Starting phenix.real_space_refine on Thu Mar 21 03:08:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwy_23560/03_2024/7lwy_23560.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwy_23560/03_2024/7lwy_23560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwy_23560/03_2024/7lwy_23560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwy_23560/03_2024/7lwy_23560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwy_23560/03_2024/7lwy_23560.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwy_23560/03_2024/7lwy_23560.pdb" } resolution = 4.0 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 250 5.16 5 C 32980 2.51 5 N 9300 2.21 5 O 9535 1.98 5 H 51395 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B ARG 329": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 572": "OE1" <-> "OE2" Residue "B GLU 578": "OE1" <-> "OE2" Residue "B ARG 619": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 676": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 315": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A ARG 620": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A ARG 676": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 271": "OE1" <-> "OE2" Residue "C ARG 329": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 416": "OE1" <-> "OE2" Residue "C ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C GLU 578": "OE1" <-> "OE2" Residue "C ARG 619": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 676": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 315": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 572": "OE1" <-> "OE2" Residue "D ARG 620": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 641": "OE1" <-> "OE2" Residue "D GLU 666": "OE1" <-> "OE2" Residue "D ARG 676": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 271": "OE1" <-> "OE2" Residue "E ARG 329": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 416": "OE1" <-> "OE2" Residue "E ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 572": "OE1" <-> "OE2" Residue "E GLU 578": "OE1" <-> "OE2" Residue "E ARG 619": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 676": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 90": "OE1" <-> "OE2" Residue "F ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 315": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 347": "OE1" <-> "OE2" Residue "F ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 572": "OE1" <-> "OE2" Residue "F ARG 620": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 641": "OE1" <-> "OE2" Residue "F GLU 666": "OE1" <-> "OE2" Residue "F ARG 676": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 271": "OE1" <-> "OE2" Residue "G ARG 329": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 416": "OE1" <-> "OE2" Residue "G ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 572": "OE1" <-> "OE2" Residue "G GLU 578": "OE1" <-> "OE2" Residue "G ARG 619": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 676": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 315": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 347": "OE1" <-> "OE2" Residue "H ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 572": "OE1" <-> "OE2" Residue "H ARG 620": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 641": "OE1" <-> "OE2" Residue "H GLU 666": "OE1" <-> "OE2" Residue "H ARG 676": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 271": "OE1" <-> "OE2" Residue "I ARG 329": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 416": "OE1" <-> "OE2" Residue "I ARG 547": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 572": "OE1" <-> "OE2" Residue "I GLU 578": "OE1" <-> "OE2" Residue "I ARG 619": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 676": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 90": "OE1" <-> "OE2" Residue "J ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 315": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 347": "OE1" <-> "OE2" Residue "J ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 572": "OE1" <-> "OE2" Residue "J ARG 620": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 641": "OE1" <-> "OE2" Residue "J GLU 666": "OE1" <-> "OE2" Residue "J ARG 676": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 103460 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 10357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 10357 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 50, 'TRANS': 614} Chain: "A" Number of atoms: 10335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 10335 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 50, 'TRANS': 613} Chain: "C" Number of atoms: 10357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 10357 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 50, 'TRANS': 614} Chain: "D" Number of atoms: 10335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 10335 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 50, 'TRANS': 613} Chain: "E" Number of atoms: 10357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 10357 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 50, 'TRANS': 614} Chain: "F" Number of atoms: 10335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 10335 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 50, 'TRANS': 613} Chain: "G" Number of atoms: 10357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 10357 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 50, 'TRANS': 614} Chain: "H" Number of atoms: 10335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 10335 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 50, 'TRANS': 613} Chain: "I" Number of atoms: 10357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 10357 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 50, 'TRANS': 614} Chain: "J" Number of atoms: 10335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 10335 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 50, 'TRANS': 613} Time building chain proxies: 32.66, per 1000 atoms: 0.32 Number of scatterers: 103460 At special positions: 0 Unit cell: (247.52, 243.44, 115.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 250 16.00 O 9535 8.00 N 9300 7.00 C 32980 6.00 H 51395 1.00 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: 58.64 Conformation dependent library (CDL) restraints added in 7.8 seconds 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12450 Finding SS restraints... Secondary structure from input PDB file: 205 helices and 70 sheets defined 34.1% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'B' and resid 38 through 51 Processing helix chain 'B' and resid 55 through 64 removed outlier: 4.326A pdb=" N ILE B 59 " --> pdb=" O ASN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 4.062A pdb=" N ASN B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 196 Processing helix chain 'B' and resid 203 through 210 Processing helix chain 'B' and resid 269 through 274 removed outlier: 3.565A pdb=" N VAL B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 269 through 274' Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 293 through 300 Processing helix chain 'B' and resid 324 through 343 Processing helix chain 'B' and resid 347 through 359 removed outlier: 3.708A pdb=" N ARG B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 429 removed outlier: 3.861A pdb=" N THR B 412 " --> pdb=" O HIS B 408 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 480 removed outlier: 4.016A pdb=" N TYR B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR B 477 " --> pdb=" O SER B 473 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLU B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 498 Processing helix chain 'B' and resid 501 through 514 removed outlier: 3.550A pdb=" N ASN B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 558 removed outlier: 4.184A pdb=" N ALA B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 584 removed outlier: 4.254A pdb=" N ASP B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 590 Processing helix chain 'B' and resid 591 through 596 removed outlier: 3.709A pdb=" N ASN B 595 " --> pdb=" O CYS B 591 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 591 through 596' Processing helix chain 'B' and resid 602 through 605 Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'A' and resid 38 through 51 Processing helix chain 'A' and resid 55 through 62 removed outlier: 4.055A pdb=" N ILE A 59 " --> pdb=" O ASN A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 163 through 172 removed outlier: 3.710A pdb=" N THR A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 196 removed outlier: 3.919A pdb=" N ALA A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 removed outlier: 3.882A pdb=" N VAL A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 269 through 274' Processing helix chain 'A' and resid 275 through 290 removed outlier: 3.674A pdb=" N GLN A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.679A pdb=" N ASN A 298 " --> pdb=" O GLN A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 343 Processing helix chain 'A' and resid 348 through 359 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.543A pdb=" N THR A 405 " --> pdb=" O PRO A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 429 Processing helix chain 'A' and resid 471 through 481 removed outlier: 4.010A pdb=" N PHE A 475 " --> pdb=" O PRO A 471 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 497 removed outlier: 3.736A pdb=" N ILE A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 514 removed outlier: 3.926A pdb=" N ILE A 504 " --> pdb=" O HIS A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 558 removed outlier: 4.325A pdb=" N ALA A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 587 through 590 Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.628A pdb=" N ASN A 595 " --> pdb=" O CYS A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'C' and resid 38 through 51 Processing helix chain 'C' and resid 55 through 64 removed outlier: 4.326A pdb=" N ILE C 59 " --> pdb=" O ASN C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 156 removed outlier: 4.063A pdb=" N ASN C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE C 156 " --> pdb=" O MET C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 196 Processing helix chain 'C' and resid 203 through 210 Processing helix chain 'C' and resid 269 through 274 removed outlier: 3.565A pdb=" N VAL C 273 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 269 through 274' Processing helix chain 'C' and resid 276 through 290 Processing helix chain 'C' and resid 293 through 300 Processing helix chain 'C' and resid 324 through 343 Processing helix chain 'C' and resid 347 through 359 removed outlier: 3.707A pdb=" N ARG C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 429 removed outlier: 3.862A pdb=" N THR C 412 " --> pdb=" O HIS C 408 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL C 423 " --> pdb=" O VAL C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 480 removed outlier: 4.016A pdb=" N TYR C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR C 477 " --> pdb=" O SER C 473 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLU C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 498 Processing helix chain 'C' and resid 501 through 514 removed outlier: 3.550A pdb=" N ASN C 514 " --> pdb=" O ASN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 558 removed outlier: 4.184A pdb=" N ALA C 554 " --> pdb=" O ASP C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 574 through 584 removed outlier: 4.254A pdb=" N ASP C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 590 Processing helix chain 'C' and resid 591 through 596 removed outlier: 3.710A pdb=" N ASN C 595 " --> pdb=" O CYS C 591 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 591 through 596' Processing helix chain 'C' and resid 602 through 605 Processing helix chain 'C' and resid 640 through 642 No H-bonds generated for 'chain 'C' and resid 640 through 642' Processing helix chain 'D' and resid 38 through 51 Processing helix chain 'D' and resid 55 through 62 removed outlier: 4.055A pdb=" N ILE D 59 " --> pdb=" O ASN D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 156 Processing helix chain 'D' and resid 163 through 172 removed outlier: 3.710A pdb=" N THR D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 196 removed outlier: 3.919A pdb=" N ALA D 180 " --> pdb=" O PRO