 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 243 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 241 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE D 242 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE D 285 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 244 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS D 287 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 27 through 29 removed outlier: 6.795A pdb=" N ALA E 27 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE E 46 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG E 29 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU E 48 " --> pdb=" O ARG E 29 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASN E 82 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE E 51 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS E 80 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR E 162 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR E 132 " --> pdb=" O THR E 165 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 65 through 66 removed outlier: 3.549A pdb=" N ARG E 71 " --> pdb=" O ASP E 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 223 through 230 removed outlier: 3.619A pdb=" N SER E 247 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 243 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 241 " --> pdb=" O GLU E 230 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE E 242 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE E 285 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 244 " --> pdb=" O ILE E 285 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS E 287 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 27 through 29 removed outlier: 6.796A pdb=" N ALA F 27 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE F 46 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG F 29 " --> pdb=" O ILE F 46 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU F 48 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN F 82 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE F 51 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS F 80 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR F 162 " --> pdb=" O TYR F 83 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR F 132 " --> pdb=" O THR F 165 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 65 through 66 removed outlier: 3.550A pdb=" N ARG F 71 " --> pdb=" O ASP F 66 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 223 through 230 removed outlier: 3.619A pdb=" N SER F 247 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU F 243 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 241 " --> pdb=" O GLU F 230 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE F 242 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE F 285 " --> pdb=" O ILE F 242 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU F 244 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS F 287 " --> pdb=" O LEU F 244 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 26 through 27 removed outlier: 5.803A pdb=" N LYS a 92 " --> pdb=" O ASN a 114 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN a 114 " --> pdb=" O LYS a 92 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET a 108 " --> pdb=" O LEU a 98 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN a 111 " --> pdb=" O MET a 146 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET a 146 " --> pdb=" O ASN a 111 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N SER a 113 " --> pdb=" O VAL a 144 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL a 144 " --> pdb=" O SER a 113 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA a 115 " --> pdb=" O ASP a 142 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP a 142 " --> pdb=" O ALA a 115 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET a 140 " --> pdb=" O PRO a 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER a 119 " --> pdb=" O THR a 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR a 62 " --> pdb=" O ALA a 141 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER a 32 " --> pdb=" O ARG a 67 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'a' and resid 26 through 27 removed outlier: 5.803A pdb=" N LYS a 92 " --> pdb=" O ASN a 114 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN a 114 " --> pdb=" O LYS a 92 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET a 108 " --> pdb=" O LEU a 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'a' and resid 37 through 38 removed outlier: 3.715A pdb=" N MET b 108 " --> pdb=" O LEU b 98 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN b 114 " --> pdb=" O LYS b 92 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS b 92 " --> pdb=" O ASN b 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 37 through 38 removed outlier: 6.890A pdb=" N ASN b 111 " --> pdb=" O MET b 146 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET b 146 " --> pdb=" O ASN b 111 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N SER b 113 " --> pdb=" O VAL b 144 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL b 144 " --> pdb=" O SER b 113 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA b 115 " --> pdb=" O ASP b 142 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP b 142 " --> pdb=" O ALA b 115 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET b 140 " --> pdb=" O PRO b 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER b 119 " --> pdb=" O THR b 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR b 62 " --> pdb=" O ALA b 141 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER b 32 " --> pdb=" O ARG b 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 40 through 44 removed outlier: 5.014A pdb=" N ASP a 41 " --> pdb=" O GLY a 57 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'a' and resid 125 through 126 removed outlier: 4.104A pdb=" N SER f 32 " --> pdb=" O ARG f 67 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR f 62 " --> pdb=" O ALA f 141 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER f 119 " --> pdb=" O THR f 138 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET f 140 " --> pdb=" O PRO f 117 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP f 142 " --> pdb=" O ALA f 115 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA f 115 " --> pdb=" O ASP f 142 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL f 144 " --> pdb=" O SER f 113 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N SER f 113 " --> pdb=" O VAL f 144 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET f 146 " --> pdb=" O ASN f 111 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN f 111 " --> pdb=" O MET f 146 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 125 through 126 removed outlier: 4.104A pdb=" N SER f 32 " --> pdb=" O ARG f 67 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR f 62 " --> pdb=" O ALA f 141 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER f 119 " --> pdb=" O THR f 138 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET f 140 " --> pdb=" O PRO f 117 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP f 142 " --> pdb=" O ALA f 115 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA f 115 " --> pdb=" O ASP f 142 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL f 144 " --> pdb=" O SER f 113 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N SER f 113 " --> pdb=" O VAL f 144 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET f 146 " --> pdb=" O ASN f 111 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN f 111 " --> pdb=" O MET f 146 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET f 108 " --> pdb=" O LEU f 98 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN f 114 " --> pdb=" O LYS f 92 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS f 92 " --> pdb=" O ASN f 114 