Starting phenix.real_space_refine on Wed Mar 20 16:52:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7okn_12962/03_2024/7okn_12962_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7okn_12962/03_2024/7okn_12962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7okn_12962/03_2024/7okn_12962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7okn_12962/03_2024/7okn_12962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7okn_12962/03_2024/7okn_12962_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7okn_12962/03_2024/7okn_12962_neut.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 187 5.16 5 C 17442 2.51 5 N 4896 2.21 5 O 5542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C GLU 400": "OE1" <-> "OE2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E GLU 326": "OE1" <-> "OE2" Residue "E GLU 371": "OE1" <-> "OE2" Residue "E GLU 400": "OE1" <-> "OE2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G GLU 255": "OE1" <-> "OE2" Residue "G ARG 270": "NH1" <-> "NH2" Residue "G GLU 326": "OE1" <-> "OE2" Residue "G GLU 371": "OE1" <-> "OE2" Residue "G GLU 400": "OE1" <-> "OE2" Residue "I GLU 207": "OE1" <-> "OE2" Residue "I GLU 255": "OE1" <-> "OE2" Residue "I ARG 270": "NH1" <-> "NH2" Residue "I GLU 326": "OE1" <-> "OE2" Residue "I GLU 371": "OE1" <-> "OE2" Residue "I GLU 400": "OE1" <-> "OE2" Residue "K GLU 207": "OE1" <-> "OE2" Residue "K GLU 255": "OE1" <-> "OE2" Residue "K ARG 270": "NH1" <-> "NH2" Residue "K GLU 326": "OE1" <-> "OE2" Residue "K GLU 371": "OE1" <-> "OE2" Residue "K GLU 400": "OE1" <-> "OE2" Residue "M GLU 207": "OE1" <-> "OE2" Residue "M GLU 255": "OE1" <-> "OE2" Residue "M ARG 270": "NH1" <-> "NH2" Residue "M GLU 326": "OE1" <-> "OE2" Residue "M GLU 371": "OE1" <-> "OE2" Residue "M GLU 400": "OE1" <-> "OE2" Residue "O GLU 207": "OE1" <-> "OE2" Residue "O GLU 255": "OE1" <-> "OE2" Residue "O ARG 270": "NH1" <-> "NH2" Residue "O GLU 326": "OE1" <-> "OE2" Residue "O GLU 371": "OE1" <-> "OE2" Residue "O GLU 400": "OE1" <-> "OE2" Residue "Q GLU 207": "OE1" <-> "OE2" Residue "Q GLU 255": "OE1" <-> "OE2" Residue "Q ARG 270": "NH1" <-> "NH2" Residue "Q GLU 326": "OE1" <-> "OE2" Residue "Q GLU 371": "OE1" <-> "OE2" Residue "Q GLU 400": "OE1" <-> "OE2" Residue "S GLU 207": "OE1" <-> "OE2" Residue "S GLU 255": "OE1" <-> "OE2" Residue "S ARG 270": "NH1" <-> "NH2" Residue "S GLU 326": "OE1" <-> "OE2" Residue "S GLU 371": "OE1" <-> "OE2" Residue "S GLU 400": "OE1" <-> "OE2" Residue "U GLU 207": "OE1" <-> "OE2" Residue "U GLU 255": "OE1" <-> "OE2" Residue "U ARG 270": "NH1" <-> "NH2" Residue "U GLU 326": "OE1" <-> "OE2" Residue "U GLU 371": "OE1" <-> "OE2" Residue "U GLU 400": "OE1" <-> "OE2" Residue "W GLU 207": "OE1" <-> "OE2" Residue "W GLU 255": "OE1" <-> "OE2" Residue "W ARG 270": "NH1" <-> "NH2" Residue "W GLU 326": "OE1" <-> "OE2" Residue "W GLU 371": "OE1" <-> "OE2" Residue "W GLU 400": "OE1" <-> "OE2" Residue "Y GLU 207": "OE1" <-> "OE2" Residue "Y GLU 255": "OE1" <-> "OE2" Residue "Y ARG 270": "NH1" <-> "NH2" Residue "Y GLU 326": "OE1" <-> "OE2" Residue "Y GLU 371": "OE1" <-> "OE2" Residue "Y GLU 400": "OE1" <-> "OE2" Residue "a GLU 207": "OE1" <-> "OE2" Residue "a GLU 255": "OE1" <-> "OE2" Residue "a ARG 270": "NH1" <-> "NH2" Residue "a GLU 326": "OE1" <-> "OE2" Residue "a GLU 371": "OE1" <-> "OE2" Residue "a GLU 400": "OE1" <-> "OE2" Residue "c GLU 207": "OE1" <-> "OE2" Residue "c GLU 255": "OE1" <-> "OE2" Residue "c ARG 270": "NH1" <-> "NH2" Residue "c GLU 326": "OE1" <-> "OE2" Residue "c GLU 371": "OE1" <-> "OE2" Residue "c GLU 400": "OE1" <-> "OE2" Residue "e GLU 207": "OE1" <-> "OE2" Residue "e GLU 255": "OE1" <-> "OE2" Residue "e ARG 270": "NH1" <-> "NH2" Residue "e GLU 326": "OE1" <-> "OE2" Residue "e GLU 371": "OE1" <-> "OE2" Residue "e GLU 400": "OE1" <-> "OE2" Residue "g GLU 207": "OE1" <-> "OE2" Residue "g GLU 255": "OE1" <-> "OE2" Residue "g ARG 270": "NH1" <-> "NH2" Residue "g GLU 326": "OE1" <-> "OE2" Residue "g GLU 371": "OE1" <-> "OE2" Residue "g GLU 400": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28067 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "B" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "C" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "D" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "E" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "F" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "G" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "H" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "I" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "J" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "K" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "L" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "M" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "N" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "O" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "P" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "Q" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "R" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "S" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "T" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "U" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "V" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "W" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "X" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "Y" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "Z" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "a" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "b" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "c" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "d" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "e" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "f" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "g" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1386 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "h" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 265 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Time building chain proxies: 13.65, per 1000 atoms: 0.49 Number of scatterers: 28067 At special positions: 0 Unit cell: (184.8, 184.8, 97.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 187 16.00 O 5542 8.00 N 4896 7.00 C 17442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 250 " - pdb=" SG CYS A 274 " distance=2.02 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS F 35 " distance=1.36 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS D 27 " distance=2.03 Simple disulfide: pdb=" SG CYS C 250 " - pdb=" SG CYS C 274 " distance=2.02 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS H 27 " distance=1.86 Simple disulfide: pdb=" SG CYS E 250 " - pdb=" SG CYS E 274 " distance=2.02 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS J 35 " distance=1.86 Simple disulfide: pdb=" SG CYS G 250 " - pdb=" SG CYS G 274 " distance=2.02 Simple disulfide: pdb=" SG CYS H 35 " - pdb=" SG CYS L 27 " distance=1.86 Simple disulfide: pdb=" SG CYS I 250 " - pdb=" SG CYS I 274 " distance=2.02 Simple disulfide: pdb=" SG CYS J 27 " - pdb=" SG CYS h 35 " distance=1.86 Simple disulfide: pdb=" SG CYS K 250 " - pdb=" SG CYS K 274 " distance=2.02 Simple disulfide: pdb=" SG CYS L 35 " - pdb=" SG CYS N 27 " distance=1.86 Simple disulfide: pdb=" SG CYS M 250 " - pdb=" SG CYS M 274 " distance=2.02 Simple disulfide: pdb=" SG CYS N 35 " - pdb=" SG CYS P 27 " distance=1.86 Simple disulfide: pdb=" SG CYS O 250 " - pdb=" SG CYS O 274 " distance=2.02 Simple disulfide: pdb=" SG CYS P 35 " - pdb=" SG CYS R 27 " distance=1.86 Simple disulfide: pdb=" SG CYS Q 250 " - pdb=" SG CYS Q 274 " distance=2.02 Simple disulfide: pdb=" SG CYS R 35 " - pdb=" SG CYS T 27 " distance=1.86 Simple disulfide: pdb=" SG CYS S 250 " - pdb=" SG CYS S 274 " distance=2.02 Simple disulfide: pdb=" SG CYS T 35 " - pdb=" SG CYS V 27 " distance=1.86 Simple disulfide: pdb=" SG CYS U 250 " - pdb=" SG CYS U 274 " distance=2.02 Simple disulfide: pdb=" SG CYS V 35 " - pdb=" SG CYS X 27 " distance=1.86 Simple disulfide: pdb=" SG CYS W 250 " - pdb=" SG CYS W 274 " distance=2.02 Simple disulfide: pdb=" SG CYS X 35 " - pdb=" SG CYS Z 27 " distance=1.86 Simple disulfide: pdb=" SG CYS Y 250 " - pdb=" SG CYS Y 274 " distance=2.02 Simple disulfide: pdb=" SG CYS Z 35 " - pdb=" SG CYS b 27 " distance=1.86 Simple disulfide: pdb=" SG CYS a 250 " - pdb=" SG CYS a 274 " distance=2.02 Simple disulfide: pdb=" SG CYS b 35 " - pdb=" SG CYS d 27 " distance=1.86 Simple disulfide: pdb=" SG CYS c 250 " - pdb=" SG CYS c 274 " distance=2.02 Simple disulfide: pdb=" SG CYS d 35 " - pdb=" SG CYS f 27 " distance=1.86 Simple disulfide: pdb=" SG CYS e 250 " - pdb=" SG CYS e 274 " distance=2.02 Simple disulfide: pdb=" SG CYS f 35 " - pdb=" SG CYS h 27 " distance=1.86 Simple disulfide: pdb=" SG CYS g 250 " - pdb=" SG CYS g 274 " distance=2.02 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: 10.46 Conformation dependent library (CDL) restraints added in 5.1 seconds 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6698 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 0 sheets defined 26.