D 176 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 274 removed outlier: 3.882A pdb=" N VAL D 273 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 269 through 274' Processing helix chain 'D' and resid 275 through 290 removed outlier: 3.675A pdb=" N GLN D 279 " --> pdb=" O ASP D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 removed outlier: 3.679A pdb=" N ASN D 298 " --> pdb=" O GLN D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 343 Processing helix chain 'D' and resid 348 through 359 Processing helix chain 'D' and resid 374 through 378 Processing helix chain 'D' and resid 402 through 406 removed outlier: 3.542A pdb=" N THR D 405 " --> pdb=" O PRO D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 429 Processing helix chain 'D' and resid 471 through 481 removed outlier: 4.010A pdb=" N PHE D 475 " --> pdb=" O PRO D 471 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS D 481 " --> pdb=" O THR D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 497 removed outlier: 3.736A pdb=" N ILE D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 514 removed outlier: 3.927A pdb=" N ILE D 504 " --> pdb=" O HIS D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 558 removed outlier: 4.326A pdb=" N ALA D 554 " --> pdb=" O ASP D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 583 Processing helix chain 'D' and resid 587 through 590 Processing helix chain 'D' and resid 591 through 597 removed outlier: 3.628A pdb=" N ASN D 595 " --> pdb=" O CYS D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 642 No H-bonds generated for 'chain 'D' and resid 640 through 642' Processing helix chain 'E' and resid 38 through 51 Processing helix chain 'E' and resid 55 through 64 removed outlier: 4.326A pdb=" N ILE E 59 " --> pdb=" O ASN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 156 removed outlier: 4.062A pdb=" N ASN E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE E 156 " --> pdb=" O MET E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 196 Processing helix chain 'E' and resid 203 through 210 Processing helix chain 'E' and resid 269 through 274 removed outlier: 3.565A pdb=" N VAL E 273 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN E 274 " --> pdb=" O PRO E 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 269 through 274' Processing helix chain 'E' and resid 276 through 290 Processing helix chain 'E' and resid 293 through 300 Processing helix chain 'E' and resid 324 through 343 Processing helix chain 'E' and resid 347 through 359 removed outlier: 3.708A pdb=" N ARG E 351 " --> pdb=" O GLU E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 429 removed outlier: 3.862A pdb=" N THR E 412 " --> pdb=" O HIS E 408 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL E 423 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 480 removed outlier: 4.017A pdb=" N TYR E 476 " --> pdb=" O LEU E 472 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR E 477 " --> pdb=" O SER E 473 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLU E 478 " --> pdb=" O ALA E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 498 Processing helix chain 'E' and resid 501 through 514 removed outlier: 3.551A pdb=" N ASN E 514 " --> pdb=" O ASN E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 550 through 558 removed outlier: 4.184A pdb=" N ALA E 554 " --> pdb=" O ASP E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 584 removed outlier: 4.255A pdb=" N ASP E 580 " --> pdb=" O LEU E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 587 through 590 Processing helix chain 'E' and resid 591 through 596 removed outlier: 3.710A pdb=" N ASN E 595 " --> pdb=" O CYS E 591 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 591 through 596' Processing helix chain 'E' and resid 602 through 605 Processing helix chain 'E' and resid 640 through 642 No H-bonds generated for 'chain 'E' and resid 640 through 642' Processing helix chain 'F' and resid 38 through 51 Processing helix chain 'F' and resid 55 through 62 removed outlier: 4.056A pdb=" N ILE F 59 " --> pdb=" O ASN F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 156 Processing helix chain 'F' and resid 163 through 172 removed outlier: 3.710A pdb=" N THR F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 196 removed outlier: 3.918A pdb=" N ALA F 180 " --> pdb=" O PRO F 176 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE F 183 " --> pdb=" O LEU F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 274 removed outlier: 3.882A pdb=" N VAL F 273 " --> pdb=" O ASN F 269 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN F 274 " --> pdb=" O PRO F 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 269 through 274' Processing helix chain 'F' and resid 275 through 290 removed outlier: 3.674A pdb=" N GLN F 279 " --> pdb=" O ASP F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 298 removed outlier: 3.680A pdb=" N ASN F 298 " --> pdb=" O GLN F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 343 Processing helix chain 'F' and resid 348 through 359 Processing helix chain 'F' and resid 374 through 378 Processing helix chain 'F' and resid 402 through 406 removed outlier: 3.542A pdb=" N THR F 405 " --> pdb=" O PRO F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 429 Processing helix chain 'F' and resid 471 through 481 removed outlier: 4.010A pdb=" N PHE F 475 " --> pdb=" O PRO F 471 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU F 478 " --> pdb=" O ALA F 474 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS F 481 " --> pdb=" O THR F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 497 removed outlier: 3.736A pdb=" N ILE F 488 " --> pdb=" O ALA F 484 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET F 491 " --> pdb=" O ARG F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 514 removed outlier: 3.926A pdb=" N ILE F 504 " --> pdb=" O HIS F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 558 removed outlier: 4.326A pdb=" N ALA F 554 " --> pdb=" O ASP F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 583 Processing helix chain 'F' and resid 587 through 590 Processing helix chain 'F' and resid 591 through 597 removed outlier: 3.627A pdb=" N ASN F 595 " --> pdb=" O CYS F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 642 No H-bonds generated for 'chain 'F' and resid 640 through 642' Processing helix chain 'G' and resid 38 through 51 Processing helix chain 'G' and resid 55 through 64 removed outlier: 4.326A pdb=" N ILE G 59 " --> pdb=" O ASN G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 156 removed outlier: 4.062A pdb=" N ASN G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE G 156 " --> pdb=" O MET G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 196 Processing helix chain 'G' and resid 203 through 210 Processing helix chain 'G' and resid 269 through 274 removed outlier: 3.564A pdb=" N VAL G 273 " --> pdb=" O ASN G 269 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN G 274 " --> pdb=" O PRO G 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 269 through 274' Processing helix chain 'G' and resid 276 through 290 Processing helix chain 'G' and resid 293 through 300 Processing helix chain 'G' and resid 324 through 343 Processing helix chain 'G' and resid 347 through 359 removed outlier: 3.708A pdb=" N ARG G 351 " --> pdb=" O GLU G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 429 removed outlier: 3.861A pdb=" N THR G 412 " --> pdb=" O HIS G 408 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP G 420 " --> pdb=" O GLU G 416 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL G 423 " --> pdb=" O VAL G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 480 removed outlier: 4.016A pdb=" N TYR G 476 " --> pdb=" O LEU G 472 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR G 477 " --> pdb=" O SER G 473 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU G 478 " --> pdb=" O ALA G 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 486 through 498 Processing helix chain 'G' and resid 501 through 514 removed outlier: 3.550A pdb=" N ASN G 514 " --> pdb=" O ASN G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 550 through 558 removed outlier: 4.183A pdb=" N ALA G 554 " --> pdb=" O ASP G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 574 through 584 removed outlier: 4.254A pdb=" N ASP G 580 " --> pdb=" O LEU G 576 " (cutoff:3.500A) Processing helix chain 'G' and resid 587 through 590 Processing helix chain 'G' and resid 591 through 596 removed outlier: 3.710A pdb=" N ASN G 595 " --> pdb=" O CYS G 591 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA G 596 " --> pdb=" O PHE G 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 591 through 596' Processing helix chain 'G' and resid 602 through 605 Processing helix chain 'G' and resid 640 through 642 No H-bonds generated for 'chain 'G' and resid 640 through 642' Processing helix chain 'H' and resid 38 through 51 Processing helix chain 'H' and resid 55 through 62 removed outlier: 4.055A pdb=" N ILE H 59 " --> pdb=" O ASN H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 156 Processing helix chain 'H' and resid 163 through 172 removed outlier: 3.710A pdb=" N THR H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 196 removed outlier: 3.919A pdb=" N ALA H 180 " --> pdb=" O PRO H 176 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE H 183 " --> pdb=" O LEU H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 274 removed outlier: 3.882A pdb=" N VAL H 273 " --> pdb=" O ASN H 269 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN H 274 " --> pdb=" O PRO H 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 269 through 274' Processing helix chain 'H' and resid 275 through 290 removed outlier: 3.675A pdb=" N GLN H 279 " --> pdb=" O ASP H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 298 removed outlier: 3.679A pdb=" N ASN H 298 " --> pdb=" O GLN H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 343 Processing helix chain 'H' and resid 348 through 359 Processing helix chain 'H' and resid 374 through 378 Processing helix chain 'H' and resid 402 through 406 removed outlier: 3.543A pdb=" N THR H 405 " --> pdb=" O PRO H 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 429 Processing helix chain 'H' and resid 471 through 481 removed outlier: 4.010A pdb=" N PHE H 475 " --> pdb=" O PRO H 471 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU H 478 " --> pdb=" O ALA H 474 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS H 481 " --> pdb=" O THR H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 482 through 497 removed outlier: 3.736A pdb=" N ILE H 488 " --> pdb=" O ALA H 484 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET H 491 " --> pdb=" O ARG H 487 " (cutoff:3.500A) Processing helix chain 'H' and resid 500 through 514 removed outlier: 3.925A pdb=" N ILE H 504 " --> pdb=" O HIS H 500 " (cutoff:3.500A) Processing helix chain 'H' and resid 550 through 558 removed outlier: 4.325A pdb=" N ALA H 554 " --> pdb=" O ASP H 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 574 through 583 Processing helix chain 'H' and resid 587 through 590 Processing helix chain 'H' and resid 591 through 597 removed outlier: 3.628A pdb=" N ASN H 595 " --> pdb=" O CYS H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 640 through 642 No H-bonds generated for 'chain 'H' and resid 640 through 642' Processing helix chain 'I' and resid 38 through 51 Processing helix chain 'I' and resid 55 through 64 removed outlier: 4.327A pdb=" N ILE I 59 " --> pdb=" O ASN I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 156 removed outlier: 4.063A pdb=" N ASN I 155 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE I 156 " --> pdb=" O MET I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 196 Processing helix chain 'I' and resid 203 through 210 Processing helix chain 'I' and resid 269 through 274 removed outlier: 3.564A pdb=" N VAL I 273 " --> pdb=" O ASN I 269 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN I 274 " --> pdb=" O PRO I 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 269 through 274' Processing helix chain 'I' and resid 276 through 290 Processing helix chain 'I' and resid 293 through 300 Processing helix chain 'I' and resid 324 through 343 Processing helix chain 'I' and resid 347 through 359 removed outlier: 3.708A pdb=" N ARG I 351 " --> pdb=" O GLU