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 37 through 38 removed outlier: 3.714A pdb=" N MET c 108 " --> pdb=" O LEU c 98 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN c 114 " --> pdb=" O LYS c 92 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS c 92 " --> pdb=" O ASN c 114 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 37 through 38 removed outlier: 6.888A pdb=" N ASN c 111 " --> pdb=" O MET c 146 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET c 146 " --> pdb=" O ASN c 111 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N SER c 113 " --> pdb=" O VAL c 144 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL c 144 " --> pdb=" O SER c 113 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA c 115 " --> pdb=" O ASP c 142 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP c 142 " --> pdb=" O ALA c 115 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET c 140 " --> pdb=" O PRO c 117 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER c 119 " --> pdb=" O THR c 138 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR c 62 " --> pdb=" O ALA c 141 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER c 32 " --> pdb=" O ARG c 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 40 through 44 removed outlier: 5.015A pdb=" N ASP b 41 " --> pdb=" O GLY b 57 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 37 through 38 removed outlier: 3.714A pdb=" N MET d 108 " --> pdb=" O LEU d 98 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN d 114 " --> pdb=" O LYS d 92 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS d 92 " --> pdb=" O ASN d 114 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 37 through 38 removed outlier: 6.890A pdb=" N ASN d 111 " --> pdb=" O MET d 146 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET d 146 " --> pdb=" O ASN d 111 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N SER d 113 " --> pdb=" O VAL d 144 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL d 144 " --> pdb=" O SER d 113 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA d 115 " --> pdb=" O ASP d 142 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP d 142 " --> pdb=" O ALA d 115 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET d 140 " --> pdb=" O PRO d 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER d 119 " --> pdb=" O THR d 138 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR d 62 " --> pdb=" O ALA d 141 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER d 32 " --> pdb=" O ARG d 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 40 through 44 removed outlier: 5.015A pdb=" N ASP c 41 " --> pdb=" O GLY c 57 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 37 through 38 removed outlier: 3.714A pdb=" N MET e 108 " --> pdb=" O LEU e 98 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN e 114 " --> pdb=" O LYS e 92 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS e 92 " --> pdb=" O ASN e 114 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 37 through 38 removed outlier: 6.890A pdb=" N ASN e 111 " --> pdb=" O MET e 146 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET e 146 " --> pdb=" O ASN e 111 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N SER e 113 " --> pdb=" O VAL e 144 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL e 144 " --> pdb=" O SER e 113 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA e 115 " --> pdb=" O ASP e 142 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP e 142 " --> pdb=" O ALA e 115 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET e 140 " --> pdb=" O PRO e 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER e 119 " --> pdb=" O THR e 138 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR e 62 " --> pdb=" O ALA e 141 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER e 32 " --> pdb=" O ARG e 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 40 through 44 removed outlier: 5.015A pdb=" N ASP d 41 " --> pdb=" O GLY d 57 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'e' and resid 40 through 44 removed outlier: 5.015A pdb=" N ASP e 41 " --> pdb=" O GLY e 57 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'f' and resid 40 through 44 removed outlier: 5.014A pdb=" N ASP f 41 " --> pdb=" O GLY f 57 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1719 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: 5.41 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6346 1.34 - 1.46: 3209 1.46 - 1.57: 9921 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 19620 Sorted by residual: bond pdb=" N LEU c 86 " pdb=" CA LEU c 86 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.23e-02 6.61e+03 6.15e+00 bond pdb=" N LEU d 86 " pdb=" CA LEU d 86 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.23e-02 6.61e+03 6.15e+00 bond pdb=" N LEU f 86 " pdb=" CA LEU f 86 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.23e-02 6.61e+03 6.14e+00 bond pdb=" N LEU a 86 " pdb=" CA LEU a 86 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.23e-02 6.61e+03 5.90e+00 bond pdb=" N LEU e 86 " pdb=" CA LEU e 86 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.23e-02 6.61e+03 5.84e+00 ... (remaining 19615 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.04: 426 106.04 - 113.02: 10803 113.02 - 120.00: 6524 120.00 - 126.98: 8701 126.98 - 133.96: 228 Bond angle restraints: 26682 Sorted by residual: angle pdb=" C GLN b 85 " pdb=" N LEU b 86 " pdb=" CA LEU b 86 " ideal model delta sigma weight residual 120.82 128.28 -7.46 1.50e+00 4.44e-01 2.47e+01 angle pdb=" C GLN e 85 " pdb=" N LEU e 86 " pdb=" CA LEU e 86 " ideal model delta sigma weight residual 120.82 128.26 -7.44 1.50e+00 4.44e-01 2.46e+01 angle pdb=" C GLN d 85 " pdb=" N LEU d 86 " pdb=" CA LEU d 86 " ideal model delta sigma weight residual 120.82 128.26 -7.44 1.50e+00 4.44e-01 2.46e+01 angle pdb=" C GLN f 85 " pdb=" N LEU f 86 " pdb=" CA LEU f 86 " ideal model delta sigma weight residual 120.82 128.23 -7.41 1.50e+00 4.44e-01 2.44e+01 angle pdb=" C GLN a 85 " pdb=" N LEU a 86 " pdb=" CA LEU a 86 " ideal model delta sigma weight residual 120.82 128.23 -7.41 1.50e+00 4.44e-01 2.44e+01 ... (remaining 26677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 10474 16.56 - 33.13: 1017 33.13 - 49.69: 275 49.69 - 66.25: 78 66.25 - 82.82: 30 Dihedral angle restraints: 11874 sinusoidal: 4680 harmonic: 7194 Sorted by residual: dihedral pdb=" CA GLN c 85 " pdb=" C GLN c 85 " pdb=" N LEU c 86 " pdb=" CA LEU c 86 " ideal model delta harmonic sigma weight residual -180.00 -145.66 -34.34 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA GLN f 85 " pdb=" C GLN f 85 " pdb=" N LEU f 86 " pdb=" CA LEU f 86 " ideal model delta harmonic sigma weight residual -180.00 -145.66 -34.34 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA GLN b 85 " pdb=" C GLN b 85 " pdb=" N LEU b 86 " pdb=" CA LEU b 86 " ideal model delta harmonic sigma weight residual 180.00 -145.67 -34.33 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 11871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2832 0.089 - 0.179: 300 0.179 - 0.268: 24 0.268 - 0.357: 0 0.357 - 0.447: 6 Chirality restraints: 3162 Sorted by residual: chirality pdb=" CB ILE D 128 " pdb=" CA ILE D 128 " pdb=" CG1 ILE D 128 " pdb=" CG2 ILE D 128 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CB ILE F 128 " pdb=" CA ILE F 128 " pdb=" CG1 ILE F 128 " pdb=" CG2 ILE F 128 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CB ILE E 128 " pdb=" CA ILE E 128 " pdb=" CG1 ILE E 128 " pdb=" CG2 ILE E 128 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.97e+00 ... (remaining 3159 not shown) Planarity restraints: 3438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP b 131 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" CG ASP b 131 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP b 131 