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 306 through 325 Processing helix chain 'A' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 325 Processing helix chain 'C' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR C 365 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN C 372 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 53 Processing helix chain 'E' and resid 306 through 325 Processing helix chain 'E' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP E 364 " --> pdb=" O LYS E 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR E 365 " --> pdb=" O THR E 361 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN E 372 " --> pdb=" O LYS E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 407 removed outlier: 3.537A pdb=" N ALA E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 53 Processing helix chain 'G' and resid 306 through 325 Processing helix chain 'G' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP G 364 " --> pdb=" O LYS G 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR G 365 " --> pdb=" O THR G 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN G 372 " --> pdb=" O LYS G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA G 407 " --> pdb=" O ALA G 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 53 Processing helix chain 'I' and resid 306 through 325 Processing helix chain 'I' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP I 364 " --> pdb=" O LYS I 360 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR I 365 " --> pdb=" O THR I 361 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN I 372 " --> pdb=" O LYS I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 407 removed outlier: 3.537A pdb=" N ALA I 407 " --> pdb=" O ALA I 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 53 Processing helix chain 'K' and resid 306 through 325 Processing helix chain 'K' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP K 364 " --> pdb=" O LYS K 360 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR K 365 " --> pdb=" O THR K 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN K 372 " --> pdb=" O LYS K 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA K 407 " --> pdb=" O ALA K 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 53 Processing helix chain 'M' and resid 306 through 325 Processing helix chain 'M' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP M 364 " --> pdb=" O LYS M 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR M 365 " --> pdb=" O THR M 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN M 372 " --> pdb=" O LYS M 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 398 through 407 removed outlier: 3.539A pdb=" N ALA M 407 " --> pdb=" O ALA M 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 53 Processing helix chain 'O' and resid 306 through 325 Processing helix chain 'O' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP O 364 " --> pdb=" O LYS O 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR O 365 " --> pdb=" O THR O 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN O 372 " --> pdb=" O LYS O 368 " (cutoff:3.500A) Processing helix chain 'O' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA O 407 " --> pdb=" O ALA O 403 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 53 Processing helix chain 'Q' and resid 306 through 325 Processing helix chain 'Q' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP Q 364 " --> pdb=" O LYS Q 360 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR Q 365 " --> pdb=" O THR Q 361 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN Q 372 " --> pdb=" O LYS Q 368 " (cutoff:3.500A) Processing helix chain 'Q' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA Q 407 " --> pdb=" O ALA Q 403 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 53 Processing helix chain 'S' and resid 306 through 325 Processing helix chain 'S' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP S 364 " --> pdb=" O LYS S 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR S 365 " --> pdb=" O THR S 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN S 372 " --> pdb=" O LYS S 368 " (cutoff:3.500A) Processing helix chain 'S' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA S 407 " --> pdb=" O ALA S 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 53 Processing helix chain 'U' and resid 306 through 325 Processing helix chain 'U' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP U 364 " --> pdb=" O LYS U 360 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR U 365 " --> pdb=" O THR U 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN U 372 " --> pdb=" O LYS U 368 " (cutoff:3.500A) Processing helix chain 'U' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA U 407 " --> pdb=" O ALA U 403 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 53 Processing helix chain 'W' and resid 306 through 325 Processing helix chain 'W' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP W 364 " --> pdb=" O LYS W 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR W 365 " --> pdb=" O THR W 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN W 372 " --> pdb=" O LYS W 368 " (cutoff:3.500A) Processing helix chain 'W' and resid 398 through 407 removed outlier: 3.539A pdb=" N ALA W 407 " --> pdb=" O ALA W 403 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 53 Processing helix chain 