I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 408 through 429 removed outlier: 3.861A pdb=" N THR I 412 " --> pdb=" O HIS I 408 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP I 420 " --> pdb=" O GLU I 416 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL I 423 " --> pdb=" O VAL I 419 " (cutoff:3.500A) Processing helix chain 'I' and resid 472 through 480 removed outlier: 4.016A pdb=" N TYR I 476 " --> pdb=" O LEU I 472 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR I 477 " --> pdb=" O SER I 473 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N GLU I 478 " --> pdb=" O ALA I 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 498 Processing helix chain 'I' and resid 501 through 514 removed outlier: 3.551A pdb=" N ASN I 514 " --> pdb=" O ASN I 510 " (cutoff:3.500A) Processing helix chain 'I' and resid 550 through 558 removed outlier: 4.184A pdb=" N ALA I 554 " --> pdb=" O ASP I 550 " (cutoff:3.500A) Processing helix chain 'I' and resid 574 through 584 removed outlier: 4.253A pdb=" N ASP I 580 " --> pdb=" O LEU I 576 " (cutoff:3.500A) Processing helix chain 'I' and resid 587 through 590 Processing helix chain 'I' and resid 591 through 596 removed outlier: 3.709A pdb=" N ASN I 595 " --> pdb=" O CYS I 591 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA I 596 " --> pdb=" O PHE I 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 591 through 596' Processing helix chain 'I' and resid 602 through 605 Processing helix chain 'I' and resid 640 through 642 No H-bonds generated for 'chain 'I' and resid 640 through 642' Processing helix chain 'J' and resid 38 through 51 Processing helix chain 'J' and resid 55 through 62 removed outlier: 4.055A pdb=" N ILE J 59 " --> pdb=" O ASN J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 156 Processing helix chain 'J' and resid 163 through 172 removed outlier: 3.711A pdb=" N THR J 167 " --> pdb=" O SER J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 196 removed outlier: 3.918A pdb=" N ALA J 180 " --> pdb=" O PRO J 176 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE J 183 " --> pdb=" O LEU J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 274 removed outlier: 3.882A pdb=" N VAL J 273 " --> pdb=" O ASN J 269 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN J 274 " --> pdb=" O PRO J 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 269 through 274' Processing helix chain 'J' and resid 275 through 290 removed outlier: 3.675A pdb=" N GLN J 279 " --> pdb=" O ASP J 275 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 298 removed outlier: 3.680A pdb=" N ASN J 298 " --> pdb=" O GLN J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 343 Processing helix chain 'J' and resid 348 through 359 Processing helix chain 'J' and resid 374 through 378 Processing helix chain 'J' and resid 402 through 406 removed outlier: 3.543A pdb=" N THR J 405 " --> pdb=" O PRO J 402 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 429 Processing helix chain 'J' and resid 471 through 481 removed outlier: 4.010A pdb=" N PHE J 475 " --> pdb=" O PRO J 471 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU J 478 " --> pdb=" O ALA J 474 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS J 481 " --> pdb=" O THR J 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 482 through 497 removed outlier: 3.735A pdb=" N ILE J 488 " --> pdb=" O ALA J 484 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET J 491 " --> pdb=" O ARG J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 500 through 514 removed outlier: 3.926A pdb=" N ILE J 504 " --> pdb=" O HIS J 500 " (cutoff:3.500A) Processing helix chain 'J' and resid 550 through 558 removed outlier: 4.326A pdb=" N ALA J 554 " --> pdb=" O ASP J 550 " (cutoff:3.500A) Processing helix chain 'J' and resid 574 through 583 Processing helix chain 'J' and resid 587 through 590 Processing helix chain 'J' and resid 591 through 597 removed outlier: 3.627A pdb=" N ASN J 595 " --> pdb=" O CYS J 591 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 642 No H-bonds generated for 'chain 'J' and resid 640 through 642' Processing sheet with id= 1, first strand: chain 'B' and resid 71 through 73 removed outlier: 3.688A pdb=" N GLN B 72 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 93 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASP B 118 " --> pdb=" O CYS B 365 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 113 through 114 removed outlier: 3.818A pdb=" N THR B 98 " --> pdb=" O ASN B 684 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN B 684 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 681 " --> pdb=" O GLY B 569 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 128 through 129 Processing sheet with id= 4, first strand: chain 'B' and resid 248 through 251 removed outlier: 6.353A pdb=" N GLY B 248 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N SER B 308 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL B 250 " --> pdb=" O SER B 308 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 266 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 307 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N CYS B 265 " --> pdb=" O TYR B 390 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR B 392 " --> pdb=" O CYS B 265 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE B 267 " --> pdb=" O TYR B 392 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 461 through 463 removed outlier: 6.912A pdb=" N VAL B 435 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TYR B 463 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA B 437 " --> pdb=" O TYR B 463 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 607 through 608 Processing sheet with id= 7, first strand: chain 'B' and resid 632 through 633 removed outlier: 3.707A pdb=" N GLY B 621 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 622 " --> pdb=" O GLN B 663 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP B 661 " --> pdb=" O THR B 624 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 92 through 95 removed outlier: 3.894A pdb=" N LEU A 117 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 113 through 114 removed outlier: 3.577A pdb=" N VAL A 99 " --> pdb=" O GLN A 113 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS A 678 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 128 through 129 removed outlier: 3.575A pdb=" N THR A 129 " --> pdb=" O VAL A 381 " (cutoff:3.500A) No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'A' and resid 248 through 251 removed outlier: 3.556A pdb=" N VAL A 307 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N CYS A 265 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR A 392 " --> pdb=" O CYS A 265 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE A 267 " --> pdb=" O TYR A 392 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 461 through 462 Processing sheet with id= 13, first strand: chain 'A' and resid 637 through 638 Processing sheet with id= 14, first strand: chain 'A' and resid 630 through 633 removed outlier: 3.554A pdb=" N GLY A 621 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 661 " --> pdb=" O THR A 624 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 71 through 73 removed outlier: 3.688A pdb=" N GLN C 72 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 93 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASP C 118 " --> pdb=" O CYS C 365 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 113 through 114 removed outlier: 3.817A pdb=" N THR C 98 " --> pdb=" O ASN C 684 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN C 684 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C 681 " --> pdb=" O GLY C 569 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'C' and resid 128 through 129 Processing sheet with id= 18, first strand: chain 'C' and resid 248 through 251 removed outlier: 6.354A pdb=" N GLY C 248 " --> pdb=" O ILE C 306 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N SER C 308 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C 250 " --> pdb=" O SER C 308 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 266 " --> pdb=" O ASN C 305 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 307 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N CYS C 265 " --> pdb=" O TYR C 390 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR C 392 " --> pdb=" O CYS C 265 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE C 267 " --> pdb=" O TYR C 392 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'C' and resid 461 through 463 removed outlier: 6.912A pdb=" N VAL C 435 " --> pdb=" O PHE C 461 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TYR C 463 " --> pdb=" O VAL C 435 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 437 " --> pdb=" O TYR C 463 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'C' and resid 607 through 608 Processing sheet with id= 21, first strand: chain 'C' and resid 632 through 633 removed outlier: 3.707A pdb=" N GLY C 621 " --> pdb=" O VAL C 633 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 622 " --> pdb=" O GLN C 663 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP C 661 " --> pdb=" O THR C 624 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'D' and resid 92 through 95 removed outlier: 3.895A pdb=" N LEU D 117 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 113 through 114 removed outlier: 3.577A pdb=" N VAL D 99 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS D 678 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 128 through 129 removed outlier: 3.575A pdb=" N THR D 129 " --> pdb=" O VAL D 381 " (cutoff:3.500A) No H-bonds generated for sheet with id= 24 Processing sheet with id= 25, first strand: chain 'D' and resid 248 through 251 removed outlier: 3.555A pdb=" N VAL D 307 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N CYS D 265 " --> pdb=" O TYR D 390 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR D 392 " --> pdb=" O CYS D 265 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE D 267 " --> pdb=" O TYR D 392 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'D' and resid 461 through 462 Processing sheet with id= 27, first strand: chain 'D' and resid 637 through 638 Processing sheet with id= 28, first strand: chain 'D' and resid 630 through 633 removed outlier: 3.554A pdb=" N GLY D 621 " --> pdb=" O VAL D 633 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP D 661 " --> pdb=" O THR D 624 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'E' and resid 71 through 73 removed outlier: 3.688A pdb=" N GLN E 72 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL E 93 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASP E 118 " --> pdb=" O CYS E 365 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'E' and resid 113 through 114 removed outlier: 3.817A pdb=" N THR E 98 " --> pdb=" O ASN E 684 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN E 684 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL E 681 " --> pdb=" O GLY E 569 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'E' and resid 128 through 129 Processing sheet with id= 32, first strand: chain 'E' and resid 248 through 251 removed outlier: 6.353A pdb=" N GLY E 248 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N SER E 308 " --> pdb=" O GLY E 248 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL E 250 " --> pdb=" O SER E 308 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 266 " --> pdb=" O ASN E 305 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL E 307 " --> pdb=" O LEU E 266 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N CYS E 265 " --> pdb=" O TYR E 390 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR E 392 " --> pdb=" O CYS E 265 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE E 267 " --> pdb=" O TYR E 392 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'E' and resid 461 through 463 removed outlier: 6.911A pdb=" N VAL E 435 " --> pdb=" O PHE E 461 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TYR E 463 " --> pdb=" O VAL E 435 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA E 437 " --> pdb=" O TYR E 463 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'E' and resid 607 through 608 Processing sheet with id= 35, first strand: chain 'E' and resid 632 through 633 removed outlier: 3.706A pdb=" N GLY E 621 " --> pdb=" O VAL E 633 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE