Starting phenix.real_space_refine (version: dev) on Thu Dec 15 03:21:27 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxo_13102/12_2022/7oxo_13102_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxo_13102/12_2022/7oxo_13102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxo_13102/12_2022/7oxo_13102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxo_13102/12_2022/7oxo_13102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxo_13102/12_2022/7oxo_13102_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxo_13102/12_2022/7oxo_13102_trim_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.060 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 476": "OE1" <-> "OE2" Residue "A PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 852": "OD1" <-> "OD2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "B ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 476": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 706": "OE1" <-> "OE2" Residue "B ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C ASP 496": "OD1" <-> "OD2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 671": "OE1" <-> "OE2" Residue "C GLU 781": "OE1" <-> "OE2" Residue "C ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 897": "OE1" <-> "OE2" Residue "D ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 412": "OD1" <-> "OD2" Residue "D GLU 441": "OE1" <-> "OE2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "D GLU 583": "OE1" <-> "OE2" Residue "D TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 733": "OE1" <-> "OE2" Residue "D ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 789": "OD1" <-> "OD2" Residue "D ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 818": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 897": "OE1" <-> "OE2" Residue "E ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 441": "OE1" <-> "OE2" Residue "E GLU 476": "OE1" <-> "OE2" Residue "E GLU 495": "OE1" <-> "OE2" Residue "E GLU 583": "OE1" <-> "OE2" Residue "E GLU 614": "OE1" <-> "OE2" Residue "E ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 897": "OE1" <-> "OE2" Residue "F ARG 131": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 205": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 381": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 583": "OE1" <-> "OE2" Residue "F ARG 785": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 786": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 801": "OE1" <-> "OE2" Residue "F GLU 812": "OE1" <-> "OE2" Residue "F ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 822": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 937": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 74729 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 12428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12428 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "B" Number of atoms: 12428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12428 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "C" Number of atoms: 12428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12428 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "D" Number of atoms: 12428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12428 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "E" Number of atoms: 12427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12427 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "F" Number of atoms: 12428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 12428 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.27, per 1000 atoms: 0.34 Number of scatterers: 74729 At special positions: 0 Unit cell: (142.83, 144.946, 221.122, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 162 16.00 P 12 15.00 O 6972 8.00 N 6426 7.00 C 23442 6.00 H 37715 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: 48.64 Conformation dependent library (CDL) restraints added in 4.5 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8736 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 183 helices and 35 sheets defined 44.1% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.13 Creating SS restraints... Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.590A pdb=" N VAL A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.915A pdb=" N LEU A 338 " --> pdb=" O MET A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 355 through 406 removed outlier: 3.761A pdb=" N LEU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 393 " --> pdb=" O GLN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 427 removed outlier: 3.901A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.830A pdb=" N ASP A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 466 Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 495 through 510 removed outlier: 3.669A pdb=" N LEU A 510 " --> pdb=" O ALA A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 540 Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 572 through 580 removed outlier: 3.634A pdb=" N CYS A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 594 No H-bonds generated for 'chain 'A' and resid 592 through 594' Processing helix chain 'A' and resid 603 through 611 removed outlier: 3.621A pdb=" N LEU A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 618 removed outlier: 3.872A pdb=" N ASN A 618 " --> pdb=" O GLN A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 615 through 618' Processing helix chain 'A' and resid 647 through 650 No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 663 through 673 removed outlier: 3.950A pdb=" N LEU A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 672 " --> pdb=" O ALA