Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 13:51:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0f_9763/07_2023/6j0f_9763.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0f_9763/07_2023/6j0f_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_9763/07_2023/6j0f_9763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0f_9763/07_2023/6j0f_9763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0f_9763/07_2023/6j0f_9763.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0f_9763/07_2023/6j0f_9763.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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-1.21rc1-5013/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: 9.29, per 1000 atoms: 0.48 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: 6.78 Conformation dependent library (CDL) restraints added in 2.9 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: 1.14 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: 5.83 Time building geometry restraints manager: 7.40 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: 0.730 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: 0.020 Extract box with map and model: 5.260 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 47.090 Find NCS groups from input model: 1.150 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.600 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 16 residues processed: 589 average time/residue: 0.3091 time to fit residues: 274.5503 Evaluate side-chains 376 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 360 time to evaluate : 2.216 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1698 time to fit residues: 8.1472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 192 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 143 optimal weight: 0.0670 chunk 223 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN B 52 HIS B 122 ASN B 268 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 ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 HIS E 122 ASN E 154 ASN E 268 ASN F 52 HIS F 122 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 19620 Z= 0.160 Angle : 0.647 14.967 26682 Z= 0.318 Chirality : 0.044 0.170 3162 Planarity : 0.004 0.057 3438 Dihedral : 5.590 23.443 2616 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 3.56 % 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: -3.32 (0.14), residues: 2412 helix: -2.42 (0.17), residues: 540 sheet: -1.43 (0.19), residues: 666 loop : -2.54 (0.15), residues: 1206 *********************** 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 501 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 423 time to evaluate : 2.237 Fit side-chains outliers start: 78 outliers final: 42 residues processed: 477 average time/residue: 0.3106 time to fit residues: 224.3650 Evaluate side-chains 395 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 353 time to evaluate : 2.167 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2018 time to fit residues: 17.7719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 0.0770 chunk 69 optimal weight: 0.9980 chunk 185 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 223 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 179 optimal weight: 4.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN E 154 ASN E 252 GLN F 39 GLN F 252 GLN c 58 GLN f 58 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 19620 Z= 0.151 Angle : 0.624 14.695 26682 Z= 0.300 Chirality : 0.044 0.184 3162 Planarity : 0.004 0.056 3438 Dihedral : 5.009 19.274 2616 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 3.38 % 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: -2.53 (0.15), residues: 2412 helix: -0.89 (0.20), residues: 528 sheet: -1.29 (0.19), residues: 690 loop : -2.28 (0.16), residues: 1194 *********************** 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 484 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 410 time to evaluate : 2.200 Fit side-chains outliers start: 74 outliers final: 33 residues processed: 464 average time/residue: 0.2836 time to fit residues: 205.5472 Evaluate side-chains 403 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 370 time to evaluate : 2.147 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1829 time to fit residues: 14.4878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 212 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN E 260 ASN F 122 ASN b 58 GLN e 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 19620 Z= 0.235 Angle : 0.642 14.784 26682 Z= 0.310 Chirality : 0.045 0.181 3162 Planarity : 0.004 0.055 3438 Dihedral : 4.947 20.879 2616 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 3.29 % 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: -2.06 (0.16), residues: 2412 helix: -0.21 (0.21), residues: 540 sheet: -1.08 (0.19), residues: 666 loop : -2.09 (0.16), residues: 1206 *********************** 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 461 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 389 time to evaluate : 2.282 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 41 residues processed: 447 average time/residue: 0.2829 time to fit residues: 198.8524 Evaluate side-chains 406 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 365 time to evaluate : 2.299 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 41 outliers final: 1 residues processed: 41 average time/residue: 0.2163 time to fit residues: 18.5472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 164 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 213 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 overall best weight: 1.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN C 252 GLN D 5 GLN ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN a 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 19620 Z= 0.243 Angle : 0.656 14.903 26682 Z= 0.313 Chirality : 0.045 0.183 3162 Planarity : 0.004 0.056 3438 Dihedral : 4.934 19.496 2616 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 3.06 % 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: -1.84 (0.16), residues: 2412 helix: 0.17 (0.22), residues: 540 sheet: -0.90 (0.20), residues: 642 loop : -2.07 (0.16), residues: 1230 *********************** 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 446 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 379 time to evaluate : 2.028 Fit side-chains outliers start: 67 outliers final: 33 residues processed: 427 average time/residue: 0.2756 time to fit residues: 187.1176 Evaluate side-chains 393 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 360 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1986 time to