E 622 " --> pdb=" O GLN E 663 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP E 661 " --> pdb=" O THR E 624 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'F' and resid 92 through 95 removed outlier: 3.894A pdb=" N LEU F 117 " --> pdb=" O ILE F 95 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'F' and resid 113 through 114 removed outlier: 3.578A pdb=" N VAL F 99 " --> pdb=" O GLN F 113 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS F 678 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'F' and resid 128 through 129 removed outlier: 3.576A pdb=" N THR F 129 " --> pdb=" O VAL F 381 " (cutoff:3.500A) No H-bonds generated for sheet with id= 38 Processing sheet with id= 39, first strand: chain 'F' and resid 248 through 251 removed outlier: 3.555A pdb=" N VAL F 307 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N CYS F 265 " --> pdb=" O TYR F 390 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR F 392 " --> pdb=" O CYS F 265 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE F 267 " --> pdb=" O TYR F 392 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'F' and resid 461 through 462 Processing sheet with id= 41, first strand: chain 'F' and resid 637 through 638 Processing sheet with id= 42, first strand: chain 'F' and resid 630 through 633 removed outlier: 3.554A pdb=" N GLY F 621 " --> pdb=" O VAL F 633 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP F 661 " --> pdb=" O THR F 624 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'G' and resid 71 through 73 removed outlier: 3.688A pdb=" N GLN G 72 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL G 93 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASP G 118 " --> pdb=" O CYS G 365 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'G' and resid 113 through 114 removed outlier: 3.818A pdb=" N THR G 98 " --> pdb=" O ASN G 684 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN G 684 " --> pdb=" O THR G 98 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL G 681 " --> pdb=" O GLY G 569 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'G' and resid 128 through 129 Processing sheet with id= 46, first strand: chain 'G' and resid 248 through 251 removed outlier: 6.353A pdb=" N GLY G 248 " --> pdb=" O ILE G 306 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N SER G 308 " --> pdb=" O GLY G 248 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL G 250 " --> pdb=" O SER G 308 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 266 " --> pdb=" O ASN G 305 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL G 307 " --> pdb=" O LEU G 266 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N CYS G 265 " --> pdb=" O TYR G 390 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N TYR G 392 " --> pdb=" O CYS G 265 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE G 267 " --> pdb=" O TYR G 392 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'G' and resid 461 through 463 removed outlier: 6.911A pdb=" N VAL G 435 " --> pdb=" O PHE G 461 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TYR G 463 " --> pdb=" O VAL G 435 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA G 437 " --> pdb=" O TYR G 463 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'G' and resid 607 through 608 Processing sheet with id= 49, first strand: chain 'G' and resid 632 through 633 removed outlier: 3.707A pdb=" N GLY G 621 " --> pdb=" O VAL G 633 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE G 622 " --> pdb=" O GLN G 663 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP G 661 " --> pdb=" O THR G 624 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'H' and resid 92 through 95 removed outlier: 3.893A pdb=" N LEU H 117 " --> pdb=" O ILE H 95 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'H' and resid 113 through 114 removed outlier: 3.577A pdb=" N VAL H 99 " --> pdb=" O GLN H 113 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS H 678 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'H' and resid 128 through 129 removed outlier: 3.576A pdb=" N THR H 129 " --> pdb=" O VAL H 381 " (cutoff:3.500A) No H-bonds generated for sheet with id= 52 Processing sheet with id= 53, first strand: chain 'H' and resid 248 through 251 removed outlier: 3.555A pdb=" N VAL H 307 " --> pdb=" O LEU H 266 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N CYS H 265 " --> pdb=" O TYR H 390 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TYR H 392 " --> pdb=" O CYS H 265 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE H 267 " --> pdb=" O TYR H 392 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'H' and resid 461 through 462 Processing sheet with id= 55, first strand: chain 'H' and resid 637 through 638 Processing sheet with id= 56, first strand: chain 'H' and resid 630 through 633 removed outlier: 3.553A pdb=" N GLY H 621 " --> pdb=" O VAL H 633 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP H 661 " --> pdb=" O THR H 624 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'I' and resid 71 through 73 removed outlier: 3.688A pdb=" N GLN I 72 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL I 93 " --> pdb=" O ILE I 119 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ASP I 118 " --> pdb=" O CYS I 365 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'I' and resid 113 through 114 removed outlier: 3.818A pdb=" N THR I 98 " --> pdb=" O ASN I 684 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN I 684 " --> pdb=" O THR I 98 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL I 681 " --> pdb=" O GLY I 569 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'I' and resid 128 through 129 Processing sheet with id= 60, first strand: chain 'I' and resid 248 through 251 removed outlier: 6.354A pdb=" N GLY I 248 " --> pdb=" O ILE I 306 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N SER I 308 " --> pdb=" O GLY I 248 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL I 250 " --> pdb=" O SER I 308 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU I 266 " --> pdb=" O ASN I 305 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL I 307 " --> pdb=" O LEU I 266 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N CYS I 265 " --> pdb=" O TYR I 390 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR I 392 " --> pdb=" O CYS I 265 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE I 267 " --> pdb=" O TYR I 392 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'I' and resid 461 through 463 removed outlier: 6.912A pdb=" N VAL I 435 " --> pdb=" O PHE I 461 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TYR I 463 " --> pdb=" O VAL I 435 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA I 437 " --> pdb=" O TYR I 463 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'I' and resid 607 through 608 Processing sheet with id= 63, first strand: chain 'I' and resid 632 through 633 removed outlier: 3.707A pdb=" N GLY I 621 " --> pdb=" O VAL I 633 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE I 622 " --> pdb=" O GLN I 663 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP I 661 " --> pdb=" O THR I 624 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'J' and resid 92 through 95 removed outlier: 3.894A pdb=" N LEU J 117 " --> pdb=" O ILE J 95 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'J' and resid 113 through 114 removed outlier: 3.578A pdb=" N VAL J 99 " --> pdb=" O GLN J 113 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS J 678 " --> pdb=" O LEU J 104 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'J' and resid 128 through 129 removed outlier: 3.575A pdb=" N THR J 129 " --> pdb=" O VAL J 381 " (cutoff:3.500A) No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain 'J' and resid 248 through 251 removed outlier: 3.555A pdb=" N VAL J 307 " --> pdb=" O LEU J 266 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N CYS J 265 " --> pdb=" O TYR J 390 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR J 392 " --> pdb=" O CYS J 265 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE J 267 " --> pdb=" O TYR J 392 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'J' and resid 461 through 462 Processing sheet with id= 69, first strand: chain 'J' and resid 637 through 638 Processing sheet with id= 70, first strand: chain 'J' and resid 630 through 633 removed outlier: 3.553A pdb=" N GLY J 621 " --> pdb=" O VAL J 633 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP J 661 " --> pdb=" O THR J 624 " (cutoff:3.500A) 1610 hydrogen bonds defined for protein. 4515 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: 39.71 Time building geometry restraints manager: 62.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 51275 1.03 - 1.23: 558 1.23 - 1.42: 22050 1.42 - 1.62: 30517 1.62 - 1.81: 380 Bond restraints: 104780 Sorted by residual: bond pdb=" N ARG H 363 " pdb=" CA ARG H 363 " ideal model delta sigma weight residual 1.453 1.488 -0.034 8.30e-03 1.45e+04 1.72e+01 bond pdb=" N ARG A 363 " pdb=" CA ARG A 363 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.68e+01 bond pdb=" N ARG D 363 " pdb=" CA ARG D 363 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.66e+01 bond pdb=" N ARG J 363 " pdb=" CA ARG J 363 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.65e+01 bond pdb=" N ARG F 363 " pdb=" CA ARG F 363 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.64e+01 ... (remaining 104775 not shown) Histogram of bond angle deviations from ideal: 97.13 - 104.57: 1477 104.57 - 112.02: 117634 112.02 - 119.46: 25804 119.46 - 126.91: 43562 126.91 - 134.35: 783 Bond angle restraints: 189260 Sorted by residual: angle pdb=" C CYS E 247 " pdb=" N GLY E 248 " pdb=" CA GLY E 248 " ideal model delta sigma weight residual 120.53 128.81 -8.28 1.13e+00 7.83e-01 5.37e+01 angle pdb=" C CYS I 247 " pdb=" N GLY I 248 " pdb=" CA GLY I 248 " ideal model delta sigma weight residual 120.53 128.81 -8.28 1.13e+00 7.83e-01 5.37e+01 angle pdb=" C CYS G 247 " pdb=" N GLY G 248 " pdb=" CA GLY G 248 " ideal model delta sigma weight residual 120.53 128.80 -8.27 1.13e+00 7.83e-01 5.35e+01 angle pdb=" C CYS B 247 " pdb=" N GLY B 248 " pdb=" CA GLY B 248 " ideal model delta sigma weight residual 120.53 128.77 -8.24 1.13e+00 7.83e-01 5.32e+01 angle pdb=" C CYS C 247 " pdb=" N GLY C 248 " pdb=" CA GLY C 248 " ideal model delta sigma weight residual 120.53 128.75 -8.22 1.13e+00 7.83e-01 5.29e+01 ... (remaining 189255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 44461 17.96 - 35.92: 4047 35.92 - 53.87: 1203 53.87 - 71.83: 244 71.83 - 89.79: 50 Dihedral angle restraints: 50005 sinusoidal: 27330 harmonic: 22675 Sorted by residual: dihedral pdb=" CA ILE I 480 " pdb=" C ILE I 480 " pdb=" N HIS I 481 " pdb=" CA HIS I 481 " ideal model delta harmonic sigma weight residual 180.00 157.30 22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ILE G 480 " pdb=" C ILE G 480 " pdb=" N HIS G 481 " pdb=" CA HIS G 481 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ILE E 480 " pdb=" C ILE E 480 " pdb=" N HIS E 481 " pdb=" CA HIS E 481 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 50002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 6482 0.064 - 0.127: 1236 0.127 - 0.191: 192 0.191 - 0.255: 65 0.255 - 0.318: 30 Chirality restraints: 8005 Sorted by residual: chirality pdb=" CA PHE E 592 " pdb=" N PHE E 592 " pdb=" C PHE E 592 " pdb=" CB PHE E 592 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA PHE B 592 " pdb=" N PHE B 592 " pdb=" C PHE B 592 " pdb=" CB PHE B 592 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CA PHE C 592 " pdb=" N PHE C 592 " pdb=" C PHE C 592 " pdb=" CB PHE C 592 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 8002 not shown) Planarity restraints: 15820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 663 " 0.222 2.00e-02 2.50e+03 4.01e-01 2.41e+03 pdb=" CD GLN C 663 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN C 663 " -0.215 2.00e-02 2.50e+03 pdb=" NE2 GLN C 663 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN C 663 " -0.654 2.00e-02 2.50e+03 pdb="HE22 GLN C 663 " 0.664 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 663 " 0.221 2.00e-02 2.50e+03 4.01e-01 2.41e+03 pdb=" CD GLN B 663 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN B 663 " -0.214 2.00e-02 2.50e+03 pdb=" NE2 GLN B 663 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 663 " -0.654 2.00e-02 2.50e+03 pdb="HE22 GLN B 663 " 0.664 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN I 663 " 0.221 2.00e-02 2.50e+03 4.01e-01 2.41e+03 pdb=" CD GLN I 663 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN I 663 " -0.214 2.00e-02 2.50e+03 pdb=" NE2 GLN I 663 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN I 663 " -0.653 2.00e-02 2.50e+03 pdb="HE22 GLN I 663 " 0.664 2.00e-02 2.50e+03 ... (remaining 15817 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 3226 2.12 - 2.74: 185623 2.74 - 3.36: 284333 3.36 - 3.98: 353252 3.98 - 4.60: 562910 Nonbonded interactions: 1389344 Sorted by model distance: nonbonded pdb=" HG SER J 88 " pdb=" HE1 TRP J 91 " model vdw 1.504 2.100 nonbonded pdb=" HG SER D 88 " pdb=" HE1 TRP D 91 " model vdw 1.504 2.100 nonbonded pdb=" HG SER F 88 " pdb=" HE1 TRP F 91 " model vdw 1.504 2.100 nonbonded pdb=" HG SER H 88 " pdb=" HE1 TRP H 91 " model vdw 1.504 2.100 nonbonded pdb=" HG SER A 88 " pdb=" HE1 TRP A 91 " model vdw 1.504 2.100 ... (remaining 1389339 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' and resid 37 through 700) selection = (chain 'C' and resid 37 through 700) selection = chain 'D' selection = (chain 'E' and resid 37 through 700) selection = chain 'F' selection = (chain 'G' and resid 37 through 700) selection = chain 'H' selection = (chain 'I' and resid 37 through 700) selection = chain 'J' } 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: 0.910 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: 1.110 Extract box with map and model: 7.710 Check model and map are aligned: 1.110 Set scattering table: 0.700 Process input model: 236.910 Find NCS groups from input model: 4.220 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 255.