A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 682 Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 693 through 702 Processing helix chain 'A' and resid 710 through 728 Processing helix chain 'A' and resid 739 through 746 removed outlier: 4.350A pdb=" N GLN A 743 " --> pdb=" O PRO A 739 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 828 removed outlier: 3.824A pdb=" N MET A 826 " --> pdb=" O ARG A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 869 Proline residue: A 854 - end of helix removed outlier: 4.224A pdb=" N CYS A 858 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 861 " --> pdb=" O CYS A 858 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A 869 " --> pdb=" O SER A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 914 through 922 removed outlier: 4.416A pdb=" N LYS A 918 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A 920 " --> pdb=" O LYS A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 928 No H-bonds generated for 'chain 'A' and resid 925 through 928' Processing helix chain 'A' and resid 939 through 944 Processing helix chain 'B' and resid 148 through 155 removed outlier: 3.974A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 291 through 306 removed outlier: 3.778A pdb=" N GLU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.961A pdb=" N LEU B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 355 through 388 Processing helix chain 'B' and resid 392 through 405 Processing helix chain 'B' and resid 414 through 427 Processing helix chain 'B' and resid 432 through 447 Processing helix chain 'B' and resid 453 through 467 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 495 through 508 Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 555 through 559 Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 592 through 594 No H-bonds generated for 'chain 'B' and resid 592 through 594' Processing helix chain 'B' and resid 603 through 611 removed outlier: 3.830A pdb=" N LEU B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 618 removed outlier: 3.745A pdb=" N ASN B 618 " --> pdb=" O GLN B 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 615 through 618' Processing helix chain 'B' and resid 647 through 650 No H-bonds generated for 'chain 'B' and resid 647 through 650' Processing helix chain 'B' and resid 663 through 673 removed outlier: 3.860A pdb=" N LEU B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 668 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 681 Processing helix chain 'B' and resid 686 through 688 No H-bonds generated for 'chain 'B' and resid 686 through 688' Processing helix chain 'B' and resid 693 through 702 Processing helix chain 'B' and resid 710 through 728 Processing helix chain 'B' and resid 739 through 746 removed outlier: 4.307A pdb=" N GLN B 743 " --> pdb=" O GLU B 740 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL B 746 " --> pdb=" O GLN B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 828 removed outlier: 3.816A pdb=" N MET B 826 " --> pdb=" O ARG B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 869 Proline residue: B 854 - end of helix removed outlier: 4.233A pdb=" N CYS B 858 " --> pdb=" O SER B 855 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 861 " --> pdb=" O CYS B 858 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET B 869 " --> pdb=" O SER B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 904 Processing helix chain 'B' and resid 914 through 922 removed outlier: 4.224A pdb=" N LYS B 918 " --> pdb=" O GLU B 915 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE B 920 " --> pdb=" O LYS B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 928 No H-bonds generated for 'chain 'B' and resid 925 through 928' Processing helix chain 'B' and resid 939 through 944 Processing helix chain 'C' and resid 148 through 154 removed outlier: 3.641A pdb=" N LEU C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 291 through 306 removed outlier: 3.764A pdb=" N GLU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 328 through 337 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 355 through 406 Processing helix chain 'C' and resid 414 through 427 Processing helix chain 'C' and resid 432 through 447 Processing helix chain 'C' and resid 453 through 466 Processing helix chain 'C' and resid 480 through 488 Processing helix chain 'C' and resid 495 through 510 removed outlier: 3.654A pdb=" N LEU C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 540 removed outlier: 3.647A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 559 Processing helix chain 'C' and resid 572 through 580 Processing helix chain 'C' and resid 592 through 594 No H-bonds generated for 'chain 'C' and resid 592 through 594' Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.839A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 650 No H-bonds generated for 'chain 'C' and resid 647 through 650' Processing helix chain 'C' and resid 663 through 673 removed outlier: 3.771A pdb=" N LEU C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 668 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG C 672 " --> pdb=" O ALA C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 681 Processing helix chain 'C' and resid 693 through 702 Processing helix chain 'C' and resid 710 through 728 Processing helix chain 'C' and resid 739 through 746 removed outlier: 4.266A pdb=" N GLN C 743 " --> pdb=" O GLU C 740 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 746 " --> pdb=" O GLN C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 828 removed outlier: 3.816A pdb=" N MET C 826 " --> pdb=" O ARG C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 