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP b 131 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP a 131 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" CG ASP a 131 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP a 131 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP a 131 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP e 131 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" CG ASP e 131 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP e 131 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP e 131 " 0.019 2.00e-02 2.50e+03 ... (remaining 3435 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4841 2.79 - 3.32: 16131 3.32 - 3.85: 29723 3.85 - 4.37: 32559 4.37 - 4.90: 58990 Nonbonded interactions: 142244 Sorted by model distance: nonbonded pdb=" OH TYR B 132 " pdb=" O ASN c 130 " model vdw 2.265 2.440 nonbonded pdb=" OH TYR A 132 " pdb=" O ASN b 130 " model vdw 2.274 2.440 nonbonded pdb=" O ARG D 123 " pdb=" OG1 THR D 133 " model vdw 2.278 2.440 nonbonded pdb=" O ARG A 123 " pdb=" OG1 THR A 133 " model vdw 2.278 2.440 nonbonded pdb=" O ARG E 123 " pdb=" OG1 THR E 133 " model vdw 2.278 2.440 ... (remaining 142239 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.460 Check model and map are aligned: 0.300 Set scattering table: 0.150 Process input model: 47.060 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.007 0.065 19620 Z= 0.441 Angle : 1.043 16.294 26682 Z= 0.557 Chirality : 0.058 0.447 3162 Planarity : 0.006 0.057 3438 Dihedral : 15.760 82.817 7194 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.19 % Allowed : 14.25 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.13), residues: 2412 helix: -4.47 (0.08), residues: 528 sheet: -1.93 (0.18), residues: 666 loop : -2.95 (0.14), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 265 HIS 0.006 0.003 HIS B 52 PHE 0.026 0.003 PHE A 262 TYR 0.021 0.002 TYR C 49 ARG 0.009 0.001 ARG E 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 553 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.6990 (tmm) cc_final: 0.6665 (tmm) REVERT: A 242 ILE cc_start: 0.6582 (mt) cc_final: 0.6299 (mt) REVERT: A 268 ASN cc_start: 0.5583 (OUTLIER) cc_final: 0.4728 (m-40) REVERT: B 242 ILE cc_start: 0.6815 (mt) cc_final: 0.6603 (mt) REVERT: B 254 TYR cc_start: 0.8458 (m-80) cc_final: 0.8087 (m-80) REVERT: B 268 ASN cc_start: 0.6325 (OUTLIER) cc_final: 0.5182 (m-40) REVERT: C 268 ASN cc_start: 0.6007 (OUTLIER) cc_final: 0.4936 (m-40) REVERT: D 38 MET cc_start: 0.6975 (tmm) cc_final: 0.6611 (tmm) REVERT: D 242 ILE cc_start: 0.6422 (mt) cc_final: 0.6152 (mt) REVERT: D 268 ASN cc_start: 0.5695 (OUTLIER) cc_final: 0.4716 (m-40) REVERT: E 38 MET cc_start: 0.7140 (tmm) cc_final: 0.6920 (tmm) REVERT: E 242 ILE cc_start: 0.6795 (mt) cc_final: 0.6554 (mt) REVERT: E 254 TYR cc_start: 0.8427 (m-80) cc_final: 0.8158 (m-80) REVERT: E 268 ASN cc_start: 0.6386 (OUTLIER) cc_final: 0.4928 (m-40) REVERT: F 5 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8268 (mm-40) REVERT: F 245 SER cc_start: 0.8397 (m) cc_final: 0.7953 (t) REVERT: F 268 ASN cc_start: 0.5915 (OUTLIER) cc_final: 0.4757 (m-40) REVERT: a 16 VAL cc_start: 0.9454 (OUTLIER) cc_final: 0.9197 (p) REVERT: a 31 ASN cc_start: 0.8946 (t0) cc_final: 0.8574 (t0) REVERT: a 41 ASP cc_start: 0.8250 (t0) cc_final: 0.8036 (t70) REVERT: a 46 ARG cc_start: 0.6892 (ptt90) cc_final: 0.5038 (ptt90) REVERT: a 82 ASN cc_start: 0.8659 (t0) cc_final: 0.8371 (t0) REVERT: a 113 SER cc_start: 0.8935 (t) cc_final: 0.8584 (p) REVERT: a 143 ARG cc_start: 0.8236 (ttt-90) cc_final: 0.7335 (ttt180) REVERT: b 31 ASN cc_start: 0.8961 (t0) cc_final: 0.8727 (t0) REVERT: b 46 ARG cc_start: 0.6443 (ptt90) cc_final: 0.4547 (mtp85) REVERT: b 82 ASN cc_start: 0.8729 (t0) cc_final: 0.8433 (t0) REVERT: b 108 MET cc_start: 0.8210 (ttm) cc_final: 0.7965 (ttm) REVERT: b 113 SER cc_start: 0.9002 (t) cc_final: 0.8704 (p) REVERT: b 143 ARG cc_start: 0.8200 (ttt-90) cc_final: 0.7454 (ttt180) REVERT: b 146 MET cc_start: 0.8629 (ttm) cc_final: 0.8404 (ttm) REVERT: c 31 ASN cc_start: 0.9026 (t0) cc_final: 0.8784 (t0) REVERT: c 41 ASP cc_start: 0.8171 (t0) cc_final: 0.7870 (t70) REVERT: c 46 ARG cc_start: 0.6682 (ptt90) cc_final: 0.4519 (mtp85) REVERT: c 82 ASN cc_start: 0.8717 (t0) cc_final: 0.8355 (t0) REVERT: c 143 ARG cc_start: 0.8292 (ttt-90) cc_final: 0.7404 (ttt180) REVERT: d 16 VAL cc_start: 0.9486 (OUTLIER) cc_final: 0.9255 (p) REVERT: d 31 ASN cc_start: 0.8930 (t0) cc_final: 0.8545 (t0) REVERT: d 46 ARG cc_start: 0.6994 (ptt90) cc_final: 0.4902 (mtp85) REVERT: d 82 ASN cc_start: 0.8666 (t0) cc_final: 0.8401 (t0) REVERT: d 113 SER cc_start: 0.8843 (t) cc_final: 0.8424 (p) REVERT: d 143 ARG cc_start: 0.8465 (ttt-90) cc_final: 0.7242 (ttt180) REVERT: e 31 ASN cc_start: 0.8926 (t0) cc_final: 0.8715 (t0) REVERT: e 41 ASP cc_start: 0.8228 (t0) cc_final: 0.8020 (t70) REVERT: e 46 ARG cc_start: 0.6540 (ptt90) cc_final: 0.3817 (mtm110) REVERT: e 82 ASN cc_start: 0.8824 (t0) cc_final: 0.8566 (t0) REVERT: e 108 MET cc_start: 0.8097 (ttm) cc_final: 0.7860 (ttm) REVERT: e 113 SER cc_start: 0.9004 (t) cc_final: 0.8632 (p) REVERT: e 143 ARG cc_start: 0.8141 (ttt-90) cc_final: 0.7317 (ttt180) REVERT: f 31 ASN cc_start: 0.9008 (t0) cc_final: 0.8807 (t0) REVERT: f 41 ASP cc_start: 0.8140 (t0) cc_final: 0.7924 (t70) REVERT: f 46 ARG cc_start: 0.6520 (ptt90) cc_final: 0.4651 (ptt90) REVERT: f 143 ARG cc_start: 0.8194 (ttt-90) cc_final: 0.7394 (ttt180) outliers start: 48 outliers final: 16 residues processed: 589 average time/residue: 0.3059 time to fit residues: 271.1107 Evaluate side-chains 402 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 378 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 22 SER Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain f residue 22 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 103 optimal weight: 0.0670 chunk 63 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 192 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 143 optimal weight: 0.0670 chunk 223 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 52 HIS A 122 ASN B 39 GLN B 52 HIS B 122 ASN C 5 GLN C 52 HIS C 122 ASN D 39 GLN D 52 HIS ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 ASN E 52 HIS E 122 ASN E 154 ASN F 52 HIS F 122 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19620 Z= 0.153 Angle : 0.638 14.969 26682 Z= 0.315 Chirality : 0.044 0.169 3162 Planarity : 0.004 0.057 3438 Dihedral : 6.645 49.353 2652 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.93 % Allowed : 19.91 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.14), residues: 2412 helix: -2.43 (0.17), residues: 534 sheet: -1.43 (0.19), residues: 666 loop : -2.56 (0.15), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 265 HIS 0.003 0.001 HIS A 200 PHE 0.030 0.002 PHE A 262 TYR 0.017 0.002 TYR f 45 ARG 0.006 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 440 time to evaluate : 2.947 Fit side-chains REVERT: A 38 MET cc_start: 0.7047 (tmm) cc_final: 0.6648 (tmm) REVERT: A 105 ASP cc_start: 0.8141 (t0) cc_final: 0.7573 (p0) REVERT: A 202 LEU cc_start: 0.9254 (mm) cc_final: 0.9046 (mm) REVERT: A 240 MET cc_start: 0.2464 (mtp) cc_final: 0.2192 (mtm) REVERT: A 256 LYS cc_start: 0.8678 (mptt) cc_final: 0.8371 (tppt) REVERT: A 268 ASN cc_start: 0.5102 (OUTLIER) cc_final: 0.4383 (m-40) REVERT: B 5 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7962 (mm-40) REVERT: B 202 LEU cc_start: 0.9210 (mm) cc_final: 0.8996 (mm) REVERT: B 254 TYR cc_start: 0.8143 (m-80) cc_final: 0.7736 (m-80) REVERT: B 268 ASN cc_start: 0.5891 (OUTLIER) cc_final: 0.4383 (m-40) REVERT: C 17 MET cc_start: 0.8928 (ttp) cc_final: 0.8691 (ttp) REVERT: C 256 LYS cc_start: 0.8656 (mptt) cc_final: 0.8372 (tppt) REVERT: D 38 MET cc_start: 0.6999 (tmm) cc_final: 0.6519 (tmm) REVERT: D 240 MET cc_start: 0.2419 (mtp) cc_final: 0.2194 (mtm) REVERT: E 254 TYR