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 0.054 53385 Z= 0.473 Angle : 0.872 9.959 72695 Z= 0.558 Chirality : 0.058 0.318 8005 Planarity : 0.005 0.053 9685 Dihedral : 13.339 86.956 19775 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.18 % Allowed : 1.29 % Favored : 98.53 % 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: -2.13 (0.10), residues: 6625 helix: 0.31 (0.12), residues: 2045 sheet: -2.43 (0.19), residues: 660 loop : -2.30 (0.10), residues: 3920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 645 HIS 0.006 0.001 HIS G 290 PHE 0.025 0.002 PHE C 583 TYR 0.012 0.001 TYR E 181 ARG 0.018 0.001 ARG F 363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 960 time to evaluate : 6.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 231 GLN cc_start: 0.8552 (pm20) cc_final: 0.8274 (pm20) REVERT: B 342 MET cc_start: 0.8343 (mtp) cc_final: 0.8084 (mtm) REVERT: B 365 CYS cc_start: 0.7722 (t) cc_final: 0.7336 (t) REVERT: B 587 ASP cc_start: 0.8058 (p0) cc_final: 0.7446 (p0) REVERT: B 684 ASN cc_start: 0.8792 (p0) cc_final: 0.7381 (t0) REVERT: C 143 SER cc_start: 0.9211 (m) cc_final: 0.8961 (t) REVERT: C 231 GLN cc_start: 0.8476 (pm20) cc_final: 0.8073 (pm20) REVERT: C 605 ILE cc_start: 0.8477 (mm) cc_final: 0.8219 (mm) REVERT: C 662 SER cc_start: 0.8371 (p) cc_final: 0.8042 (p) REVERT: C 684 ASN cc_start: 0.8568 (p0) cc_final: 0.7925 (t0) REVERT: D 62 MET cc_start: 0.7620 (ppp) cc_final: 0.7291 (tmm) REVERT: D 373 LEU cc_start: 0.8817 (mp) cc_final: 0.8528 (mm) REVERT: D 429 SER cc_start: 0.8791 (m) cc_final: 0.8499 (m) REVERT: D 627 ASP cc_start: 0.8413 (p0) cc_final: 0.8212 (p0) REVERT: E 143 SER cc_start: 0.9257 (m) cc_final: 0.8866 (t) REVERT: E 572 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7698 (mm-30) REVERT: E 662 SER cc_start: 0.8355 (p) cc_final: 0.8104 (p) REVERT: E 678 LYS cc_start: 0.8129 (mttp) cc_final: 0.7914 (mmmt) REVERT: E 684 ASN cc_start: 0.8468 (p0) cc_final: 0.7685 (t0) REVERT: F 359 GLU cc_start: 0.7369 (mp0) cc_final: 0.6914 (mp0) REVERT: F 444 GLN cc_start: 0.7816 (mp10) cc_final: 0.7300 (tp40) REVERT: F 508 VAL cc_start: 0.9490 (p) cc_final: 0.9255 (t) REVERT: F 519 ILE cc_start: 0.8903 (mt) cc_final: 0.8703 (mt) REVERT: G 152 MET cc_start: 0.8569 (tmm) cc_final: 0.8322 (tmm) REVERT: G 181 TYR cc_start: 0.8947 (t80) cc_final: 0.8686 (t80) REVERT: G 390 TYR cc_start: 0.8060 (m-80) cc_final: 0.7770 (m-10) REVERT: G 530 ARG cc_start: 0.4861 (ttt180) cc_final: 0.4465 (ttt90) REVERT: G 632 PRO cc_start: 0.9384 (OUTLIER) cc_final: 0.9132 (Cg_endo) REVERT: G 678 LYS cc_start: 0.7917 (mttp) cc_final: 0.7716 (mttp) REVERT: G 684 ASN cc_start: 0.8551 (p0) cc_final: 0.7358 (t0) REVERT: H 444 GLN cc_start: 0.7648 (mp10) cc_final: 0.6993 (tp40) REVERT: H 493 MET cc_start: 0.8610 (mmm) cc_final: 0.8288 (mmt) REVERT: I 181 TYR cc_start: 0.8973 (t80) cc_final: 0.8732 (t80) REVERT: I 262 LEU cc_start: 0.7596 (mp) cc_final: 0.7352 (mp) REVERT: I 329 ARG cc_start: 0.8337 (ttm170) cc_final: 0.8131 (mtm-85) REVERT: I 390 TYR cc_start: 0.8030 (m-80) cc_final: 0.7718 (m-10) REVERT: I 587 ASP cc_start: 0.7886 (p0) cc_final: 0.7364 (p0) REVERT: I 684 ASN cc_start: 0.8371 (p0) cc_final: 0.7283 (t0) REVERT: J 429 SER cc_start: 0.8741 (m) cc_final: 0.8199 (p) REVERT: J 444 GLN cc_start: 0.7278 (mp10) cc_final: 0.6649 (tp40) REVERT: J 491 MET cc_start: 0.7854 (ttt) cc_final: 0.7566 (ttp) REVERT: J 656 SER cc_start: 0.8807 (p) cc_final: 0.8587 (p) outliers start: 10 outliers final: 2 residues processed: 970 average time/residue: 1.2613 time to fit residues: 1989.5139 Evaluate side-chains 713 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 710 time to evaluate : 6.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 632 PRO Chi-restraints excluded: chain G residue 632 PRO Chi-restraints excluded: chain I residue 567 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 557 optimal weight: 6.9990 chunk 500 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 337 optimal weight: 7.9990 chunk 267 optimal weight: 4.9990 chunk 517 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 314 optimal weight: 0.6980 chunk 385 optimal weight: 8.9990 chunk 599 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN B 171 GLN B 316 GLN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN C 316 GLN ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN E 69 GLN E 113 GLN F 584 ASN G 113 GLN G 316 GLN H 584 ASN I 113 GLN I 316 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 53385 Z= 0.270 Angle : 0.595 6.265 72695 Z= 0.311 Chirality : 0.042 0.157 8005 Planarity : 0.004 0.064 9685 Dihedral : 4.778 51.465 7283 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.04 % Favored : 90.88 % Rotamer: Outliers : 0.99 % Allowed : 7.14 % Favored : 91.87 % 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: -1.83 (0.10), residues: 6625 helix: 0.76 (0.12), residues: 2055 sheet: -2.36 (0.18), residues: 720 loop : -2.21 (0.10), residues: 3850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 645 HIS 0.006 0.001 HIS A 408 PHE 0.026 0.001 PHE D 367 TYR 0.015 0.001 TYR F 390 ARG 0.009 0.000 ARG I 619 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 744 time to evaluate : 6.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 MET cc_start: 0.8312 (mtp) cc_final: 0.8048 (mtm) REVERT: B 365 CYS cc_start: 0.7787 (t) cc_final: 0.7452 (t) REVERT: B 449 MET cc_start: 0.3920 (tpt) cc_final: 0.3028 (tpt) REVERT: B 684 ASN cc_start: 0.9086 (p0) cc_final: 0.7404 (t0) REVERT: A 368 TYR cc_start: 0.7972 (m-80) cc_final: 0.7733 (m-80) REVERT: C 143 SER cc_start: 0.9209 (m) cc_final: 0.8946 (t) REVERT: C 231 GLN cc_start: 0.8685 (pm20) cc_final: 0.8233 (pm20) REVERT: C 445 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8149 (tp) REVERT: C 662 SER cc_start: 0.8425 (p) cc_final: 0.8127 (p) REVERT: C 684 ASN cc_start: 0.8501 (p0) cc_final: 0.7765 (t0) REVERT: D 361 MET cc_start: 0.8256 (mmt) cc_final: 0.7846 (mmp) REVERT: D 367 PHE cc_start: 0.7761 (t80) cc_final: 0.7487 (t80) REVERT: D 627 ASP cc_start: 0.8428 (p0) cc_final: 0.8059 (p0) REVERT: E 354 GLN cc_start: 0.8935 (tt0) cc_final: 0.8621 (mt0) REVERT: E 651 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8222 (mp) REVERT: E 662 SER cc_start: 0.8409 (p) cc_final: 0.8151 (p) REVERT: E 684 ASN cc_start: 0.8559 (p0) cc_final: 0.7688 (t0) REVERT: F 444 GLN cc_start: 0.7775 (mp10) cc_final: 0.7216 (tp40) REVERT: F 493 MET cc_start: 0.8602 (mmm) cc_final: 0.8195 (mmt) REVERT: F 519 ILE cc_start: 0.8840 (mt) cc_final: 0.8601 (mt) REVERT: F 620 ARG cc_start: 0.5430 (mmt180) cc_final: 0.5009 (mpt180) REVERT: G 152 MET cc_start: 0.8533 (tmm) cc_final: 0.8299 (tmm) REVERT: G 329 ARG cc_start: 0.8105 (ttp-170) cc_final: 0.7887 (mtm-85) REVERT: G 390 TYR cc_start: 0.8113 (m-80) cc_final: 0.7747 (m-10) REVERT: G 605 ILE cc_start: 0.8567 (mm) cc_final: 0.8253 (mm) REVERT: G 684 ASN cc_start: 0.8676 (p0) cc_final: 0.7416 (t0) REVERT: H 368 TYR cc_start: 0.7823 (m-80) cc_final: 0.7529 (m-80) REVERT: H 444 GLN cc_start: 0.7587 (mp10) cc_final: 0.6917 (tp40) REVERT: I 390 TYR cc_start: 0.8031 (m-80) cc_final: 0.7744 (m-80) REVERT: I 587 ASP cc_start: 0.7940 (p0) cc_final: 0.7396 (p0) REVERT: I 684 ASN cc_start: 0.8457 (p0) cc_final: 0.7325 (t0) REVERT: J 429 SER cc_start: 0.8578 (m) cc_final: 0.8355 (p) REVERT: J 491 MET cc_start: 0.7815 (ttt) cc_final: 0.7554 (ttp) outliers start: 56 outliers final: 40 residues processed: 777 average time/residue: 1.3439 time to fit residues: 1722.8925 Evaluate side-chains 723 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 681 time to evaluate : 6.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 690 CYS Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 319 HIS Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 647 ASP Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 690 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 509 ILE Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 365 CYS Chi-restraints excluded: chain G residue 457 GLU Chi-restraints excluded: chain G residue 587 ASP Chi-restraints excluded: chain G residue 690 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 538 LEU Chi-restraints excluded: chain I residue 66 PHE Chi-restraints excluded: chain I residue 230 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 365 CYS Chi-restraints excluded: chain I residue 542 THR Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 640 ASP Chi-restraints excluded: chain J residue 308 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 333 optimal weight: 0.3980 chunk 186 optimal weight: 8.9990 chunk 498 optimal weight: 8.9990 chunk 408 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 chunk 600 optimal weight: 10.0000 chunk 648 optimal weight: 3.9990 chunk 534 optimal weight: 4.9990 chunk 595 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 481 optimal weight: 10.0000 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 584 ASN H 584 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 53385 Z= 0.258 Angle : 0.555 7.348 72695 Z= 0.285 Chirality : 0.041 0.143 8005 Planarity : 0.004 0.060 9685 Dihedral : 4.589 52.971 7277 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.71 % Favored : 90.22 % Rotamer: Outliers : 1.03 % Allowed : 8.45 % Favored : 90.52 % 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: -1.64 (0.11), residues: 6625 helix: 1.01 (0.12), residues: 2075 sheet: -2.23 (0.18), residues: 720 loop : -2.17 (0.10), residues: 3830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 645 HIS 0.005 0.001 HIS B 290 PHE 0.022 0.001 PHE C 66 TYR 0.021 0.001 TYR H 476 ARG 0.012 0.000 ARG E 619 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 697 time to evaluate : 6.