869 Proline residue: C 854 - end of helix removed outlier: 4.261A pdb=" N CYS C 858 " --> pdb=" O SER C 855 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 861 " --> pdb=" O CYS C 858 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET C 869 " --> pdb=" O SER C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 914 through 922 removed outlier: 4.605A pdb=" N LYS C 918 " --> pdb=" O GLU C 915 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE C 920 " --> pdb=" O LYS C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 928 No H-bonds generated for 'chain 'C' and resid 925 through 928' Processing helix chain 'C' and resid 939 through 945 Processing helix chain 'D' and resid 149 through 155 Processing helix chain 'D' and resid 175 through 180 removed outlier: 4.178A pdb=" N VAL D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 306 Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 328 through 337 Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 355 through 388 Processing helix chain 'D' and resid 392 through 403 Processing helix chain 'D' and resid 414 through 427 Processing helix chain 'D' and resid 432 through 447 Processing helix chain 'D' and resid 453 through 467 Processing helix chain 'D' and resid 480 through 488 Processing helix chain 'D' and resid 495 through 510 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 572 through 580 Processing helix chain 'D' and resid 592 through 594 No H-bonds generated for 'chain 'D' and resid 592 through 594' Processing helix chain 'D' and resid 603 through 611 removed outlier: 3.904A pdb=" N LEU D 608 " --> pdb=" O SER D 604 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 610 " --> pdb=" O ALA D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 650 No H-bonds generated for 'chain 'D' and resid 647 through 650' Processing helix chain 'D' and resid 663 through 673 removed outlier: 3.785A pdb=" N LEU D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG D 672 " --> pdb=" O ALA D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 682 Processing helix chain 'D' and resid 693 through 702 Processing helix chain 'D' and resid 710 through 728 Processing helix chain 'D' and resid 739 through 746 removed outlier: 3.885A pdb=" N GLN D 743 " --> pdb=" O PRO D 739 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP D 744 " --> pdb=" O GLU D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 808 through 828 removed outlier: 3.649A pdb=" N MET D 826 " --> pdb=" O ARG D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 869 Proline residue: D 854 - end of helix removed outlier: 4.165A pdb=" N CYS D 858 " --> pdb=" O SER D 855 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D 861 " --> pdb=" O CYS D 858 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET D 869 " --> pdb=" O SER D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 904 Processing helix chain 'D' and resid 914 through 922 removed outlier: 4.503A pdb=" N LYS D 918 " --> pdb=" O GLU D 915 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE D 920 " --> pdb=" O LYS D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 928 No H-bonds generated for 'chain 'D' and resid 925 through 928' Processing helix chain 'D' and resid 939 through 944 Processing helix chain 'E' and resid 150 through 155 Processing helix chain 'E' and resid 175 through 180 removed outlier: 4.103A pdb=" N VAL E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 306 removed outlier: 3.580A pdb=" N GLU E 295 " --> pdb=" O ALA E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 328 through 338 removed outlier: 3.678A pdb=" N LEU E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 351 Processing helix chain 'E' and resid 355 through 404 removed outlier: 3.740A pdb=" N LEU E 372 " --> pdb=" O LYS E 368 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS E 393 " --> pdb=" O GLN E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 427 Processing helix chain 'E' and resid 432 through 447 removed outlier: 3.522A pdb=" N GLY E 446 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU E 447 " --> pdb=" O SER E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 466 removed outlier: 3.656A pdb=" N VAL E 457 " --> pdb=" O SER E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 488 Processing helix chain 'E' and resid 495 through 511 removed outlier: 3.771A pdb=" N ARG E 511 " --> pdb=" O VAL E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 540 Processing helix chain 'E' and resid 555 through 559 Processing helix chain 'E' and resid 572 through 580 Processing helix chain 'E' and resid 592 through 594 No H-bonds generated for 'chain 'E' and resid 592 through 594' Processing helix chain 'E' and resid 603 through 611 removed outlier: 3.800A pdb=" N LEU E 608 " --> pdb=" O SER E 604 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU E 610 " --> pdb=" O ALA E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 618 Processing helix chain 'E' and resid 647 through 650 No H-bonds generated for 'chain 'E' and resid 647 through 650' Processing helix chain 'E' and resid 663 through 673 removed outlier: 3.715A pdb=" N LEU E 667 " --> pdb=" O ALA E 663 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG E 672 " --> pdb=" O ALA E 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 682 Processing helix chain 'E' and resid 693 through 702 Processing helix chain 'E' and resid 710 through 728 Processing helix chain 'E' and resid 742 through 746 removed outlier: 4.083A pdb=" N VAL E 746 " --> pdb=" O GLN E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 808 through 828 removed outlier: 3.747A