cc_start: 0.8118 (m-80) cc_final: 0.7821 (m-80) REVERT: E 256 LYS cc_start: 0.8582 (mptt) cc_final: 0.8236 (tppt) REVERT: E 268 ASN cc_start: 0.5832 (OUTLIER) cc_final: 0.4093 (m-40) REVERT: F 256 LYS cc_start: 0.8672 (mptt) cc_final: 0.8293 (tppt) REVERT: a 16 VAL cc_start: 0.9419 (OUTLIER) cc_final: 0.9204 (p) REVERT: a 31 ASN cc_start: 0.8901 (t0) cc_final: 0.8545 (t0) REVERT: a 46 ARG cc_start: 0.6860 (ptt90) cc_final: 0.4943 (ptt90) REVERT: a 81 ILE cc_start: 0.9201 (tt) cc_final: 0.8925 (tt) REVERT: a 113 SER cc_start: 0.8943 (t) cc_final: 0.8706 (p) REVERT: a 132 ILE cc_start: 0.8851 (pt) cc_final: 0.8630 (pt) REVERT: a 143 ARG cc_start: 0.8353 (ttt-90) cc_final: 0.7059 (ttt180) REVERT: b 31 ASN cc_start: 0.8961 (t0) cc_final: 0.8721 (t0) REVERT: b 46 ARG cc_start: 0.6435 (ptt90) cc_final: 0.4594 (ptt90) REVERT: b 77 LEU cc_start: 0.9240 (mt) cc_final: 0.8839 (mt) REVERT: b 82 ASN cc_start: 0.8780 (t0) cc_final: 0.8494 (t0) REVERT: b 143 ARG cc_start: 0.8290 (ttt-90) cc_final: 0.7477 (ttt180) REVERT: c 31 ASN cc_start: 0.8969 (t0) cc_final: 0.8741 (t0) REVERT: c 41 ASP cc_start: 0.8153 (t0) cc_final: 0.7931 (t0) REVERT: c 45 TYR cc_start: 0.8980 (t80) cc_final: 0.8698 (t80) REVERT: c 46 ARG cc_start: 0.6281 (ptt90) cc_final: 0.4331 (ptt90) REVERT: c 143 ARG cc_start: 0.8184 (ttt-90) cc_final: 0.7173 (ttt180) REVERT: d 16 VAL cc_start: 0.9456 (OUTLIER) cc_final: 0.9253 (p) REVERT: d 31 ASN cc_start: 0.8879 (t0) cc_final: 0.8531 (t0) REVERT: d 81 ILE cc_start: 0.9227 (tt) cc_final: 0.8958 (tt) REVERT: d 82 ASN cc_start: 0.8706 (t0) cc_final: 0.8470 (t0) REVERT: d 113 SER cc_start: 0.8904 (t) cc_final: 0.8600 (p) REVERT: d 143 ARG cc_start: 0.8422 (ttt-90) cc_final: 0.7045 (ttt180) REVERT: e 31 ASN cc_start: 0.8918 (t0) cc_final: 0.8664 (t0) REVERT: e 46 ARG cc_start: 0.6261 (ptt90) cc_final: 0.4378 (ptt90) REVERT: e 77 LEU cc_start: 0.9218 (mt) cc_final: 0.8752 (mt) REVERT: e 82 ASN cc_start: 0.8844 (t0) cc_final: 0.8612 (t0) REVERT: e 113 SER cc_start: 0.9051 (t) cc_final: 0.8720 (p) REVERT: e 143 ARG cc_start: 0.8217 (ttt-90) cc_final: 0.7288 (ttt180) REVERT: f 31 ASN cc_start: 0.8968 (t0) cc_final: 0.8757 (t0) REVERT: f 46 ARG cc_start: 0.6276 (ptt90) cc_final: 0.4604 (ptt90) REVERT: f 81 ILE cc_start: 0.9274 (tt) cc_final: 0.9060 (tt) REVERT: f 143 ARG cc_start: 0.8174 (ttt-90) cc_final: 0.7237 (ttt180) outliers start: 86 outliers final: 45 residues processed: 499 average time/residue: 0.3124 time to fit residues: 235.0876 Evaluate side-chains 426 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 376 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 85 GLN Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 27 LYS Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 113 SER Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 chunk 152 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 241 optimal weight: 3.9990 chunk 199 optimal weight: 0.0980 chunk 221 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 179 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 154 ASN F 39 GLN c 58 GLN f 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19620 Z= 0.180 Angle : 0.619 14.691 26682 Z= 0.300 Chirality : 0.043 0.158 3162 Planarity : 0.004 0.055 3438 Dihedral : 5.597 43.192 2636 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.62 % Allowed : 21.55 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.15), residues: 2412 helix: -0.86 (0.21), residues: 528 sheet: -1.29 (0.19), residues: 690 loop : -2.24 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 265 HIS 0.002 0.001 HIS F 200 PHE 0.031 0.002 PHE B 262 TYR 0.022 0.002 TYR f 17 ARG 0.006 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 428 time to evaluate : 2.267 Fit side-chains REVERT: A 38 MET cc_start: 0.7141 (tmm) cc_final: 0.6656 (tmm) REVERT: A 105 ASP cc_start: 0.7954 (t0) cc_final: 0.7687 (p0) REVERT: B 254 TYR cc_start: 0.8097 (m-80) cc_final: 0.7744 (m-80) REVERT: C 31 ASP cc_start: 0.8068 (t0) cc_final: 0.7703 (t0) REVERT: D 30 PHE cc_start: 0.8732 (m-80) cc_final: 0.8475 (m-80) REVERT: D 38 MET cc_start: 0.7029 (tmm) cc_final: 0.6493 (tmm) REVERT: D 105 ASP cc_start: 0.7864 (t0) cc_final: 0.7300 (p0) REVERT: E 57 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9191 (mt) REVERT: E 254 TYR cc_start: 0.8096 (m-80) cc_final: 0.7734 (m-80) REVERT: E 256 LYS cc_start: 0.8562 (mptt) cc_final: 0.8254 (tppt) REVERT: F 17 MET cc_start: 0.8883 (ttp) cc_final: 0.8626 (ttp) REVERT: F 105 ASP cc_start: 0.8068 (t0) cc_final: 0.7687 (p0) REVERT: F 256 LYS cc_start: 0.8656 (mptt) cc_final: 0.8358 (tppt) REVERT: a 31 ASN cc_start: 0.8908 (t0) cc_final: 0.8563 (t0) REVERT: a 46 ARG cc_start: 0.6900 (ptt90) cc_final: 0.5299 (ptt90) REVERT: a 81 ILE cc_start: 0.9200 (tt) cc_final: 0.8994 (tt) REVERT: a 113 SER cc_start: 0.8920 (t) cc_final: 0.8694 (p) REVERT: a 143 ARG cc_start: 0.8475 (ttt-90) cc_final: 0.7143 (ttt180) REVERT: b 31 ASN cc_start: 0.8956 (t0) cc_final: 0.8726 (t0) REVERT: b 46 ARG cc_start: 0.6298 (ptt90) cc_final: 0.4398 (ptt90) REVERT: b 77 LEU cc_start: 0.9150 (mt) cc_final: 0.8744 (mt) REVERT: b 82 ASN cc_start: 0.8678 (t0) cc_final: 0.8394 (t0) REVERT: b 85 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: b 143 ARG cc_start: 0.8377 (ttt-90) cc_final: 0.7528 (ttt180) REVERT: c 31 ASN cc_start: 0.9035 (t0) cc_final: 0.8816 (t0) REVERT: c 46 ARG cc_start: 0.6411 (ptt90) cc_final: 0.4534 (ptt90) REVERT: c 113 SER cc_start: 0.8873 (t) cc_final: 0.8646 (p) REVERT: c 143 ARG cc_start: 0.8256 (ttt-90) cc_final: 0.7141 (ttt180) REVERT: d 31 ASN cc_start: 0.8898 (t0) cc_final: 0.8514 (t0) REVERT: d 46 ARG cc_start: 0.6874 (ptt90) cc_final: 0.4975 (ptt90) REVERT: d 81 ILE cc_start: 0.9231 (tt) cc_final: 0.9029 (tt) REVERT: d 82 ASN cc_start: 0.8602 (t0) cc_final: 0.8361 (t0) REVERT: d 113 SER cc_start: 0.8884 (t) cc_final: 0.8628 (p) REVERT: d 143 ARG cc_start: 0.8518 (ttt-90) cc_final: 0.7108 (ttt180) REVERT: e 31 ASN cc_start: 0.8916 (t0) cc_final: 0.8637 (t0) REVERT: e 46 ARG cc_start: 0.6357 (ptt90) cc_final: 0.4406 (ptt90) REVERT: e 77 LEU cc_start: 0.9121 (mt) cc_final: 0.8703 (mt) REVERT: e 85 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8086 (mt0) REVERT: e 113 SER cc_start: 0.9026 (t) cc_final: 0.8777 (p) REVERT: e 143 ARG cc_start: 0.8318 (ttt-90) cc_final: 0.7407 (ttt180) REVERT: e 145 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8788 (pt) REVERT: f 31 ASN cc_start: 0.8989 (t0) cc_final: 0.8769 (t0) REVERT: f 46 ARG cc_start: 0.6342 (ptt90) cc_final: 0.4668 (ptt90) REVERT: f 143 ARG cc_start: 0.8220 (ttt-90) cc_final: 0.7255 (ttt180) outliers start: 123 outliers final: 76 residues processed: 516 average time/residue: 0.2805 time to fit residues: 225.0162 Evaluate side-chains 478 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 398 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain a residue 22 SER Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 130 ASN Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 27 LYS Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 85 GLN Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 130 ASN Chi-restraints excluded: chain c residue 145 ILE Chi-restraints excluded: chain d residue 27 LYS Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 85 GLN Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 106 LEU Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain e residue 145 ILE Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 106 optimal weight: 0.0570 chunk 150 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 212 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN b 58 GLN e 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19620 Z= 0.171 Angle : 0.599 14.357 26682 Z= 0.287 Chirality : 0.043 0.153 3162 Planarity : 0.004 0.055 3438 Dihedral : 5.121 31.723 2628 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.57 % Allowed : 22.92 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.16), residues: 2412 helix: -0.06 (0.22), residues: 528 sheet: -0.91 (0.20), residues: 642 loop : -2.11 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 265 HIS 0.002 0.001 HIS B 200 PHE 0.029 0.002 PHE B 262 TYR 0.021 0.002 TYR b 17 ARG 0.004 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 439 time to evaluate : 2.227 Fit side-chains REVERT: A 38 MET cc_start: 0.7040 (tmm) cc_final: 0.6525 (tmm) REVERT: A 121 ASN cc_start: 0.8052 (m-40) cc_final: 0.7515 (m-40) REVERT: A 193 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7654 (pp) REVERT: A 256 LYS cc_start: 0.8651 (mptt) cc_final: 0.8362 (tppt) REVERT: B 105 ASP cc_start: 0.7741 (t0) cc_final: 0.7395 (p0) REVERT: B 254 TYR cc_start: 0.8149 (m-80) cc_final: 0.7788 (m-80) REVERT: D 14 MET cc_start: 0.8712 (mmm) cc_final: 0.8388 (tpp) REVERT: D 38 MET cc_start: 0.7024 (tmm) cc_final: 0.6503 (tmm) REVERT: D 105 ASP cc_start: 0.7822 (t0) cc_final: 0.7543 (p0) REVERT: D 193 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7583 (pp) REVERT: E 105 ASP cc_start: 0.7798 (t0) cc_final: 0.7527 (p0) REVERT: E 193 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7377 (pp) REVERT: E 240 MET cc_start: 0.2163 (mtp) cc_final: 0.1895 (mtp) REVERT: E 254 TYR cc_start: 0.8081 (m-80) cc_final: 0.7747 (m-80) REVERT: F 17 MET cc_start: 0.8958 (ttp) cc_final: 0.8696 (ttp) REVERT: F 105 ASP cc_start: 0.8150 (t0) cc_final: 0.7934 (p0) REVERT: F 256 LYS cc_start: 0.8657 (mptt) cc_final: 0.8276 (tppt) REVERT: a 31 ASN cc_start: 0.8911 (t0) cc_final: 0.8566 (t0) REVERT: a 46 ARG cc_start: 0.6872 (ptt90) cc_final: 0.5121 (ptt90) REVERT: a 81 ILE cc_start: 0.9217 (tt) cc_final: 0.8978 (tt) REVERT: a 113 SER cc_start: 0.8933 (t) cc_final: 0.8632 (p) REVERT: a 143 ARG cc_start: 0.8407 (ttt-90) cc_final: 0.7133 (ttt180) REVERT: b 31 ASN cc_start: 0.8959 (t0) cc_final: 0.8703 (t0) REVERT: b 46 ARG cc_start: 0.6296 (ptt90) cc_final: 0.4337 (ptt90) REVERT: b 77 LEU cc_start: 0.9079 (mt) cc_final: 0.8698 (mt) REVERT: b 143 ARG cc_start: 0.8343 (ttt-90) cc_final: 0.7456 (ttt180) REVERT: c 31 ASN cc_start: 0.9032 (t0) cc_final: 0.8789 (t0) REVERT: c 46 ARG cc_start: 0.6365 (ptt90) cc_final: 0.4667 (ptt90) REVERT: c 143 ARG cc_start: 0.8384 (ttt-90) cc_final: 0.7101 (ttt180) REVERT: d 31 ASN cc_start: 0.8900 (t0) cc_final: 0.8512 (t0) REVERT: d 46 ARG cc_start: 0.6856 (ptt90) cc_final: 0.5076 (ptt90) REVERT: d 81 ILE cc_start: 0.9236 (tt) cc_final: 0.8965 (tt) REVERT: d 82 ASN cc_start: 0.8591 (t0) cc_final: 0.8339 (t0) REVERT: d 113 SER cc_start: 0.8889 (t) cc_final: 0.8653 (p) REVERT: d 143 ARG cc_start: 0.8501 (ttt-90) cc_final: 0.7147 (ttt180) REVERT: e 31 ASN cc_start: 0.8924 (t0) cc_final: 0.8674 (t0) REVERT: e 46 ARG cc_start: 0.6430 (ptt90) cc_final: 0.4534 (ptt90) REVERT: e 77 LEU cc_start: 0.9088 (mt) cc_final: 0.8743 (mt) REVERT: e 82 ASN cc_start: 0.8676 (t0) cc_final: 0.8444 (t0) REVERT: e 113 SER cc_start: 0.9033 (t) cc_final: 0.8801 (p) REVERT: e 143 ARG cc_start: 0.8297 (ttt-90) cc_final: 0.7339 (ttt180) REVERT: e 145 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8778 (pt) REVERT: f 31 ASN cc_start: 0.9016 (t0) cc_final: 0.8773 (t0) REVERT: f 46 ARG cc_start: 0.6252 (ptt90) cc_final: 0.4555 (ptt90) REVERT: f 143 ARG cc_start: 0.8351 (ttt-90) cc_final: 0.7188 (ttt180) outliers start: 122 outliers final: 94 residues processed: 525 average time/residue: 0.2899 time to fit residues: 237.7151 Evaluate side-chains 508 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 410 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 287 LYS Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain a residue 22 SER Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 120 LEU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 130 ASN Chi-restraints excluded: chain c residue 145 ILE Chi-restraints excluded: chain d residue 27 LYS Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 106 LEU Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 145 ILE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 154 ASN E 260 ASN a 85 GLN d 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19620 Z= 0.147 Angle : 0.587 14.133 26682 Z= 0.280 Chirality : 0.043 0.169 3162 Planarity : 0.004 0.055 3438 Dihedral : 4.892 27.481 2628 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.98 % Allowed : 22.74 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.16), residues: 2412 helix: 0.49 (0.23), residues: 522 sheet: -0.87 (0.19), residues: 696 loop : -2.02 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 265 HIS 0.001 0.000 HIS F 200 PHE 0.033 0.002 PHE D 262 TYR 0.016 0.001 TYR e 45 ARG 0.003 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 427 time to evaluate : 2.305 Fit side-chains REVERT: A 38 MET cc_start: 0.7060 (tmm) cc_final: 0.6591 (tmm) REVERT: A 50 ASP cc_start: 0.7944 (t0) cc_final: 0.7684 (t0) REVERT: A 121 ASN cc_start: 0.8070 (m-40) cc_final: 0.7821 (m-40) REVERT: A 193 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8048 (pp) REVERT: B 193 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7473 (pp) REVERT: B 254 TYR cc_start: 0.8155 (m-80) cc_final: 0.7806 (m-80) REVERT: D 38 MET cc_start: 0.7077 (tmm) cc_final: 0.6620 (tmm) REVERT: D 193 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7807 (pp) REVERT: E 105 ASP cc_start: 0.7955 (t0) cc_final: 0.7653 (p0) REVERT: E 193 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7458 (pp) REVERT: E 254 TYR cc_start: 0.8077 (m-80) cc_final: 0.7692 (m-80) REVERT: E 256 LYS cc_start: 0.8535 (mptt) cc_final: 0.8244 (tppt) REVERT: E 262 PHE cc_start: 0.7093 (p90) cc_final: 0.6885 (p90) REVERT: F 193 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7434 (pp) REVERT: F 230 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: F 256 LYS cc_start: 0.8621 (mptt) cc_final: 0.8230 (tppt) REVERT: a 31 ASN cc_start: 0.8896 (t0) cc_final: 0.8605 (t0) REVERT: a 46 ARG cc_start: 0.6817 (ptt90) cc_final: 0.5035 (ptt90) REVERT: a 81 ILE cc_start: 0.9217 (tt) cc_final: 0.8966 (tt) REVERT: a 113 SER cc_start: 0.8948 (t) cc_final: 0.8625 (p) REVERT: a 143 ARG cc_start: 0.8373 (ttt-90) cc_final: 0.7133 (ttt180) REVERT: b 31 ASN cc_start: 0.8958 (t0) cc_final: 0.8701 (t0) REVERT: b 46 ARG cc_start: 0.6392 (ptt90) cc_final: 0.4532 (ptt90) REVERT: b 77 LEU cc_start: 0.9045 (mt) cc_final: 0.8661 (mt) REVERT: b 143 ARG cc_start: 0.8341 (ttt-90) cc_final: 0.7355 (ttt180) REVERT: c 31 ASN cc_start: 0.9050 (t0) cc_final: 0.8794 (t0) REVERT: c 46 ARG cc_start: 0.6326 (ptt90) cc_final: 0.4597 (ptt90) REVERT: c 143 ARG cc_start: 0.8386 (ttt-90) cc_final: 0.7085 (ttt180) REVERT: d 31 ASN cc_start: 0.8923 (t0) cc_final: 0.8503 (t0) REVERT: d 46 ARG cc_start: 0.6769 (ptt90) cc_final: 0.4990 (ptt90) REVERT: d 82 ASN cc_start: 0.8555 (t0) cc_final: 0.8304 (t0) REVERT: d 113 SER cc_start: 0.8841 (t) cc_final: 0.8612 (p) REVERT: d 143 ARG cc_start: 0.8483 (ttt-90) cc_final: 0.7141 (ttt180) REVERT: e 31 ASN cc_start: 0.8924 (t0) cc_final: 0.8655 (t0) REVERT: e 46 ARG cc_start: 0.6580 (ptt90) cc_final: 0.4733 (ptt90) REVERT: e 77 LEU cc_start: 0.9068 (mt) cc_final: 0.8699 (mt) REVERT: e 82 ASN cc_start: 0.8633 (t0) cc_final: 0.8371 (t0) REVERT: e 143 ARG cc_start: 0.8290 (ttt-90) cc_final: 0.7371 (ttt180) REVERT: e 145 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8727 (pt) REVERT: f 27 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8397 (mtmm) REVERT: f 31 ASN cc_start: 0.9043 (t0) cc_final: 0.8796 (t0) REVERT: f 46 ARG cc_start: 0.6180 (ptt90) cc_final: 0.4436 (ptt90) REVERT: f 143 ARG cc_start: 0.8367 (ttt-90) cc_final: 0.7206 (ttt180) outliers start: 131 outliers final: 95 residues processed: 530 average time/residue: 0.2635 time to fit residues: 219.9533 Evaluate side-chains 501 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 398 