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 ASN cc_start: 0.8374 (t0) cc_final: 0.8130 (t0) REVERT: B 342 MET cc_start: 0.8252 (mtp) cc_final: 0.7871 (mtm) REVERT: B 365 CYS cc_start: 0.7825 (t) cc_final: 0.7454 (t) REVERT: B 449 MET cc_start: 0.3968 (tpt) cc_final: 0.3133 (tpt) REVERT: B 684 ASN cc_start: 0.9090 (p0) cc_final: 0.7314 (t0) REVERT: C 143 SER cc_start: 0.9183 (m) cc_final: 0.8920 (t) REVERT: C 231 GLN cc_start: 0.8668 (pm20) cc_final: 0.8235 (pm20) REVERT: C 605 ILE cc_start: 0.8264 (mm) cc_final: 0.8003 (mm) REVERT: C 662 SER cc_start: 0.8445 (p) cc_final: 0.8162 (p) REVERT: C 684 ASN cc_start: 0.8572 (p0) cc_final: 0.7716 (t0) REVERT: D 361 MET cc_start: 0.8248 (mmt) cc_final: 0.7823 (mmp) REVERT: D 513 HIS cc_start: 0.8168 (t-90) cc_final: 0.7957 (t-90) REVERT: D 627 ASP cc_start: 0.8419 (p0) cc_final: 0.8083 (p0) REVERT: E 143 SER cc_start: 0.9262 (m) cc_final: 0.8844 (t) REVERT: E 572 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7385 (mm-30) REVERT: E 651 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8265 (mp) REVERT: E 662 SER cc_start: 0.8380 (p) cc_final: 0.8134 (p) REVERT: E 678 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8343 (mmmt) REVERT: E 684 ASN cc_start: 0.8684 (p0) cc_final: 0.7702 (t0) REVERT: F 383 MET cc_start: 0.8225 (tpp) cc_final: 0.7996 (mmm) REVERT: F 444 GLN cc_start: 0.7790 (mp10) cc_final: 0.7185 (tp40) REVERT: F 519 ILE cc_start: 0.8838 (mt) cc_final: 0.8582 (mt) REVERT: F 620 ARG cc_start: 0.5713 (mmt180) cc_final: 0.5186 (mpt180) REVERT: G 152 MET cc_start: 0.8553 (tmm) cc_final: 0.8342 (tmm) REVERT: G 390 TYR cc_start: 0.8075 (m-80) cc_final: 0.7710 (m-10) REVERT: G 605 ILE cc_start: 0.8582 (mm) cc_final: 0.8268 (mm) REVERT: G 684 ASN cc_start: 0.8688 (p0) cc_final: 0.7382 (t0) REVERT: H 368 TYR cc_start: 0.7892 (m-80) cc_final: 0.7616 (m-80) REVERT: H 383 MET cc_start: 0.7671 (ttm) cc_final: 0.7416 (mmm) REVERT: H 472 LEU cc_start: 0.9059 (tp) cc_final: 0.8755 (tp) REVERT: H 476 TYR cc_start: 0.9210 (m-10) cc_final: 0.8954 (m-10) REVERT: I 390 TYR cc_start: 0.8026 (m-80) cc_final: 0.7745 (m-80) REVERT: I 467 ARG cc_start: 0.8056 (mtp85) cc_final: 0.7809 (mtp85) REVERT: I 478 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7501 (tm-30) REVERT: I 684 ASN cc_start: 0.8538 (p0) cc_final: 0.7188 (t0) REVERT: J 429 SER cc_start: 0.8629 (m) cc_final: 0.8380 (p) REVERT: J 491 MET cc_start: 0.7805 (ttt) cc_final: 0.7574 (ttp) outliers start: 58 outliers final: 47 residues processed: 728 average time/residue: 1.3413 time to fit residues: 1609.3266 Evaluate side-chains 709 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 661 time to evaluate : 6.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 690 CYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 690 CYS Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 365 CYS Chi-restraints excluded: chain G residue 690 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 538 LEU Chi-restraints excluded: chain H residue 546 ASN Chi-restraints excluded: chain I residue 66 PHE Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 230 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 365 CYS Chi-restraints excluded: chain I residue 542 THR Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain J residue 259 THR Chi-restraints excluded: chain J residue 308 SER Chi-restraints excluded: chain J residue 325 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 593 optimal weight: 8.9990 chunk 451 optimal weight: 5.9990 chunk 311 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 403 optimal weight: 0.9980 chunk 602 optimal weight: 9.9990 chunk 637 optimal weight: 5.9990 chunk 314 optimal weight: 7.9990 chunk 571 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN F 584 ASN H 584 ASN I 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 53385 Z= 0.321 Angle : 0.564 6.738 72695 Z= 0.290 Chirality : 0.041 0.144 8005 Planarity : 0.004 0.069 9685 Dihedral : 4.588 53.362 7277 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.40 % Favored : 89.52 % Rotamer: Outliers : 1.41 % Allowed : 9.83 % Favored : 88.75 % 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: -1.64 (0.11), residues: 6625 helix: 1.00 (0.12), residues: 2085 sheet: -2.20 (0.18), residues: 720 loop : -2.18 (0.10), residues: 3820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 645 HIS 0.006 0.001 HIS B 290 PHE 0.023 0.001 PHE C 66 TYR 0.023 0.001 TYR H 390 ARG 0.016 0.000 ARG I 619 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 678 time to evaluate : 6.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 ASN cc_start: 0.8383 (t0) cc_final: 0.8127 (t0) REVERT: B 342 MET cc_start: 0.8301 (mtp) cc_final: 0.7930 (mtm) REVERT: B 365 CYS cc_start: 0.7845 (t) cc_final: 0.7443 (t) REVERT: B 449 MET cc_start: 0.4064 (tpt) cc_final: 0.3099 (tpt) REVERT: C 143 SER cc_start: 0.9143 (m) cc_final: 0.8917 (t) REVERT: C 231 GLN cc_start: 0.8619 (pm20) cc_final: 0.8198 (pm20) REVERT: C 552 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8643 (tp30) REVERT: C 605 ILE cc_start: 0.8367 (mm) cc_final: 0.8103 (mm) REVERT: C 684 ASN cc_start: 0.9041 (p0) cc_final: 0.7670 (t0) REVERT: D 361 MET cc_start: 0.8271 (mmt) cc_final: 0.7795 (mmp) REVERT: D 627 ASP cc_start: 0.8433 (p0) cc_final: 0.8065 (p0) REVERT: E 143 SER cc_start: 0.9257 (m) cc_final: 0.8859 (t) REVERT: E 651 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8485 (mp) REVERT: E 684 ASN cc_start: 0.8663 (p0) cc_final: 0.7720 (t0) REVERT: F 444 GLN cc_start: 0.7880 (mp10) cc_final: 0.7218 (tp40) REVERT: F 519 ILE cc_start: 0.8795 (mt) cc_final: 0.8557 (mt) REVERT: F 620 ARG cc_start: 0.5663 (mmt180) cc_final: 0.4885 (mpt180) REVERT: G 123 ASP cc_start: 0.7712 (t0) cc_final: 0.7184 (t0) REVERT: G 152 MET cc_start: 0.8522 (tmm) cc_final: 0.8311 (tmm) REVERT: G 347 GLU cc_start: 0.8191 (tp30) cc_final: 0.7915 (tp30) REVERT: G 390 TYR cc_start: 0.8050 (m-80) cc_final: 0.7811 (m-10) REVERT: G 449 MET cc_start: 0.3787 (tpt) cc_final: 0.2859 (tpt) REVERT: G 605 ILE cc_start: 0.8619 (mm) cc_final: 0.8326 (mm) REVERT: G 684 ASN cc_start: 0.9151 (p0) cc_final: 0.7391 (t0) REVERT: H 368 TYR cc_start: 0.8020 (m-80) cc_final: 0.7710 (m-80) REVERT: H 472 LEU cc_start: 0.9083 (tp) cc_final: 0.8820 (tp) REVERT: H 476 TYR cc_start: 0.9192 (m-10) cc_final: 0.8957 (m-10) REVERT: I 70 PHE cc_start: 0.8788 (p90) cc_final: 0.8583 (p90) REVERT: I 467 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7810 (mtp85) REVERT: J 290 HIS cc_start: 0.7418 (OUTLIER) cc_final: 0.7080 (m90) REVERT: J 429 SER cc_start: 0.8507 (m) cc_final: 0.7884 (p) REVERT: J 491 MET cc_start: 0.7865 (ttt) cc_final: 0.7659 (ttp) REVERT: J 546 ASN cc_start: 0.8492 (m-40) cc_final: 0.8209 (t0) REVERT: J 620 ARG cc_start: 0.5589 (mpt180) cc_final: 0.5383 (mpt180) outliers start: 80 outliers final: 65 residues processed: 727 average time/residue: 1.2921 time to fit residues: 1542.9785 Evaluate side-chains 718 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 651 time to evaluate : 6.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 690 CYS Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 690 CYS Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain G residue 365 CYS Chi-restraints excluded: chain G residue 457 GLU Chi-restraints excluded: chain G residue 588 ILE Chi-restraints excluded: chain G residue 690 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 290 HIS Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 538 LEU Chi-restraints excluded: chain H residue 546 ASN Chi-restraints excluded: chain I residue 66 PHE Chi-restraints excluded: chain I residue 75 ASN Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 230 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 365 CYS Chi-restraints excluded: chain I residue 542 THR Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 640 ASP Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain I residue 690 CYS Chi-restraints excluded: chain J residue 259 THR Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 308 SER Chi-restraints excluded: chain J residue 325 ASP Chi-restraints excluded: chain J residue 373 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 531 optimal weight: 3.9990 chunk 362 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 475 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 544 optimal weight: 8.9990 chunk 440 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 325 optimal weight: 5.9990 chunk 572 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN C 521 ASN D 598 ASN H 584 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 53385 Z= 0.314 Angle : 0.558 6.484 72695 Z= 0.287 Chirality : 0.041 0.145 8005 Planarity : 0.004 0.073 9685 Dihedral : 4.562 52.640 7277 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.63 % Favored : 89.30 % Rotamer: Outliers : 1.57 % Allowed : 10.52 % Favored : 87.90 % 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: -1.57 (0.11), residues: 6625 helix: 1.07 (0.12), residues: 2085 sheet: -2.12 (0.19), residues: 680 loop : -2.16 (0.10), residues: 3860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 645 HIS 0.005 0.001 HIS B 290 PHE 0.023 0.001 PHE C 66 TYR 0.009 0.001 TYR G 221 ARG 0.009 0.000 ARG I 619 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 669 time to evaluate : 6.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 ASN cc_start: 0.8407 (t0) cc_final: 0.8173 (t0) REVERT: B 342 MET cc_start: 0.8273 (mtp) cc_final: 0.7906 (mtm) REVERT: B 365 CYS cc_start: 0.7847 (t) cc_final: 0.7463 (t) REVERT: B 449 MET cc_start: 0.3964 (tpt) cc_final: 0.3196 (tpt) REVERT: C 69 GLN cc_start: 0.8323 (tp40) cc_final: 0.8092 (tp-100) REVERT: C 143 SER cc_start: 0.9124 (m) cc_final: 0.8912 (t) REVERT: C 231 GLN cc_start: 0.8625 (pm20) cc_final: 0.8213 (pm20) REVERT: C 552 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8608 (tp30) REVERT: C 605 ILE cc_start: 0.8440 (mm) cc_final: 0.8232 (mm) REVERT: C 684 ASN cc_start: 0.9050 (p0) cc_final: 0.7648 (t0) REVERT: D 361 MET cc_start: 0.8359 (mmt) cc_final: 0.7909 (mmp) REVERT: D 627 ASP cc_start: 0.8432 (p0) cc_final: 0.8062 (p0) REVERT: E 143 SER cc_start: 0.9255 (m) cc_final: 0.8858 (t) REVERT: E 651 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8530 (mp) REVERT: F 444 GLN cc_start: 0.7892 (mp10) cc_final: 0.7216 (tp40) REVERT: F 519 ILE cc_start: 0.8784 (mt) cc_final: 0.8544 (mt) REVERT: F 620 ARG cc_start: 0.5541 (mmt180) cc_final: 0.4761 (mpt180) REVERT: G 66 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8017 (p90) REVERT: G 123 ASP cc_start: 0.7732 (t0) cc_final: 0.7222 (t0) REVERT: G 347 GLU cc_start: 0.8238 (tp30) cc_final: 0.7971 (tp30) REVERT: G 449 MET cc_start: 0.3496 (tpt) cc_final: 0.2449 (tpt) REVERT: G 605 ILE cc_start: 0.8606 (mm) cc_final: 0.8304 (mm) REVERT: G 684 ASN cc_start: 0.9144 (p0) cc_final: 0.7397 (t0) REVERT: H 422 MET cc_start: 0.8575 (mmp) cc_final: 0.8311 (mmp) REVERT: I 75 ASN cc_start: 0.8375 (t0) cc_final: 0.8129 (m-40) REVERT: I 467 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7840 (mtp85) REVERT: I 592 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7229 (p90) REVERT: J 290 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.7055 (m90) REVERT: J 429 SER cc_start: 0.8503 (m) cc_final: 0.7895 (p) REVERT: J 546 ASN cc_start: 0.8488 (m-40) cc_final: 0.8230 (t0) outliers start: 89 outliers final: 76 residues processed: 727 average time/residue: 1.2554 time to fit residues: 1490.2504 Evaluate side-chains 721 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 641 time to evaluate : 6.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 690 CYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain E residue 636 ASP Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 690 CYS Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 568 ASP Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain G residue 66 PHE Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 365 CYS Chi-restraints excluded: chain G residue 457 GLU Chi-restraints excluded: chain G residue 588 ILE Chi-restraints excluded: chain G residue 690 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 290 HIS Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 538 LEU Chi-restraints excluded: chain H residue 546 ASN Chi-restraints excluded: chain I residue 66 PHE Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 230 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 365 CYS Chi-restraints excluded: chain I residue 542 THR Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 592 PHE Chi-restraints excluded: chain I residue 640 ASP Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain I residue 690 CYS Chi-restraints excluded: chain J residue 259 THR Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 308 SER Chi-restraints excluded: chain J residue 365 CYS Chi-restraints excluded: chain J residue 373 LEU Chi-restraints excluded: chain J residue 505 ILE Chi-restraints excluded: chain J residue 662 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 214 optimal weight: 5.9990 chunk 574 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 374 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 638 optimal weight: 5.9990 chunk 530 optimal weight: 5.9990 chunk 295 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 335 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 GLN H 507 ASN H 584 ASN ** I 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 53385 Z= 0.223 Angle : 0.530 5.817 72695 Z= 0.269 Chirality : 0.041 0.140 8005 Planarity : 0.004 0.072 9685 Dihedral : 4.404 51.559 7277 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.06 % Favored : 90.87 % Rotamer: Outliers : 1.56 % Allowed : 11.42 % Favored : 87.02 % 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: -1.37 (0.11), residues: 6625 helix: 1.32 (0.12), residues: 2085 sheet: -2.06 (0.19), residues: 680 loop : -2.08 (0.10), residues: 3860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 645 HIS 0.007 0.001 HIS F 290 PHE 0.025 0.001 PHE G 70 TYR 0.029 0.001 TYR H 476 ARG 0.010 0.000 ARG J 674 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 699 time to evaluate : 6.