pdb=" N MET E 826 " --> pdb=" O ARG E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 850 through 869 Proline residue: E 854 - end of helix removed outlier: 4.729A pdb=" N GLY E 857 " --> pdb=" O GLY E 853 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N CYS E 858 " --> pdb=" O PRO E 854 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N THR E 859 " --> pdb=" O SER E 855 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE E 860 " --> pdb=" O ALA E 856 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL E 861 " --> pdb=" O GLY E 857 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR E 862 " --> pdb=" O CYS E 858 " (cutoff:3.500A) Processing helix chain 'E' and resid 895 through 904 Processing helix chain 'E' and resid 914 through 922 removed outlier: 4.823A pdb=" N LYS E 918 " --> pdb=" O GLU E 915 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE E 920 " --> pdb=" O LYS E 917 " (cutoff:3.500A) Processing helix chain 'E' and resid 925 through 928 No H-bonds generated for 'chain 'E' and resid 925 through 928' Processing helix chain 'E' and resid 939 through 946 removed outlier: 3.781A pdb=" N ALA E 946 " --> pdb=" O PHE E 943 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 155 removed outlier: 3.665A pdb=" N LEU F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 Processing helix chain 'F' and resid 291 through 306 removed outlier: 3.520A pdb=" N GLU F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 328 through 338 removed outlier: 3.522A pdb=" N LEU F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 351 Processing helix chain 'F' and resid 355 through 388 Processing helix chain 'F' and resid 392 through 404 Processing helix chain 'F' and resid 414 through 425 removed outlier: 3.961A pdb=" N LYS F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE F 421 " --> pdb=" O ILE F 417 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 447 removed outlier: 3.729A pdb=" N GLY F 446 " --> pdb=" O LEU F 442 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU F 447 " --> pdb=" O SER F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 466 Processing helix chain 'F' and resid 480 through 488 Processing helix chain 'F' and resid 495 through 510 removed outlier: 3.545A pdb=" N LEU F 510 " --> pdb=" O ALA F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 540 Processing helix chain 'F' and resid 555 through 559 Processing helix chain 'F' and resid 572 through 580 Processing helix chain 'F' and resid 592 through 594 No H-bonds generated for 'chain 'F' and resid 592 through 594' Processing helix chain 'F' and resid 603 through 611 removed outlier: 3.665A pdb=" N LEU F 608 " --> pdb=" O SER F 604 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU F 609 " --> pdb=" O SER F 605 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 618 removed outlier: 3.507A pdb=" N ASN F 618 " --> pdb=" O GLN F 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 615 through 618' Processing helix chain 'F' and resid 647 through 650 No H-bonds generated for 'chain 'F' and resid 647 through 650' Processing helix chain 'F' and resid 663 through 673 removed outlier: 3.633A pdb=" N LEU F 667 " --> pdb=" O ALA F 663 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG F 672 " --> pdb=" O ALA F 668 " (cutoff:3.500A) Processing helix chain 'F' and resid 675 through 681 Processing helix chain 'F' and resid 686 through 688 No H-bonds generated for 'chain 'F' and resid 686 through 688' Processing helix chain 'F' and resid 693 through 702 Processing helix chain 'F' and resid 710 through 728 Processing helix chain 'F' and resid 739 through 746 removed outlier: 4.153A pdb=" N GLN F 743 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL F 746 " --> pdb=" O GLN F 743 " (cutoff:3.500A) Processing helix chain 'F' and resid 808 through 828 removed outlier: 3.825A pdb=" N MET F 826 " --> pdb=" O ARG F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 869 Proline residue: F 854 - end of helix removed outlier: 4.266A pdb=" N CYS F 858 " --> pdb=" O SER F 855 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL F 861 " --> pdb=" O CYS F 858 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET F 869 " --> pdb=" O SER F 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 895 through 904 Processing helix chain 'F' and resid 914 through 922 removed outlier: 4.285A pdb=" N LYS F 918 " --> pdb=" O GLU F 915 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE F 920 " --> pdb=" O LYS F 917 " (cutoff:3.500A) Processing helix chain 'F' and resid 925 through 928 No H-bonds generated for 'chain 'F' and resid 925 through 928' Processing helix chain 'F' and resid 939 through 945 Processing sheet with id= A, first strand: chain 'A' and resid 140 through 142 Processing sheet with id= B, first strand: chain 'A' and resid 164 through 166 Processing sheet with id= C, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.180A pdb=" N CYS A 637 " --> pdb=" O PHE A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 544 through 548 removed outlier: 6.708A pdb=" N LEU A 586 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE A 547 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU A 588 " --> pdb=" O PHE A 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 689 through 691 removed outlier: 7.124A pdb=" N VAL A 735 " --> pdb=" O LYS A 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 764 through 766 Processing sheet with id= G, first strand: chain 'A' and resid 910 through 913 removed outlier: 3.783A pdb=" N LEU A 912 " --> pdb=" O HIS A 934 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 140 through 142 Processing sheet