fit residues: 14.9531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 10.0000 chunk 214 optimal weight: 0.9980 chunk 47 optimal weight: 0.0050 chunk 139 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 19620 Z= 0.177 Angle : 0.635 14.676 26682 Z= 0.299 Chirality : 0.044 0.206 3162 Planarity : 0.004 0.056 3438 Dihedral : 4.747 21.286 2616 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 1.92 % 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: 0.48 (0.23), residues: 534 sheet: -0.83 (0.21), residues: 642 loop : -1.99 (0.16), residues: 1236 *********************** 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 426 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 384 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 22 residues processed: 408 average time/residue: 0.2936 time to fit residues: 187.1768 Evaluate side-chains 386 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 364 time to evaluate : 2.096 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2054 time to fit residues: 11.2034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 109 optimal weight: 0.1980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN C 122 ASN ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN e 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3614 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= 0.159 Angle : 0.627 14.634 26682 Z= 0.294 Chirality : 0.044 0.194 3162 Planarity : 0.004 0.056 3438 Dihedral : 4.547 18.729 2616 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 0.96 % 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: -1.47 (0.17), residues: 2412 helix: 0.80 (0.23), residues: 522 sheet: -0.90 (0.19), residues: 708 loop : -1.86 (0.17), residues: 1182 *********************** 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 413 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 392 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 404 average time/residue: 0.2811 time to fit residues: 178.3841 Evaluate side-chains 371 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 358 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1850 time to fit residues: 7.0785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 161 optimal weight: 20.0000 chunk 117 optimal weight: 0.0040 chunk 22 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN D 171 ASN ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 58 GLN d 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 19620 Z= 0.179 Angle : 0.641 14.600 26682 Z= 0.300 Chirality : 0.044 0.186 3162 Planarity : 0.004 0.056 3438 Dihedral : 4.562 19.507 2616 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 1.42 % 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: -1.31 (0.17), residues: 2412 helix: 0.97 (0.23), residues: 522 sheet: -0.66 (0.21), residues: 642 loop : -1.83 (0.16), residues: 1248 *********************** 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 402 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 371 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 385 average time/residue: 0.2857 time to fit residues: 173.5813 Evaluate side-chains 383 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 368 time to evaluate : 2.341 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2004 time to fit residues: 8.5215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 207 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 67 optimal weight: 0.2980 chunk 199 optimal weight: 6.9990 chunk 208 optimal weight: 0.0770 chunk 145 optimal weight: 0.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN C 39 GLN D 39 GLN D 171 ASN ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3910 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= 0.142 Angle : 0.644 14.560 26682 Z= 0.298 Chirality : 0.044 0.192 3162 Planarity : 0.004 0.056 3438 Dihedral : 4.485 24.501 2616 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 0.78 % 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: -1.17 (0.17), residues: 2412 helix: 1.21 (0.24), residues: 522 sheet: -0.73 (0.20), residues: 702 loop : -1.73 (0.17), residues: 1188 *********************** 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 418 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 401 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 407 average time/residue: 0.2642 time to fit residues: 171.1119 Evaluate side-chains 379 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 370 time to evaluate : 1.974 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3037 time to fit residues: 6.8955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 225 optimal weight: 0.0770 chunk 195 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 19620 Z= 0.186 Angle : 0.665 14.161 26682 Z= 0.309 Chirality : 0.045 0.193 3162 Planarity : 0.004 0.056 3438 Dihedral : 4.555 24.386 2616 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 0.64 % 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: -1.06 (0.17), residues: 2412 helix: 1.25 (0.24), residues: 534 sheet: -0.61 (0.21), residues: 642 loop : -1.68 (0.17), residues: 1236 ********************** 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 395 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 381 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 384 average time/residue: 0.2837 time to fit residues: 171.0400 Evaluate side-chains 380 residues out of total 2190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 374 time to evaluate : 2.084 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1686 time to fit residues: 5.0937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 200 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 171 optimal weight: 0.2980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.105025 restraints weight = 27985.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.106246 restraints weight = 20474.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.106940 restraints weight = 16357.922| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4001 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= 0.200 Angle : 0.674 14.183 26682 Z= 0.313 Chirality : 0.045 0.183 3162 Planarity : 0.004 0.056 3438 Dihedral : 4.565 22.851 2616 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 0.59 % 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: -1.05 (0.17), residues: 2412 helix: 1.32 (0.24), residues: 534 sheet: -0.71 (0.20), residues: 702 loop : -1.66 (0.17), residues: 1176 =============================================================================== Job complete usr+sys time: 4006.47 seconds wall clock time: 73 minutes 29.57 seconds (4409.57 seconds total)