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 ASN cc_start: 0.8414 (t0) cc_final: 0.8175 (t0) REVERT: B 342 MET cc_start: 0.8242 (mtp) cc_final: 0.7810 (mtm) REVERT: B 365 CYS cc_start: 0.7856 (t) cc_final: 0.7453 (t) REVERT: B 449 MET cc_start: 0.3936 (tpt) cc_final: 0.3191 (tpt) REVERT: C 69 GLN cc_start: 0.8299 (tp40) cc_final: 0.8069 (tp-100) REVERT: C 143 SER cc_start: 0.9111 (m) cc_final: 0.8893 (t) REVERT: C 231 GLN cc_start: 0.8593 (pm20) cc_final: 0.8197 (pm20) REVERT: C 605 ILE cc_start: 0.8442 (mm) cc_final: 0.8226 (mm) REVERT: C 684 ASN cc_start: 0.9049 (p0) cc_final: 0.7634 (t0) REVERT: D 627 ASP cc_start: 0.8421 (p0) cc_final: 0.8054 (p0) REVERT: E 143 SER cc_start: 0.9251 (m) cc_final: 0.8848 (t) REVERT: E 651 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8503 (mp) REVERT: F 444 GLN cc_start: 0.7794 (mp10) cc_final: 0.7195 (tp40) REVERT: F 519 ILE cc_start: 0.8779 (mt) cc_final: 0.8525 (mt) REVERT: F 620 ARG cc_start: 0.5745 (mmt180) cc_final: 0.5033 (mpt180) REVERT: G 66 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7957 (p90) REVERT: G 123 ASP cc_start: 0.7716 (t0) cc_final: 0.7208 (t0) REVERT: G 347 GLU cc_start: 0.8116 (tp30) cc_final: 0.7833 (tp30) REVERT: G 383 MET cc_start: 0.9173 (tpp) cc_final: 0.8962 (tpp) REVERT: G 449 MET cc_start: 0.3398 (tpt) cc_final: 0.2393 (tpt) REVERT: G 605 ILE cc_start: 0.8594 (mm) cc_final: 0.8295 (mm) REVERT: G 684 ASN cc_start: 0.9135 (p0) cc_final: 0.7413 (t0) REVERT: H 422 MET cc_start: 0.8608 (mmp) cc_final: 0.8400 (mmp) REVERT: H 476 TYR cc_start: 0.9237 (m-10) cc_final: 0.8960 (m-80) REVERT: I 74 ARG cc_start: 0.7869 (ttt90) cc_final: 0.7522 (ttt-90) REVERT: I 592 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.7180 (p90) REVERT: J 290 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.7038 (m90) REVERT: J 429 SER cc_start: 0.8437 (m) cc_final: 0.7778 (p) REVERT: J 546 ASN cc_start: 0.8468 (m-40) cc_final: 0.8214 (t0) outliers start: 88 outliers final: 72 residues processed: 758 average time/residue: 1.3314 time to fit residues: 1671.5197 Evaluate side-chains 736 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 660 time to evaluate : 6.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 690 CYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 365 CYS Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 690 CYS Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 568 ASP Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain G residue 66 PHE Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 365 CYS Chi-restraints excluded: chain G residue 457 GLU Chi-restraints excluded: chain G residue 588 ILE Chi-restraints excluded: chain G residue 690 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 290 HIS Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 538 LEU Chi-restraints excluded: chain H residue 546 ASN Chi-restraints excluded: chain I residue 66 PHE Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 230 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 365 CYS Chi-restraints excluded: chain I residue 542 THR Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 592 PHE Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain I residue 690 CYS Chi-restraints excluded: chain J residue 259 THR Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 308 SER Chi-restraints excluded: chain J residue 325 ASP Chi-restraints excluded: chain J residue 365 CYS Chi-restraints excluded: chain J residue 373 LEU Chi-restraints excluded: chain J residue 505 ILE Chi-restraints excluded: chain J residue 662 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 615 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 363 optimal weight: 9.9990 chunk 466 optimal weight: 6.9990 chunk 361 optimal weight: 6.9990 chunk 537 optimal weight: 0.6980 chunk 356 optimal weight: 0.9990 chunk 636 optimal weight: 10.0000 chunk 398 optimal weight: 5.9990 chunk 387 optimal weight: 9.9990 chunk 293 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 507 ASN H 584 ASN ** I 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 53385 Z= 0.248 Angle : 0.534 6.218 72695 Z= 0.271 Chirality : 0.041 0.139 8005 Planarity : 0.004 0.044 9685 Dihedral : 4.359 51.528 7277 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.80 % Favored : 90.13 % Rotamer: Outliers : 1.63 % Allowed : 11.87 % Favored : 86.51 % 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: -1.34 (0.11), residues: 6625 helix: 1.37 (0.12), residues: 2075 sheet: -2.06 (0.19), residues: 680 loop : -2.06 (0.10), residues: 3870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 645 HIS 0.006 0.001 HIS F 290 PHE 0.023 0.001 PHE C 66 TYR 0.017 0.001 TYR H 476 ARG 0.011 0.000 ARG F 674 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 672 time to evaluate : 6.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 MET cc_start: 0.8235 (mtp) cc_final: 0.7814 (mtm) REVERT: B 365 CYS cc_start: 0.7876 (t) cc_final: 0.7458 (t) REVERT: B 449 MET cc_start: 0.3921 (tpt) cc_final: 0.3205 (tpt) REVERT: C 69 GLN cc_start: 0.8254 (tp40) cc_final: 0.8035 (tp-100) REVERT: C 143 SER cc_start: 0.9097 (m) cc_final: 0.8892 (t) REVERT: C 231 GLN cc_start: 0.8592 (pm20) cc_final: 0.8209 (pm20) REVERT: C 605 ILE cc_start: 0.8453 (mm) cc_final: 0.8233 (mm) REVERT: C 684 ASN cc_start: 0.9043 (p0) cc_final: 0.8700 (p0) REVERT: D 627 ASP cc_start: 0.8420 (p0) cc_final: 0.8052 (p0) REVERT: E 143 SER cc_start: 0.9255 (m) cc_final: 0.8861 (t) REVERT: E 651 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8524 (mp) REVERT: F 444 GLN cc_start: 0.7814 (mp10) cc_final: 0.7193 (tp40) REVERT: F 519 ILE cc_start: 0.8769 (mt) cc_final: 0.8544 (mt) REVERT: F 620 ARG cc_start: 0.5500 (mmt180) cc_final: 0.4820 (mpt180) REVERT: G 66 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8083 (p90) REVERT: G 123 ASP cc_start: 0.7727 (t0) cc_final: 0.7219 (t0) REVERT: G 347 GLU cc_start: 0.8215 (tp30) cc_final: 0.7919 (tp30) REVERT: G 449 MET cc_start: 0.3393 (tpt) cc_final: 0.2365 (tpt) REVERT: G 605 ILE cc_start: 0.8590 (mm) cc_final: 0.8286 (mm) REVERT: H 422 MET cc_start: 0.8633 (mmp) cc_final: 0.8423 (mmp) REVERT: H 476 TYR cc_start: 0.9214 (m-10) cc_final: 0.8887 (m-80) REVERT: I 74 ARG cc_start: 0.7860 (ttt90) cc_final: 0.7525 (ttt-90) REVERT: I 75 ASN cc_start: 0.8481 (t0) cc_final: 0.7836 (m-40) REVERT: I 592 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7175 (p90) REVERT: J 290 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.7040 (m90) REVERT: J 429 SER cc_start: 0.8454 (m) cc_final: 0.7791 (p) REVERT: J 546 ASN cc_start: 0.8543 (m-40) cc_final: 0.8195 (t0) outliers start: 92 outliers final: 80 residues processed: 732 average time/residue: 1.2530 time to fit residues: 1500.2845 Evaluate side-chains 743 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 659 time to evaluate : 6.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 690 CYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 365 CYS Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 365 CYS Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain E residue 515 CYS Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 690 CYS Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 568 ASP Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain G residue 66 PHE Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 365 CYS Chi-restraints excluded: chain G residue 457 GLU Chi-restraints excluded: chain G residue 690 CYS Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 290 HIS Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 538 LEU Chi-restraints excluded: chain H residue 546 ASN Chi-restraints excluded: chain I residue 66 PHE Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 230 CYS Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 365 CYS Chi-restraints excluded: chain I residue 542 THR Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 592 PHE Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain I residue 690 CYS Chi-restraints excluded: chain J residue 259 THR Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 325 ASP Chi-restraints excluded: chain J residue 365 CYS Chi-restraints excluded: chain J residue 373 LEU Chi-restraints excluded: chain J residue 505 ILE Chi-restraints excluded: chain J residue 662 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 393 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 chunk 379 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 404 optimal weight: 1.9990 chunk 433 optimal weight: 0.7980 chunk 314 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 500 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 595 ASN H 354 GLN H 584 ASN I 55 ASN I 57 ASN ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 53385 Z= 0.161 Angle : 0.514 6.978 72695 Z= 0.258 Chirality : 0.040 0.142 8005 Planarity : 0.004 0.058 9685 Dihedral : 4.216 50.815 7277 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.06 % Favored : 91.86 % Rotamer: Outliers : 1.56 % Allowed : 12.20 % Favored : 86.24 % 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 (0.11), residues: 6625 helix: 1.59 (0.12), residues: 2070 sheet: -2.04 (0.18), residues: 725 loop : -1.98 (0.10), residues: 3830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 645 HIS 0.006 0.001 HIS F 290 PHE 0.027 0.001 PHE G 70 TYR 0.020 0.001 TYR F 368 ARG 0.015 0.000 ARG I 619 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 700 time to evaluate : 6.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 MET cc_start: 0.8168 (mtp) cc_final: 0.7676 (mtm) REVERT: B 365 CYS cc_start: 0.7859 (t) cc_final: 0.7457 (t) REVERT: B 449 MET cc_start: 0.3889 (tpt) cc_final: 0.3199 (tpt) REVERT: C 69 GLN cc_start: 0.8193 (tp40) cc_final: 0.7990 (tp-100) REVERT: C 143 SER cc_start: 0.9085 (m) cc_final: 0.8861 (t) REVERT: C 231 GLN cc_start: 0.8562 (pm20) cc_final: 0.8186 (pm20) REVERT: C 605 ILE cc_start: 0.8422 (mm) cc_final: 0.8205 (mm) REVERT: C 684 ASN cc_start: 0.9180 (p0) cc_final: 0.8785 (p0) REVERT: D 627 ASP cc_start: 0.8385 (p0) cc_final: 0.8050 (p0) REVERT: E 143 SER cc_start: 0.9235 (m) cc_final: 0.8855 (t) REVERT: E 651 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8500 (mp) REVERT: F 444 GLN cc_start: 0.7723 (mp10) cc_final: 0.7148 (tp40) REVERT: F 519 ILE cc_start: 0.8757 (mt) cc_final: 0.8518 (mt) REVERT: F 620 ARG cc_start: 0.5482 (mmt180) cc_final: 0.4816 (mpt180) REVERT: G 66 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8083 (p90) REVERT: G 347 GLU cc_start: 0.8077 (tp30) cc_final: 0.7804 (tp30) REVERT: G 449 MET cc_start: 0.3402 (tpt) cc_final: 0.2237 (tpt) REVERT: G 605 ILE cc_start: 0.8590 (mm) cc_final: 0.8276 (mm) REVERT: H 476 TYR cc_start: 0.9252 (m-10) cc_final: 0.8883 (m-80) REVERT: I 74 ARG cc_start: 0.7785 (ttt90) cc_final: 0.7516 (ttt-90) REVERT: I 75 ASN cc_start: 0.8476 (t0) cc_final: 0.7827 (m-40) REVERT: I 592 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7134 (p90) REVERT: J 290 HIS cc_start: 0.7379 (OUTLIER) cc_final: 0.7016 (m90) REVERT: J 429 SER cc_start: 0.8460 (m) cc_final: 0.7988 (p) outliers start: 88 outliers final: 74 residues processed: 756 average time/residue: 1.2989 time to fit residues: 1618.1751 Evaluate side-chains 759 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 681 time to evaluate : 6.