with id= I, first strand: chain 'B' and resid 164 through 167 removed outlier: 3.750A pdb=" N VAL B 164 " --> pdb=" O ALA B 192 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.128A pdb=" N CYS B 637 " --> pdb=" O PHE B 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 544 through 548 removed outlier: 6.385A pdb=" N LEU B 586 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N PHE B 547 " --> pdb=" O LEU B 586 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU B 588 " --> pdb=" O PHE B 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 689 through 691 removed outlier: 6.922A pdb=" N VAL B 735 " --> pdb=" O LYS B 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 764 through 766 Processing sheet with id= N, first strand: chain 'B' and resid 910 through 913 removed outlier: 3.754A pdb=" N LEU B 912 " --> pdb=" O HIS B 934 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 140 through 142 Processing sheet with id= P, first strand: chain 'C' and resid 164 through 166 Processing sheet with id= Q, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.118A pdb=" N CYS C 637 " --> pdb=" O PHE C 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 544 through 548 removed outlier: 6.121A pdb=" N LEU C 586 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE C 547 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU C 588 " --> pdb=" O PHE C 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 764 through 766 Processing sheet with id= T, first strand: chain 'D' and resid 140 through 142 Processing sheet with id= U, first strand: chain 'D' and resid 163 through 166 Processing sheet with id= V, first strand: chain 'D' and resid 544 through 548 removed outlier: 7.082A pdb=" N LEU D 586 " --> pdb=" O PHE D 545 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N PHE D 547 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU D 588 " --> pdb=" O PHE D 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 764 through 766 Processing sheet with id= X, first strand: chain 'D' and resid 910 through 913 Processing sheet with id= Y, first strand: chain 'E' and resid 140 through 142 Processing sheet with id= Z, first strand: chain 'E' and resid 163 through 166 Processing sheet with id= AA, first strand: chain 'E' and resid 544 through 548 removed outlier: 6.485A pdb=" N LEU E 586 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N PHE E 547 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU E 588 " --> pdb=" O PHE E 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.657A pdb=" N VAL E 735 " --> pdb=" O LYS E 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 780 through 784 Processing sheet with id= AD, first strand: chain 'F' and resid 140 through 142 Processing sheet with id= AE, first strand: chain 'F' and resid 188 through 191 Processing sheet with id= AF, first strand: chain 'F' and resid 520 through 522 removed outlier: 6.094A pdb=" N CYS F 637 " --> pdb=" O PHE F 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.464A pdb=" N LEU F 586 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE F 547 " --> pdb=" O LEU F 586 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU F 588 " --> pdb=" O PHE F 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'F' and resid 689 through 691 removed outlier: 7.203A pdb=" N VAL F 735 " --> pdb=" O LYS F 690 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 764 through 769 1351 hydrogen bonds defined for protein. 3645 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: 24.39 Time building geometry restraints manager: 51.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 37673 1.02 - 1.22: 109 1.22 - 1.42: 14913 1.42 - 1.62: 22375 1.62 - 1.81: 283 Bond restraints: 75353 Sorted by residual: bond pdb=" CB MET F 879 " pdb=" CG MET F 879 " ideal model delta sigma weight residual 1.520 1.416 0.104 3.00e-02 1.11e+03 1.20e+01 bond pdb=" CA SER F 838 " pdb=" CB SER F 838 " ideal model delta sigma weight residual 1.534 1.475 0.059 1.78e-02 3.16e+03 1.08e+01 bond pdb=" C5 ADP A1001 " pdb=" C6 ADP A1001 " ideal model delta sigma weight residual 1.490 1.425 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" CG1 ILE F 900 " pdb=" CD1 ILE F 900 " ideal model delta sigma weight residual 1.513 1.387 0.126 3.90e-02 6.57e+02 1.05e+01 bond pdb=" CG GLU A 665 " pdb=" CD GLU A 665 " ideal model delta sigma weight residual 1.516 1.438 0.078 2.50e-02 1.60e+03 9.65e+00 ... (remaining 75348 not shown) Histogram of bond angle deviations from ideal: 93.91 - 102.60: 172 102.60 - 111.29: 84032 111.29 - 119.98: 30216 119.98 - 128.67: 22233 128.67 - 137.36: 306 Bond angle restraints: 136959 Sorted by residual: angle pdb=" N GLY E 601 " pdb=" CA GLY E 601 " pdb=" C GLY E 601 " ideal model delta sigma weight residual 113.18 98.68 14.50 2.37e+00 1.78e-01 3.74e+01 angle pdb=" N GLY D 601 " pdb=" CA GLY D 601 " pdb=" C GLY D 601 " ideal model delta sigma weight residual 113.18 100.00 13.18 2.37e+00 1.78e-01 3.09e+01 angle pdb=" N GLN D 515 " pdb=" CA GLN D 515 " pdb=" C GLN D 515 " ideal model delta sigma weight residual 109.23 100.62 8.61 1.55e+00 4.16e-01 3.09e+01 angle pdb=" CB MET E 435 " pdb=" CG MET E 435 " pdb=" SD MET E 435 " ideal model delta sigma weight residual 112.70 128.43 -15.73 3.00e+00 1.11e-01 2.75e+01 angle pdb=" N MET E 435 " pdb=" CA MET E 435 " pdb=" CB MET E 435 " ideal model delta sigma weight residual 109.94 117.38 -7.44 1.49e+00 4.50e-01 2.49e+01 ... (remaining 136954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.13: 29285 32.13 - 64.26: 515 64.26 - 96.39: 57 96.39 - 128.52: 1 128.52 - 160.65: 4 Dihedral angle restraints: 29862 sinusoidal: 14622 harmonic: 15240 Sorted