'Y' and resid 306 through 325 Processing helix chain 'Y' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP Y 364 " --> pdb=" O LYS Y 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR Y 365 " --> pdb=" O THR Y 361 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN Y 372 " --> pdb=" O LYS Y 368 " (cutoff:3.500A) Processing helix chain 'Y' and resid 398 through 407 removed outlier: 3.537A pdb=" N ALA Y 407 " --> pdb=" O ALA Y 403 " (cutoff:3.500A) Processing helix chain 'X' and resid 38 through 53 Processing helix chain 'Z' and resid 38 through 53 Processing helix chain 'a' and resid 306 through 325 Processing helix chain 'a' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP a 364 " --> pdb=" O LYS a 360 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR a 365 " --> pdb=" O THR a 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN a 372 " --> pdb=" O LYS a 368 " (cutoff:3.500A) Processing helix chain 'a' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA a 407 " --> pdb=" O ALA a 403 " (cutoff:3.500A) Processing helix chain 'c' and resid 306 through 325 Processing helix chain 'c' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP c 364 " --> pdb=" O LYS c 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR c 365 " --> pdb=" O THR c 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN c 372 " --> pdb=" O LYS c 368 " (cutoff:3.500A) Processing helix chain 'c' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA c 407 " --> pdb=" O ALA c 403 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 53 Processing helix chain 'e' and resid 306 through 325 Processing helix chain 'e' and resid 360 through 372 removed outlier: 4.506A pdb=" N ASP e 364 " --> pdb=" O LYS e 360 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR e 365 " --> pdb=" O THR e 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN e 372 " --> pdb=" O LYS e 368 " (cutoff:3.500A) Processing helix chain 'e' and resid 398 through 407 removed outlier: 3.538A pdb=" N ALA e 407 " --> pdb=" O ALA e 403 " (cutoff:3.500A) Processing helix chain 'd' and resid 38 through 53 Processing helix chain 'g' and resid 306 through 325 Processing helix chain 'g' and resid 360 through 372 removed outlier: 4.507A pdb=" N ASP g 364 " --> pdb=" O LYS g 360 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TYR g 365 " --> pdb=" O THR g 361 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN g 372 " --> pdb=" O LYS g 368 " (cutoff:3.500A) Processing helix chain 'g' and resid 398 through 407 removed outlier: 3.537A pdb=" N ALA g 407 " --> pdb=" O ALA g 403 " (cutoff:3.500A) Processing helix chain 'f' and resid 38 through 53 Processing helix chain 'h' and resid 38 through 53 663 hydrogen bonds defined for protein. 1989 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: 6.03 Time building geometry restraints manager: 11.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9571 1.34 - 1.46: 6083 1.46 - 1.58: 12498 1.58 - 1.71: 0 1.71 - 1.83: 289 Bond restraints: 28441 Sorted by residual: bond pdb=" CB ARG I 232 " pdb=" CG ARG I 232 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.23e+00 bond pdb=" CB ARG S 232 " pdb=" CG ARG S 232 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.17e+00 bond pdb=" CB ARG g 232 " pdb=" CG ARG g 232 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.16e+00 bond pdb=" CB ARG Y 232 " pdb=" CG ARG Y 232 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" CB ARG c 232 " pdb=" CG ARG c 232 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.11e+00 ... (remaining 28436 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.09: 675 107.09 - 113.81: 15890 113.81 - 120.54: 10616 120.54 - 127.27: 10865 127.27 - 134.00: 187 Bond angle restraints: 38233 Sorted by residual: angle pdb=" CB ARG T 46 " pdb=" CG ARG T 46 " pdb=" CD ARG T 46 " ideal model delta sigma weight residual 111.30 102.72 8.58 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CB ARG J 46 " pdb=" CG ARG J 46 " pdb=" CD ARG J 46 " ideal model delta sigma weight residual 111.30 102.73 8.57 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CB ARG F 46 " pdb=" CG ARG F 46 " pdb=" CD ARG F 46 " ideal model delta sigma weight residual 111.30 102.73 8.57 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CB ARG h 46 " pdb=" CG ARG h 46 " pdb=" CD ARG h 46 " ideal model delta sigma weight residual 111.30 102.74 8.56 2.30e+00 1.89e-01 1.38e+01 angle pdb=" CB ARG N 46 " pdb=" CG ARG N 46 " pdb=" CD ARG N 46 " ideal model delta sigma weight residual 111.30 102.76 8.54 2.30e+00 1.89e-01 1.38e+01 ... (remaining 38228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 14783 17.67 - 35.34: 1741 35.34 - 53.02: 459 53.02 - 70.69: 153 70.69 - 88.36: 85 Dihedral angle restraints: 17221 sinusoidal: 6749 harmonic: 10472 Sorted by residual: dihedral pdb=" CB CYS B 27 " pdb=" SG