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 690 CYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 365 CYS Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 365 CYS Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 690 CYS Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 568 ASP Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain G residue 66 PHE Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 365 CYS Chi-restraints excluded: chain G residue 457 GLU Chi-restraints excluded: chain G residue 690 CYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 290 HIS Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 538 LEU Chi-restraints excluded: chain H residue 546 ASN Chi-restraints excluded: chain I residue 66 PHE Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 365 CYS Chi-restraints excluded: chain I residue 542 THR Chi-restraints excluded: chain I residue 567 LEU Chi-restraints excluded: chain I residue 592 PHE Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain I residue 690 CYS Chi-restraints excluded: chain J residue 259 THR Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 325 ASP Chi-restraints excluded: chain J residue 505 ILE Chi-restraints excluded: chain J residue 662 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 578 optimal weight: 9.9990 chunk 609 optimal weight: 5.9990 chunk 556 optimal weight: 9.9990 chunk 592 optimal weight: 2.9990 chunk 356 optimal weight: 0.9980 chunk 258 optimal weight: 0.8980 chunk 465 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 chunk 535 optimal weight: 7.9990 chunk 560 optimal weight: 0.7980 chunk 590 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 ASN B 57 ASN ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 ASN C 57 ASN ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 ASN E 57 ASN ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 507 ASN H 584 ASN ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 53385 Z= 0.164 Angle : 0.512 6.559 72695 Z= 0.256 Chirality : 0.040 0.142 8005 Planarity : 0.004 0.083 9685 Dihedral : 4.101 50.380 7277 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.85 % Favored : 92.08 % Rotamer: Outliers : 1.50 % Allowed : 12.57 % Favored : 85.92 % 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: -1.08 (0.11), residues: 6625 helix: 1.70 (0.12), residues: 2070 sheet: -1.96 (0.18), residues: 725 loop : -1.95 (0.10), residues: 3830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 645 HIS 0.005 0.001 HIS F 290 PHE 0.026 0.001 PHE E 70 TYR 0.016 0.001 TYR H 476 ARG 0.011 0.000 ARG I 619 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 706 time to evaluate : 6.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 MET cc_start: 0.8152 (mtp) cc_final: 0.7666 (mtm) REVERT: B 365 CYS cc_start: 0.7859 (t) cc_final: 0.7445 (t) REVERT: B 449 MET cc_start: 0.3888 (tpt) cc_final: 0.3211 (tpt) REVERT: C 69 GLN cc_start: 0.8186 (tp40) cc_final: 0.7982 (tp-100) REVERT: C 143 SER cc_start: 0.9083 (m) cc_final: 0.8882 (t) REVERT: C 231 GLN cc_start: 0.8589 (pm20) cc_final: 0.8174 (pm20) REVERT: C 605 ILE cc_start: 0.8406 (mm) cc_final: 0.8183 (mm) REVERT: C 684 ASN cc_start: 0.9175 (p0) cc_final: 0.8799 (p0) REVERT: D 627 ASP cc_start: 0.8350 (p0) cc_final: 0.8017 (p0) REVERT: E 69 GLN cc_start: 0.8157 (tp40) cc_final: 0.7681 (tp40) REVERT: E 143 SER cc_start: 0.9222 (m) cc_final: 0.8841 (t) REVERT: E 651 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8512 (mp) REVERT: F 383 MET cc_start: 0.8262 (tpp) cc_final: 0.7960 (mmm) REVERT: F 444 GLN cc_start: 0.7685 (mp10) cc_final: 0.7131 (tp40) REVERT: F 620 ARG cc_start: 0.5279 (mmt180) cc_final: 0.4643 (mpt180) REVERT: G 66 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.8126 (p90) REVERT: G 347 GLU cc_start: 0.8083 (tp30) cc_final: 0.7786 (tp30) REVERT: G 449 MET cc_start: 0.3422 (tpt) cc_final: 0.2193 (tpt) REVERT: G 605 ILE cc_start: 0.8574 (mm) cc_final: 0.8263 (mm) REVERT: H 476 TYR cc_start: 0.9250 (m-10) cc_final: 0.8888 (m-80) REVERT: I 74 ARG cc_start: 0.7786 (ttt90) cc_final: 0.7449 (ttt90) REVERT: I 75 ASN cc_start: 0.8477 (t0) cc_final: 0.7863 (m-40) REVERT: I 592 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.7111 (p90) REVERT: J 290 HIS cc_start: 0.7388 (OUTLIER) cc_final: 0.7054 (m90) outliers start: 85 outliers final: 71 residues processed: 757 average time/residue: 1.2670 time to fit residues: 1583.9789 Evaluate side-chains 745 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 670 time to evaluate : 6.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 690 CYS Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 365 CYS Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 365 CYS Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 690 CYS Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 568 ASP Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain G residue 66 PHE Chi-restraints excluded: chain G residue 365 CYS Chi-restraints excluded: chain G residue 457 GLU Chi-restraints excluded: chain G residue 690 CYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 290 HIS Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 365 CYS Chi-restraints excluded: chain H residue 538 LEU Chi-restraints excluded: chain H residue 546 ASN Chi-restraints excluded: chain I residue 66 PHE Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 592 PHE Chi-restraints excluded: chain I residue 633 VAL Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain J residue 259 THR Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 325 ASP Chi-restraints excluded: chain J residue 365 CYS Chi-restraints excluded: chain J residue 505 ILE Chi-restraints excluded: chain J residue 662 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 389 optimal weight: 5.9990 chunk 626 optimal weight: 3.9990 chunk 382 optimal weight: 8.9990 chunk 297 optimal weight: 9.9990 chunk 435 optimal weight: 4.9990 chunk 657 optimal weight: 1.9990 chunk 605 optimal weight: 2.9990 chunk 523 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 404 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 584 ASN ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 584 ASN ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 53385 Z= 0.195 Angle : 0.518 10.194 72695 Z= 0.259 Chirality : 0.040 0.145 8005 Planarity : 0.004 0.091 9685 Dihedral : 4.037 26.359 7275 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.24 % Favored : 91.68 % Rotamer: Outliers : 1.36 % Allowed : 12.98 % Favored : 85.66 % 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: -1.07 (0.11), residues: 6625 helix: 1.69 (0.12), residues: 2075 sheet: -1.94 (0.19), residues: 725 loop : -1.94 (0.10), residues: 3825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 645 HIS 0.006 0.001 HIS F 290 PHE 0.031 0.001 PHE G 70 TYR 0.022 0.001 TYR J 368 ARG 0.012 0.000 ARG I 619 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13250 Ramachandran restraints generated. 6625 Oldfield, 0 Emsley, 6625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 663 time to evaluate : 6.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 MET cc_start: 0.8176 (mtp) cc_final: 0.7686 (mtm) REVERT: B 365 CYS cc_start: 0.7863 (t) cc_final: 0.7456 (t) REVERT: B 449 MET cc_start: 0.3903 (tpt) cc_final: 0.3222 (tpt) REVERT: C 143 SER cc_start: 0.9102 (m) cc_final: 0.8901 (t) REVERT: C 231 GLN cc_start: 0.8603 (pm20) cc_final: 0.8198 (pm20) REVERT: C 449 MET cc_start: 0.3264 (tpt) cc_final: 0.1956 (tpt) REVERT: C 552 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8584 (tp30) REVERT: C 605 ILE cc_start: 0.8397 (mm) cc_final: 0.8175 (mm) REVERT: C 684 ASN cc_start: 0.9183 (p0) cc_final: 0.8764 (p0) REVERT: D 627 ASP cc_start: 0.8356 (p0) cc_final: 0.8032 (p0) REVERT: E 69 GLN cc_start: 0.8150 (tp40) cc_final: 0.7692 (tp40) REVERT: E 143 SER cc_start: 0.9229 (m) cc_final: 0.8858 (t) REVERT: E 651 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8515 (mp) REVERT: F 444 GLN cc_start: 0.7705 (mp10) cc_final: 0.7133 (tp40) REVERT: F 620 ARG cc_start: 0.5276 (mmt180) cc_final: 0.4633 (mpt180) REVERT: G 66 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8208 (p90) REVERT: G 347 GLU cc_start: 0.8201 (tp30) cc_final: 0.7869 (tp30) REVERT: G 449 MET cc_start: 0.3457 (tpt) cc_final: 0.2189 (tpt) REVERT: G 605 ILE cc_start: 0.8584 (mm) cc_final: 0.8276 (mm) REVERT: H 476 TYR cc_start: 0.9262 (m-10) cc_final: 0.8931 (m-80) REVERT: I 74 ARG cc_start: 0.7847 (ttt90) cc_final: 0.7401 (ttt90) REVERT: I 75 ASN cc_start: 0.8488 (t0) cc_final: 0.7838 (m-40) REVERT: I 592 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7156 (p90) REVERT: J 290 HIS cc_start: 0.7402 (OUTLIER) cc_final: 0.7066 (m90) outliers start: 77 outliers final: 72 residues processed: 712 average time/residue: 1.3065 time to fit residues: 1535.1836 Evaluate side-chains 728 residues out of total 5655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 652 time to evaluate : 6.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 584 ASN Chi-restraints excluded: chain B residue 587 ASP Chi-restraints excluded: chain B residue 690 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 251 GLN Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 365 CYS Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 584 ASN Chi-restraints excluded: chain C residue 690 CYS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 365 CYS Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 365 CYS Chi-restraints excluded: chain E residue 396 THR Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain E residue 651 LEU Chi-restraints excluded: chain E residue 690 CYS Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 118 ASP Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 568 ASP Chi-restraints excluded: chain F residue 662 SER Chi-restraints excluded: chain G residue 66 PHE Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 365 CYS Chi-restraints excluded: chain G residue 457 GLU Chi-restraints excluded: chain G residue 690 CYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 136 SER Chi-restraints excluded: chain H residue 290 HIS Chi-restraints excluded: chain H residue 296 MET Chi-restraints excluded: chain H residue 365 CYS Chi-restraints excluded: chain H residue 538 LEU Chi-restraints excluded: chain H residue 546 ASN Chi-restraints excluded: chain I residue 66 PHE Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 199 SER Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 542 THR Chi-restraints excluded: chain I residue 592 PHE Chi-restraints excluded: chain I residue 633 VAL Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain J residue 259 THR Chi-restraints excluded: chain J residue 285 ILE Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 325 ASP Chi-restraints excluded: chain J residue 365 CYS Chi-restraints excluded: chain J residue 373 LEU Chi-restraints excluded: chain J residue 505 ILE Chi-restraints excluded: chain J residue 662 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 415 optimal weight: 10.0000 chunk 557 optimal weight: 7.9990 chunk 160 optimal weight: 0.0000 chunk 482 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 145 optimal weight: 6.9990 chunk 524 optimal weight: 7.9990 chunk 219 optimal weight: 5.9990 chunk 538 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 overall best weight: 4.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 584 ASN ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 546 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 = 0.2770 r_free = 0.2770 target = 0.077749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.063303 restraints weight = 343158.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.066692 restraints weight = 140215.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.068921 restraints weight = 77962.079| |-----------------------------------------------------------------------------| r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.229 53385 Z= 0.235 Angle : 0.585 59.200 72695 Z= 0.314 Chirality : 0.041 0.522 8005 Planarity : 0.004 0.088 9685 Dihedral : 4.044 26.340 7275 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.35 % Favored : 91.56 % Rotamer: Outliers : 1.45 % Allowed : 13.09 % Favored : 85.46 % Cbeta Deviations : 0.02 % 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: -1.07 (0.11), residues: 6625 helix: 1.69 (0.12), residues: 2075 sheet: -1.94 (0.19), residues: 725 loop : -1.94 (0.10), residues: 3825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 645 HIS 0.005 0.001 HIS F 290 PHE 0.023 0.001 PHE C 66 TYR 0.016 0.001 TYR J 368 ARG 0.010 0.000 ARG I 619 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22732.47 seconds wall clock time: 394 minutes 35.05 seconds (23675.05 seconds total)