by residual: dihedral pdb=" O1B ADP C1001 " pdb=" O3A ADP C1001 " pdb=" PB ADP C1001 " pdb=" PA ADP C1001 " ideal model delta sinusoidal sigma weight residual -60.00 100.65 -160.65 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O1B ADP D1001 " pdb=" O3A ADP D1001 " pdb=" PB ADP D1001 " pdb=" PA ADP D1001 " ideal model delta sinusoidal sigma weight residual 300.00 144.33 155.66 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O1B ADP B1001 " pdb=" O3A ADP B1001 " pdb=" PB ADP B1001 " pdb=" PA ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 80.89 -140.90 1 2.00e+01 2.50e-03 4.26e+01 ... (remaining 29859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4765 0.089 - 0.178: 979 0.178 - 0.267: 80 0.267 - 0.357: 7 0.357 - 0.446: 1 Chirality restraints: 5832 Sorted by residual: chirality pdb=" CB ILE B 532 " pdb=" CA ILE B 532 " pdb=" CG1 ILE B 532 " pdb=" CG2 ILE B 532 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CB ILE D 558 " pdb=" CA ILE D 558 " pdb=" CG1 ILE D 558 " pdb=" CG2 ILE D 558 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CB VAL A 802 " pdb=" CA VAL A 802 " pdb=" CG1 VAL A 802 " pdb=" CG2 VAL A 802 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 5829 not shown) Planarity restraints: 10974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 421 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C PHE E 421 " 0.071 2.00e-02 2.50e+03 pdb=" O PHE E 421 " -0.027 2.00e-02 2.50e+03 pdb=" N ARG E 422 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 615 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C GLN E 615 " -0.068 2.00e-02 2.50e+03 pdb=" O GLN E 615 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN E 616 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 464 " 0.025 2.00e-02 2.50e+03 1.93e-02 1.49e+01 pdb=" CG TRP D 464 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP D 464 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 464 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 464 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 464 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 464 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 464 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 464 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 464 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP D 464 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 TRP D 464 " 0.005 2.00e-02 2.50e+03 pdb=" HE3 TRP D 464 " -0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 464 " -0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 464 " 0.003 2.00e-02 2.50e+03 pdb=" HH2 TRP D 464 " 0.001 2.00e-02 2.50e+03 ... (remaining 10971 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 3239 2.17 - 2.77: 151299 2.77 - 3.38: 205238 3.38 - 3.99: 250602 3.99 - 4.60: 398127 Nonbonded interactions: 1008505 Sorted by model distance: nonbonded pdb=" O PHE F 619 " pdb=" H VAL F 628 " model vdw 1.556 1.850 nonbonded pdb=" O VAL F 166 " pdb=" H THR F 190 " model vdw 1.589 1.850 nonbonded pdb=" O LYS E 414 " pdb=" H GLU E 418 " model vdw 1.590 1.850 nonbonded pdb=" O ALA B 856 " pdb=" HG1 THR B 859 " model vdw 1.596 1.850 nonbonded pdb=" O ASP B 852 " pdb=" HG SER B 855 " model vdw 1.597 1.850 ... (remaining 1008500 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' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'B' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'C' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = (chain 'D' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) selection = chain 'E' selection = (chain 'F' and (resid 123 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ or name H \ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name H \ D3 or name HE2 or name HE3 or name HZ2 or name HZ3)) or resid 415 through 948 or \ resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 162 5.16 5 C 23442 2.51 5 N 6426 2.21 5 O 6972 1.98 5 H 37715 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.820 Extract box with map and model: 16.740 Check model and map are aligned: 0.830 Convert atoms to be neutral: 0.500 Process input model: 173.840 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.013 0.136 37638 Z= 0.865 Angle : 1.336 15.727 50844 Z= 0.737 Chirality : 0.069 0.446 5832 Planarity : 0.008 0.056 6522 Dihedral : 13.053 160.653 14460 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.30 % Favored : 90.67 % Rotamer Outliers : 0.02 % 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: -2.64 (0.12), residues: 4632 helix: -2.04 (0.09), residues: 1956 sheet: -3.77 (0.18), residues: 585 loop : -0.54 (0.15), residues: 2091 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 4.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.8921 time to fit residues: 237.8701 Evaluate side-chains 134 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 4.432 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 2.9990 chunk 350 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 119 optimal weight: 0.1980 chunk 236 optimal weight: 30.0000 chunk 187 optimal weight: 0.9980 chunk 362 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 220 optimal weight: 0.6980 chunk 269 optimal weight: 4.9990 chunk 419 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 37638 Z= 0.178 Angle : 0.661 8.145 50844 Z= 0.339 Chirality : 0.041 0.160 5832 Planarity : 0.004 0.044 6522 Dihedral : 7.677 167.490 5124 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 0.15 % 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: -1.81 (0.12), residues: 4632 helix: -0.74 (0.11), residues: 1952 sheet: -3.46 (0.18), residues: 586 loop : -0.75 (0.15), residues: 2094 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 4.