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain a residue 22 SER Chi-restraints excluded: chain a residue 60 GLN Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 130 ASN Chi-restraints excluded: chain c residue 145 ILE Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain d residue 139 LEU Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 106 LEU Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain e residue 145 ILE Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 238 optimal weight: 0.0970 chunk 197 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 GLN B 260 ASN C 122 ASN F 39 GLN F 122 ASN c 58 GLN f 58 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19620 Z= 0.296 Angle : 0.651 13.891 26682 Z= 0.318 Chirality : 0.045 0.167 3162 Planarity : 0.004 0.054 3438 Dihedral : 5.255 30.774 2628 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 6.67 % Allowed : 22.47 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.17), residues: 2412 helix: 0.38 (0.23), residues: 540 sheet: -0.98 (0.20), residues: 678 loop : -1.87 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 110 HIS 0.002 0.001 HIS F 200 PHE 0.027 0.002 PHE A 262 TYR 0.020 0.002 TYR b 45 ARG 0.003 0.000 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 406 time to evaluate : 2.418 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7203 (tmm) cc_final: 0.6894 (tmm) REVERT: A 121 ASN cc_start: 0.8220 (m-40) cc_final: 0.7871 (m-40) REVERT: A 193 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8132 (pp) REVERT: A 256 LYS cc_start: 0.8640 (mptt) cc_final: 0.8372 (tppt) REVERT: B 193 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7458 (pp) REVERT: B 230 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7503 (pm20) REVERT: B 254 TYR cc_start: 0.8296 (m-80) cc_final: 0.7871 (m-80) REVERT: C 31 ASP cc_start: 0.8071 (t0) cc_final: 0.7662 (t0) REVERT: C 193 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7449 (pp) REVERT: D 38 MET cc_start: 0.7319 (tmm) cc_final: 0.6916 (tmm) REVERT: D 193 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7871 (pp) REVERT: D 254 TYR cc_start: 0.8309 (m-80) cc_final: 0.7776 (m-80) REVERT: D 256 LYS cc_start: 0.8706 (mptt) cc_final: 0.8394 (tppt) REVERT: E 105 ASP cc_start: 0.8052 (t0) cc_final: 0.7756 (p0) REVERT: E 193 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7447 (pp) REVERT: E 230 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7585 (pm20) REVERT: E 254 TYR cc_start: 0.8200 (m-80) cc_final: 0.7763 (m-80) REVERT: E 256 LYS cc_start: 0.8601 (mptt) cc_final: 0.8332 (tppt) REVERT: E 262 PHE cc_start: 0.7065 (p90) cc_final: 0.6790 (p90) REVERT: F 193 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7547 (pp) REVERT: F 256 LYS cc_start: 0.8694 (mptt) cc_final: 0.8351 (tppt) REVERT: a 31 ASN cc_start: 0.8887 (t0) cc_final: 0.8564 (t0) REVERT: a 85 GLN cc_start: 0.8487 (mt0) cc_final: 0.8270 (mt0) REVERT: a 113 SER cc_start: 0.8916 (t) cc_final: 0.8499 (p) REVERT: a 143 ARG cc_start: 0.8508 (ttt-90) cc_final: 0.7144 (ttt180) REVERT: b 31 ASN cc_start: 0.8973 (t0) cc_final: 0.8763 (t0) REVERT: b 46 ARG cc_start: 0.6559 (ptt90) cc_final: 0.4673 (ptt90) REVERT: b 77 LEU cc_start: 0.9195 (mt) cc_final: 0.8875 (mt) REVERT: b 143 ARG cc_start: 0.8629 (ttt-90) cc_final: 0.7440 (ttt180) REVERT: c 31 ASN cc_start: 0.8987 (t0) cc_final: 0.8744 (t0) REVERT: c 46 ARG cc_start: 0.6324 (ptt90) cc_final: 0.4336 (ptt90) REVERT: c 143 ARG cc_start: 0.8586 (ttt-90) cc_final: 0.7347 (ttt180) REVERT: d 31 ASN cc_start: 0.8882 (t0) cc_final: 0.8560 (t0) REVERT: d 82 ASN cc_start: 0.8717 (t0) cc_final: 0.8401 (t0) REVERT: d 113 SER cc_start: 0.8838 (t) cc_final: 0.8488 (p) REVERT: d 143 ARG cc_start: 0.8560 (ttt-90) cc_final: 0.7244 (ttt180) REVERT: e 31 ASN cc_start: 0.8962 (t0) cc_final: 0.8754 (t0) REVERT: e 46 ARG cc_start: 0.6555 (ptt90) cc_final: 0.4543 (ptt90) REVERT: e 77 LEU cc_start: 0.9230 (mt) cc_final: 0.8920 (mt) REVERT: e 82 ASN cc_start: 0.8766 (t0) cc_final: 0.8531 (t0) REVERT: e 143 ARG cc_start: 0.8370 (ttt-90) cc_final: 0.7466 (ttt180) REVERT: e 145 ILE cc_start: 0.9086 (pt) cc_final: 0.8850 (pt) REVERT: f 31 ASN cc_start: 0.8995 (t0) cc_final: 0.8748 (t0) REVERT: f 46 ARG cc_start: 0.6441 (ptt90) cc_final: 0.4457 (ptt90) REVERT: f 143 ARG cc_start: 0.8506 (ttt-90) cc_final: 0.7328 (ttt180) outliers start: 146 outliers final: 116 residues processed: 526 average time/residue: 0.2788 time to fit residues: 229.0712 Evaluate side-chains 513 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 389 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 287 LYS Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 22 SER Chi-restraints excluded: chain a residue 28 ILE Chi-restraints excluded: chain a residue 60 GLN Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 120 LEU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 130 ASN Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain d residue 10 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain d residue 139 LEU Chi-restraints excluded: chain e residue 14 ILE Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 106 LEU Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 1.9990 chunk 26 optimal weight: 0.0040 chunk 135 optimal weight: 0.0020 chunk 173 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 144 optimal weight: 0.0470 chunk 109 optimal weight: 1.9990 overall best weight: 0.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN B 260 ASN a 58 GLN d 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19620 Z= 0.139 Angle : 0.612 14.136 26682 Z= 0.289 Chirality : 0.043 0.158 3162 Planarity : 0.004 0.054 3438 Dihedral : 4.885 29.126 2628 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.53 % Allowed : 24.02 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2412 helix: 0.84 (0.23), residues: 522 sheet: -0.67 (0.21), residues: 642 loop : -1.89 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP f 110 HIS 0.001 0.000 HIS F 200 PHE 0.033 0.001 PHE D 262 TYR 0.017 0.001 TYR e 45 ARG 0.002 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 439 time to evaluate : 2.424 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7118 (tmm) cc_final: 0.6904 (tmm) REVERT: A 121 ASN cc_start: 0.8015 (m-40) cc_final: 0.7379 (m-40) REVERT: B 193 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7490 (pp) REVERT: B 230 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7460 (pm20) REVERT: B 254 TYR cc_start: 0.8244 (m-80) cc_final: 0.7878 (m-80) REVERT: C 43 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6850 (mtt) REVERT: C 193 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7379 (pp) REVERT: D 38 MET cc_start: 0.7200 (tmm) cc_final: 0.6862 (tmm) REVERT: D 193 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8124 (pp) REVERT: D 256 LYS cc_start: 0.8664 (mptt) cc_final: 0.8341 (tppt) REVERT: E 193 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7451 (pp) REVERT: E 230 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: E 254 TYR cc_start: 0.8146 (m-80) cc_final: 0.7747 (m-80) REVERT: E 256 LYS cc_start: 0.8570 (mptt) cc_final: 0.8307 (tppt) REVERT: F 193 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7442 (pp) REVERT: F 220 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8817 (mp) REVERT: F 256 LYS cc_start: 0.8665 (mptt) cc_final: 0.8341 (tppt) REVERT: a 31 ASN cc_start: 0.8901 (t0) cc_final: 0.8593 (t0) REVERT: a 46 ARG cc_start: 0.6954 (ptt90) cc_final: 0.4772 (ptt90) REVERT: a 81 ILE cc_start: 0.9252 (tt) cc_final: 0.9010 (tt) REVERT: a 113 SER cc_start: 0.8870 (t) cc_final: 0.8511 (p) REVERT: a 143 ARG cc_start: 0.8344 (ttt-90) cc_final: 0.7129 (ttt180) REVERT: b 31 ASN cc_start: 0.8935 (t0) cc_final: 0.8713 (t0) REVERT: b 46 ARG cc_start: 0.6480 (ptt90) cc_final: 0.4530 (ptt90) REVERT: b 143 ARG cc_start: 0.8541 (ttt-90) cc_final: 0.7437 (ttt180) REVERT: c 46 ARG