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 148 average time/residue: 0.8986 time to fit residues: 227.8110 Evaluate side-chains 139 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 5.263 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.8102 time to fit residues: 15.2934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 30.0000 chunk 130 optimal weight: 4.9990 chunk 349 optimal weight: 8.9990 chunk 285 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 420 optimal weight: 1.9990 chunk 454 optimal weight: 0.8980 chunk 374 optimal weight: 2.9990 chunk 416 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 337 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 37638 Z= 0.253 Angle : 0.599 8.321 50844 Z= 0.303 Chirality : 0.039 0.145 5832 Planarity : 0.004 0.043 6522 Dihedral : 7.250 163.717 5124 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.10 % 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: -1.43 (0.12), residues: 4632 helix: -0.14 (0.11), residues: 1975 sheet: -3.26 (0.19), residues: 582 loop : -0.88 (0.14), residues: 2075 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 4.523 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 outliers start: 4 outliers final: 2 residues processed: 137 average time/residue: 0.9244 time to fit residues: 215.8550 Evaluate side-chains 135 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 4.431 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.7875 time to fit residues: 8.5713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 8.9990 chunk 316 optimal weight: 9.9990 chunk 218 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 282 optimal weight: 20.0000 chunk 421 optimal weight: 2.9990 chunk 446 optimal weight: 0.1980 chunk 220 optimal weight: 3.9990 chunk 399 optimal weight: 30.0000 chunk 120 optimal weight: 4.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 477 ASN ** F 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 37638 Z= 0.259 Angle : 0.584 8.754 50844 Z= 0.294 Chirality : 0.038 0.145 5832 Planarity : 0.004 0.044 6522 Dihedral : 7.087 166.414 5124 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.15 % 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: -1.28 (0.12), residues: 4632 helix: 0.13 (0.12), residues: 1976 sheet: -3.20 (0.19), residues: 594 loop : -0.95 (0.14), residues: 2062 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 135 time to evaluate : 4.497 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 outliers start: 6 outliers final: 5 residues processed: 138 average time/residue: 0.9096 time to fit residues: 214.0576 Evaluate side-chains 136 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 4.522 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.7285 time to fit residues: 12.5355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 3.9990 chunk 253 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 332 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 381 optimal weight: 0.7980 chunk 308 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 228 optimal weight: 0.0000 chunk 400 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 overall best weight: 2.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 37638 Z= 0.277 Angle : 0.579 8.994 50844 Z= 0.291 Chirality : 0.038 0.143 5832 Planarity : 0.003 0.044 6522 Dihedral : 6.844 166.793 5124 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 0.25 % 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: -1.22 (0.12), residues: 4632 helix: 0.24 (0.12), residues: 1984 sheet: -3.14 (0.20), residues: 591 loop : -1.00 (0.14), residues: 2057 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 4.553 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 outliers start: 10 outliers final: 6 residues processed: 140 average time/residue: 0.9323 time to fit residues: 221.3424 Evaluate side-chains 137 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 4.606 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.7682 time to fit residues: 14.3037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 1.9990 chunk 402 optimal weight: 50.0000 chunk 88 optimal weight: 30.0000 chunk 262 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 447 optimal weight: 2.9990 chunk 371 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 234 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 37638 Z= 0.177 Angle : 0.539 8.177 50844 Z= 0.265 Chirality : 0.038 0.149 5832 Planarity : 0.003 0.037 6522 Dihedral : 6.613 166.883 5124 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.17 % 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: -0.96 (0.13), residues: 4632 helix: 0.49 (0.12), residues: 1985 sheet: -2.97 (0.20), residues: 591 loop : -0.92 (0.14), residues: 2056 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 4.659 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 outliers start: 7 outliers final: 3 residues processed: 140 average time/residue: 0.8990 time to fit residues: 215.2200 Evaluate side-chains 133 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 4.481 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.6742 time to fit residues: 9.5996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 5.9990 chunk 50 optimal weight: 0.0970 chunk 254 optimal weight: 3.9990 chunk 326 optimal weight: 30.0000 chunk 252 optimal weight: 20.0000 chunk 376 optimal weight: 3.9990 chunk 249 optimal weight: 10.0000 chunk 445 optimal weight: 0.7980 chunk 278 optimal weight: 0.3980 chunk 271 optimal weight: 6.9990 chunk 205 optimal weight: 0.7980 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 37638 Z= 0.159 Angle : 0.525 8.716 50844 Z= 0.256 Chirality : 0.037 0.149 5832 Planarity : 0.003 0.034 6522 Dihedral : 6.401 164.254 5124 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.20 % 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: -0.75 (0.13), residues: 4632 helix: 0.69 (0.12), residues: 1976 sheet: -2.79 (0.21), residues: 577 loop : -0.88 (0.14), residues: 2079 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 4.543 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 outliers start: 8 outliers final: 2 residues processed: 143 average time/residue: 0.9138 time to fit residues: 223.6050 Evaluate side-chains 134 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 4.554 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.7279 time to fit residues: 8.8393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 chunk 265 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 87 optimal weight: 30.0000 chunk 86 optimal weight: 9.9990 chunk 283 optimal weight: 0.8980 chunk 303 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 350 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 37638 Z= 0.198 Angle : 0.530 8.562 50844 Z= 0.260 Chirality : 0.037 0.147 5832 Planarity : 0.003 0.033 6522 Dihedral : 6.284 160.899 5124 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 0.02 % 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: -0.74 (0.13), residues: 4632 helix: 0.75 (0.12), residues: 1978 sheet: -2.82 (0.21), residues: 586 loop : -0.90 (0.14), residues: 2068 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 4.692 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 outliers start: 1 outliers final: 1 residues processed: 134 average time/residue: 0.9313 time to fit residues: 213.2124 Evaluate side-chains 134 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 4.533 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.8011 time to fit residues: 7.4356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 10.0000 chunk 426 optimal weight: 1.9990 chunk 389 optimal weight: 6.9990 chunk 414 optimal weight: 0.8980 chunk 249 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 325 optimal weight: 40.0000 chunk 127 optimal weight: 2.9990 chunk 374 optimal weight: 3.9990 chunk 392 optimal weight: 10.0000 chunk 413 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 37638 Z= 0.294 Angle : 0.574 9.153 50844 Z= 0.287 Chirality : 0.038 0.146 5832 Planarity : 0.003 0.035 6522 Dihedral : 6.273 154.253 5124 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 0.20 % 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: -0.92 (0.13), residues: 4632 helix: 0.61 (0.12), residues: 1981 sheet: -3.00 (0.20), residues: 598 loop : -0.97 (0.14), residues: 2053 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 4.778 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 outliers start: 8 outliers final: 2 residues processed: 139 average time/residue: 0.8821 time to fit residues: 209.8021 Evaluate side-chains 134 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 4.546 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.7056 time to fit residues: 8.5604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 10.0000 chunk 438 optimal weight: 2.9990 chunk 267 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 305 optimal weight: 4.9990 chunk 460 optimal weight: 2.9990 chunk 423 optimal weight: 8.9990 chunk 366 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 283 optimal weight: 0.7980 chunk 224 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 37638 Z= 0.184 Angle : 0.534 9.662 50844 Z= 0.261 Chirality : 0.038 0.150 5832 Planarity : 0.003 0.037 6522 Dihedral : 6.152 150.166 5124 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.07 % 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: -0.72 (0.13), residues: 4632 helix: 0.78 (0.12), residues: 1981 sheet: -2.80 (0.21), residues: 586 loop : -0.91 (0.14), residues: 2065 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 414 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 4.498 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 outliers start: 3 outliers final: 2 residues processed: 138 average time/residue: 0.9174 time to fit residues: 217.3502 Evaluate side-chains 136 residues out of total 4050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 4.495 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.8148 time to fit residues: 8.9238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 8.9990 chunk 390 optimal weight: 6.9990 chunk 112 optimal weight: 0.1980 chunk 337 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 367 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 376 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.156582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.111711 restraints weight = 433774.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.110631 restraints weight = 251788.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.110373 restraints weight = 190389.381| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.048 37638 Z= 0.139 Angle : 0.527 16.520 50844 Z= 0.252 Chirality : 0.037 0.223 5832 Planarity : 0.003 0.038 6522 Dihedral : 5.965 147.626 5124 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.05 % 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: -0.51 (0.13), residues: 4632 helix: 0.96 (0.12), residues: 1979 sheet: -2.67 (0.21), residues: 578 loop : -0.82 (0.14), residues: 2075 =============================================================================== Job complete usr+sys time: 7732.06 seconds wall clock time: 137 minutes 29.88 seconds (8249.88 seconds total)