cc_start: 0.6163 (ptt90) cc_final: 0.4335 (ptt90) REVERT: c 143 ARG cc_start: 0.8422 (ttt-90) cc_final: 0.7188 (ttt180) REVERT: d 31 ASN cc_start: 0.8887 (t0) cc_final: 0.8460 (t0) REVERT: d 46 ARG cc_start: 0.6954 (ptt90) cc_final: 0.4766 (ptt90) REVERT: d 81 ILE cc_start: 0.9268 (tt) cc_final: 0.9013 (tt) REVERT: d 82 ASN cc_start: 0.8606 (t0) cc_final: 0.8390 (t0) REVERT: d 113 SER cc_start: 0.8860 (t) cc_final: 0.8546 (p) REVERT: d 143 ARG cc_start: 0.8391 (ttt-90) cc_final: 0.7150 (ttt180) REVERT: e 31 ASN cc_start: 0.8933 (t0) cc_final: 0.8664 (t0) REVERT: e 46 ARG cc_start: 0.6559 (ptt90) cc_final: 0.4615 (ptt90) REVERT: e 82 ASN cc_start: 0.8655 (t0) cc_final: 0.8405 (t0) REVERT: e 143 ARG cc_start: 0.8207 (ttt-90) cc_final: 0.7378 (ttt180) REVERT: e 145 ILE cc_start: 0.8898 (pt) cc_final: 0.8688 (pt) REVERT: f 46 ARG cc_start: 0.6157 (ptt90) cc_final: 0.4327 (ptt90) REVERT: f 143 ARG cc_start: 0.8334 (ttt-90) cc_final: 0.7240 (ttt180) outliers start: 121 outliers final: 93 residues processed: 524 average time/residue: 0.2839 time to fit residues: 229.0948 Evaluate side-chains 509 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 407 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 22 SER Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 60 GLN Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 27 LYS Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 120 LEU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 130 ASN Chi-restraints excluded: chain c residue 145 ILE Chi-restraints excluded: chain d residue 10 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 0.2980 chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN E 260 ASN d 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19620 Z= 0.285 Angle : 0.659 14.192 26682 Z= 0.318 Chirality : 0.045 0.166 3162 Planarity : 0.004 0.054 3438 Dihedral : 5.136 29.540 2628 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 6.85 % Allowed : 22.74 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2412 helix: 0.79 (0.23), residues: 528 sheet: -0.67 (0.22), residues: 600 loop : -1.83 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 110 HIS 0.002 0.001 HIS D 52 PHE 0.028 0.002 PHE D 262 TYR 0.019 0.002 TYR b 45 ARG 0.005 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 401 time to evaluate : 2.273 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7179 (tmm) cc_final: 0.6922 (tmm) REVERT: B 193 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7564 (pp) REVERT: B 230 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: B 254 TYR cc_start: 0.8338 (m-80) cc_final: 0.7940 (m-80) REVERT: C 31 ASP cc_start: 0.7992 (t0) cc_final: 0.7774 (t0) REVERT: C 193 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7451 (pp) REVERT: D 38 MET cc_start: 0.7340 (tmm) cc_final: 0.6892 (tmm) REVERT: D 193 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8149 (pp) REVERT: D 256 LYS cc_start: 0.8692 (mptt) cc_final: 0.8392 (tppt) REVERT: E 193 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7540 (pp) REVERT: E 230 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7471 (pm20) REVERT: E 254 TYR cc_start: 0.8250 (m-80) cc_final: 0.7857 (m-80) REVERT: E 256 LYS cc_start: 0.8695 (mptt) cc_final: 0.8344 (tppt) REVERT: E 262 PHE cc_start: 0.7092 (p90) cc_final: 0.6851 (p90) REVERT: F 31 ASP cc_start: 0.7928 (t0) cc_final: 0.7703 (t0) REVERT: F 193 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7535 (pp) REVERT: F 220 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8842 (mp) REVERT: F 256 LYS cc_start: 0.8645 (mptt) cc_final: 0.8343 (tppt) REVERT: a 31 ASN cc_start: 0.8929 (t0) cc_final: 0.8658 (t0) REVERT: a 81 ILE cc_start: 0.9351 (tt) cc_final: 0.9098 (tt) REVERT: a 108 MET cc_start: 0.8176 (ttm) cc_final: 0.7892 (ttt) REVERT: a 111 ASN cc_start: 0.9018 (p0) cc_final: 0.8637 (p0) REVERT: a 113 SER cc_start: 0.8900 (t) cc_final: 0.8431 (p) REVERT: a 143 ARG cc_start: 0.8498 (ttt-90) cc_final: 0.7231 (ttt180) REVERT: b 31 ASN cc_start: 0.8987 (t0) cc_final: 0.8772 (t0) REVERT: b 46 ARG cc_start: 0.6591 (ptt90) cc_final: 0.4696 (ptt90) REVERT: b 77 LEU cc_start: 0.9166 (mt) cc_final: 0.8871 (mt) REVERT: b 143 ARG cc_start: 0.8650 (ttt-90) cc_final: 0.7305 (ttt180) REVERT: b 146 MET cc_start: 0.7058 (ttt) cc_final: 0.6850 (ttt) REVERT: c 46 ARG cc_start: 0.6287 (ptt90) cc_final: 0.4511 (ptt90) REVERT: c 82 ASN cc_start: 0.8614 (t0) cc_final: 0.8235 (t0) REVERT: c 143 ARG cc_start: 0.8611 (ttt-90) cc_final: 0.7386 (ttt180) REVERT: d 31 ASN cc_start: 0.8901 (t0) cc_final: 0.8568 (t0) REVERT: d 81 ILE cc_start: 0.9370 (tt) cc_final: 0.9106 (tt) REVERT: d 82 ASN cc_start: 0.8684 (t0) cc_final: 0.8403 (t0) REVERT: d 111 ASN cc_start: 0.8918 (p0) cc_final: 0.8673 (p0) REVERT: d 113 SER cc_start: 0.8848 (t) cc_final: 0.8416 (p) REVERT: d 143 ARG cc_start: 0.8541 (ttt-90) cc_final: 0.7277 (ttt180) REVERT: e 31 ASN cc_start: 0.8971 (t0) cc_final: 0.8764 (t0) REVERT: e 46 ARG cc_start: 0.6826 (ptt90) cc_final: 0.4765 (ptt90) REVERT: e 77 LEU cc_start: 0.9174 (mt) cc_final: 0.8884 (mt) REVERT: e 82 ASN cc_start: 0.8791 (t0) cc_final: 0.8540 (t0) REVERT: e 143 ARG cc_start: 0.8315 (ttt-90) cc_final: 0.7860 (ttt180) REVERT: e 145 ILE cc_start: 0.9044 (pt) cc_final: 0.8476 (mt) REVERT: f 46 ARG cc_start: 0.6291 (ptt90) cc_final: 0.4511 (ptt90) REVERT: f 82 ASN cc_start: 0.8628 (t0) cc_final: 0.8262 (t0) REVERT: f 143 ARG cc_start: 0.8486 (ttt-90) cc_final: 0.7280 (ttt180) outliers start: 150 outliers final: 121 residues processed: 512 average time/residue: 0.2807 time to fit residues: 223.1291 Evaluate side-chains 520 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 391 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 22 SER Chi-restraints excluded: chain a residue 60 GLN Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 130 ASN Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 120 LEU Chi-restraints excluded: chain b residue 142 ASP Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain d residue 10 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain d residue 139 LEU Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 171 ASN E 260 ASN F 171 ASN d 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19620 Z= 0.214 Angle : 0.650 14.014 26682 Z= 0.310 Chirality : 0.044 0.164 3162 Planarity : 0.004 0.054 3438 Dihedral : 5.074 28.324 2628 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.84 % Allowed : 24.38 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2412 helix: 0.93 (0.23), residues: 534 sheet: -0.90 (0.20), residues: 660 loop : -1.74 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 88 HIS 0.002 0.001 HIS A 52 PHE 0.025 0.002 PHE A 262 TYR 0.017 0.002 TYR f 17 ARG 0.009 0.000 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 406 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7093 (tmm) cc_final: 0.6856 (tmm) REVERT: B 43 MET cc_start: 0.7330 (mtt) cc_final: 0.6917 (mtp) REVERT: B 193 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7542 (pp) REVERT: B 230 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7429 (pm20) REVERT: B 254 TYR cc_start: 0.8321 (m-80) cc_final: 0.7929 (m-80) REVERT: C 31 ASP cc_start: 0.7948 (t0) cc_final: 0.7724 (t0) REVERT: C 193 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7446 (pp) REVERT: D 193 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8201 (pp) REVERT: D 254 TYR cc_start: 0.8332 (m-80) cc_final: 0.7911 (m-80) REVERT: D 256 LYS cc_start: 0.8689 (mptt) cc_final: 0.8390 (tppt) REVERT: E 193 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7516 (pp) REVERT: E 230 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7458 (pm20) REVERT: E 254 TYR cc_start: 0.8264 (m-80) cc_final: 0.7907 (m-80) REVERT: E 256 LYS cc_start: 0.8607 (mptt) cc_final: 0.8350 (tppt) REVERT: E 262 PHE cc_start: 0.7053 (p90) cc_final: 0.6791 (p90) REVERT: F 193 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7234 (pp) REVERT: F 256 LYS cc_start: 0.8672 (mptt) cc_final: 0.8364 (tppt) REVERT: a 31 ASN cc_start: 0.8899 (t0) cc_final: 0.8556 (t0) REVERT: a 46 ARG cc_start: 0.6983 (ptt90) cc_final: 0.4902 (ptt90) REVERT: a 81 ILE cc_start: 0.9324 (tt) cc_final: 0.9072 (tt) REVERT: a 111 ASN cc_start: 0.8944 (p0) cc_final: 0.8684 (p0) REVERT: a 113 SER cc_start: 0.8905 (t) cc_final: 0.8453 (p) REVERT: a 143 ARG cc_start: 0.8447 (ttt-90) cc_final: 0.7136 (ttt180) REVERT: b 31 ASN cc_start: 0.8986 (t0) cc_final: 0.8757 (t0) REVERT: b 46 ARG cc_start: 0.6668 (ptt90) cc_final: 0.4609 (ptt90) REVERT: b 143 ARG cc_start: 0.8612 (ttt-90) cc_final: 0.7365 (ttt180) REVERT: c 46 ARG cc_start: 0.6214 (ptt90) cc_final: 0.4382 (ptt90) REVERT: c 82 ASN cc_start: 0.8594 (t0) cc_final: 0.8236 (t0) REVERT: c 143 ARG cc_start: 0.8504 (ttt-90) cc_final: 0.7277 (ttt180) REVERT: d 31 ASN cc_start: 0.8890 (t0) cc_final: 0.8593 (t0) REVERT: d 46 ARG cc_start: 0.6851 (ptt90) cc_final: 0.4752 (ptt90) REVERT: d 82 ASN cc_start: 0.8668 (t0) cc_final: 0.8425 (t0) REVERT: d 113 SER cc_start: 0.8848 (t) cc_final: 0.8422 (p) REVERT: d 143 ARG cc_start: 0.8488 (ttt-90) cc_final: 0.7183 (ttt180) REVERT: e 31 ASN cc_start: 0.8965 (t0) cc_final: 0.8719 (t0) REVERT: e 46 ARG cc_start: 0.6847 (ptt90) cc_final: 0.4685 (ptt90) REVERT: e 82 ASN cc_start: 0.8751 (t0) cc_final: 0.8531 (t0) REVERT: e 143 ARG cc_start: 0.8238 (ttt-90) cc_final: 0.7451 (ttt180) REVERT: f 46 ARG cc_start: 0.6274 (ptt90) cc_final: 0.4480 (ptt90) REVERT: f 82 ASN cc_start: 0.8608 (t0) cc_final: 0.8252 (t0) REVERT: f 143 ARG cc_start: 0.8422 (ttt-90) cc_final: 0.7263 (ttt180) outliers start: 128 outliers final: 114 residues processed: 501 average time/residue: 0.2762 time to fit residues: 215.6918 Evaluate side-chains 508 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 387 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain F residue 287 LYS Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 22 SER Chi-restraints excluded: chain a residue 60 GLN Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 130 ASN Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 27 LYS Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 120 LEU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 145 ILE Chi-restraints excluded: chain d residue 10 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain d residue 139 LEU Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 162 optimal weight: 0.6980 chunk 245 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 119 optimal weight: 0.2980 chunk 155 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN E 260 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 ASN d 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19620 Z= 0.153 Angle : 0.638 14.196 26682 Z= 0.300 Chirality : 0.043 0.169 3162 Planarity : 0.004 0.055 3438 Dihedral : 4.850 28.244 2628 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.21 % Allowed : 25.34 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.17), residues: 2412 helix: 1.26 (0.24), residues: 522 sheet: -0.66 (0.21), residues: 624 loop : -1.70 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 88 HIS 0.001 0.000 HIS F 200 PHE 0.033 0.002 PHE D 262 TYR 0.021 0.002 TYR b 45 ARG 0.007 0.000 ARG F 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 425 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.8214 (m-40) cc_final: 0.7681 (m-40) REVERT: B 43 MET cc_start: 0.7293 (mtt) cc_final: 0.6936 (mtp) REVERT: B 193 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7467 (pp) REVERT: B 230 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7484 (pm20) REVERT: B 254 TYR cc_start: 0.8247 (m-80) cc_final: 0.7858 (m-80) REVERT: C 31 ASP cc_start: 0.7810 (t0) cc_final: 0.7597 (t0) REVERT: C 193 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7344 (pp) REVERT: D 254 TYR cc_start: 0.8301 (m-80) cc_final: 0.7905 (m-80) REVERT: D 256 LYS cc_start: 0.8696 (mptt) cc_final: 0.8388 (tppt) REVERT: E 230 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7411 (pm20) REVERT: E 254 TYR cc_start: 0.8264 (m-80) cc_final: 0.7927 (m-80) REVERT: E 256 LYS cc_start: 0.8604 (mptt) cc_final: 0.8341 (tppt) REVERT: E 262 PHE cc_start: 0.7068 (p90) cc_final: 0.6815 (p90) REVERT: F 193 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7223 (pp) REVERT: F 256 LYS cc_start: 0.8661 (mptt) cc_final: 0.8354 (tppt) REVERT: a 17 TYR cc_start: 0.9269 (p90) cc_final: 0.9016 (p90) REVERT: a 31 ASN cc_start: 0.8888 (t0) cc_final: 0.8577 (t0) REVERT: a 46 ARG cc_start: 0.6821 (ptt90) cc_final: 0.4640 (ptt90) REVERT: a 113 SER cc_start: 0.8816 (t) cc_final: 0.8471 (p) REVERT: a 143 ARG cc_start: 0.8404 (ttt-90) cc_final: 0.7180 (ttt180) REVERT: b 31 ASN cc_start: 0.8932 (t0) cc_final: 0.8688 (t0) REVERT: b 46 ARG cc_start: 0.6537 (ptt90) cc_final: 0.4468 (ptt90) REVERT: b 143 ARG cc_start: 0.8554 (ttt-90) cc_final: 0.7356 (ttt180) REVERT: c 46 ARG cc_start: 0.6098 (ptt90) cc_final: 0.4225 (ptt90) REVERT: c 82 ASN cc_start: 0.8517 (t0) cc_final: 0.8147 (t0) REVERT: c 143 ARG cc_start: 0.8403 (ttt-90) cc_final: 0.7165 (ttt180) REVERT: d 31 ASN cc_start: 0.8894 (t0) cc_final: 0.8601 (t0) REVERT: d 46 ARG cc_start: 0.6850 (ptt90) cc_final: 0.4896 (ptt90) REVERT: d 81 ILE cc_start: 0.9255 (tt) cc_final: 0.8996 (tt) REVERT: d 82 ASN cc_start: 0.8575 (t0) cc_final: 0.8358 (t0) REVERT: d 113 SER cc_start: 0.8747 (t) cc_final: 0.8489 (p) REVERT: d 143 ARG cc_start: 0.8483 (ttt-90) cc_final: 0.7203 (ttt180) REVERT: e 31 ASN cc_start: 0.8923 (t0) cc_final: 0.8676 (t0) REVERT: e 46 ARG cc_start: 0.6710 (ptt90) cc_final: 0.4476 (ptt90) REVERT: e 82 ASN cc_start: 0.8709 (t0) cc_final: 0.8394 (t0) REVERT: e 143 ARG cc_start: 0.8153 (ttt-90) cc_final: 0.7394 (ttt180) REVERT: f 46 ARG cc_start: 0.6131 (ptt90) cc_final: 0.4314 (ptt90) REVERT: f 82 ASN cc_start: 0.8483 (t0) cc_final: 0.8148 (t0) REVERT: f 143 ARG cc_start: 0.8365 (ttt-90) cc_final: 0.7242 (ttt180) outliers start: 114 outliers final: 99 residues processed: 510 average time/residue: 0.2787 time to fit residues: 219.7378 Evaluate side-chains 501 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 397 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 161 ASN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 161 ASN Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 247 SER Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 60 GLN Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 130 ASN Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain b residue 27 LYS Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 120 LEU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 130 ASN Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain d residue 10 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 200 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 85 GLN d 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.095578 restraints weight = 28384.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.094939 restraints weight = 22467.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.095199 restraints weight = 19462.496| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 19620 Z= 0.322 Angle : 0.709 13.964 26682 Z= 0.340 Chirality : 0.046 0.172 3162 Planarity : 0.004 0.055 3438 Dihedral : 5.282 30.453 2628 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 5.84 % Allowed : 24.61 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.17), residues: 2412 helix: 1.05 (0.24), residues: 534 sheet: -0.74 (0.22), residues: 606 loop : -1.73 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 110 HIS 0.003 0.001 HIS A 52 PHE 0.027 0.002 PHE D 262 TYR 0.030 0.002 TYR a 45 ARG 0.007 0.000 ARG F 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4513.80 seconds wall clock time: 81 minutes 23.81 seconds (4883.81 seconds total)