CYS B 27 " pdb=" SG CYS F 35 " pdb=" CB CYS F 35 " ideal model delta sinusoidal sigma weight residual -86.00 -144.57 58.57 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS B 35 " pdb=" SG CYS B 35 " pdb=" SG CYS D 27 " pdb=" CB CYS D 27 " ideal model delta sinusoidal sigma weight residual -86.00 -141.61 55.61 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS J 27 " pdb=" SG CYS J 27 " pdb=" SG CYS h 35 " pdb=" CB CYS h 35 " ideal model delta sinusoidal sigma weight residual -86.00 -141.02 55.02 1 1.00e+01 1.00e-02 4.10e+01 ... (remaining 17218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2300 0.029 - 0.058: 1236 0.058 - 0.087: 423 0.087 - 0.116: 265 0.116 - 0.145: 43 Chirality restraints: 4267 Sorted by residual: chirality pdb=" CA PRO M 240 " pdb=" N PRO M 240 " pdb=" C PRO M 240 " pdb=" CB PRO M 240 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA PRO E 240 " pdb=" N PRO E 240 " pdb=" C PRO E 240 " pdb=" CB PRO E 240 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA PRO S 240 " pdb=" N PRO S 240 " pdb=" C PRO S 240 " pdb=" CB PRO S 240 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 4264 not shown) Planarity restraints: 5015 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 199 " 0.011 2.00e-02 2.50e+03 8.52e-03 1.81e+00 pdb=" CG TRP I 199 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP I 199 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP I 199 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP I 199 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 199 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 199 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 199 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 199 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP I 199 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 199 " -0.011 2.00e-02 2.50e+03 8.51e-03 1.81e+00 pdb=" CG TRP Q 199 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 199 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 199 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 199 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 199 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 199 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 199 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 199 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 199 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 199 " -0.011 2.00e-02 2.50e+03 8.49e-03 1.80e+00 pdb=" CG TRP K 199 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP K 199 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP K 199 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP K 199 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP K 199 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 199 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 199 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 199 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP K 199 " -0.001 2.00e-02 2.50e+03 ... (remaining 5012 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 124 2.50 - 3.10: 20789 3.10 - 3.70: 40469 3.70 - 4.30: 55956 4.30 - 4.90: 99825 Nonbonded interactions: 217163 Sorted by model distance: nonbonded pdb=" OG SER B 23 " pdb=" O MET E 303 " model vdw 1.898 2.440 nonbonded pdb=" O CYS D 18 " pdb=" OH TYR E 366 " model vdw 1.968 2.440 nonbonded pdb=" O CYS B 18 " pdb=" OH TYR I 366 " model vdw 2.104 2.440 nonbonded pdb=" OD1 ASN A 241 " pdb=" N LYS E 275 " model vdw 2.149 2.520 nonbonded pdb=" OH TYR C 366 " pdb=" O CYS L 18 " model vdw 2.220 2.440 ... (remaining 217158 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 24.850 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 64.890 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 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 : 0.006 0.045 28441 Z= 0.411 Angle : 0.923 8.582 38233 Z= 0.514 Chirality : 0.045 0.145 4267 Planarity : 0.004 0.030 5015 Dihedral : 17.962 88.360 10421 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 1.03 % Allowed : 36.73 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.13), residues: 3655 helix: 1.14 (0.17), residues: 1020 sheet: -2.70 (0.16), residues: 901 loop : -3.39 (0.12), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K 199 HIS 0.003 0.001 HIS Q 288 PHE 0.012 0.001 PHE e 251 TYR 0.011 0.002 TYR E 373 ARG 0.021 0.003 ARG c 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 981 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 279 ASP cc_start: 0.7649 (p0) cc_final: 0.7360 (p0) REVERT: A 303 MET cc_start: 0.8385 (tpt) cc_final: 0.8004 (tpt) REVERT: A 364 ASP cc_start: 0.8682 (m-30) cc_final: 0.8460 (p0) REVERT: B 43 GLN cc_start: 0.7627 (mt0) cc_final: 0.7216 (mt0) REVERT: C 244 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7742 (mt-10) REVERT: C 303 MET cc_start: 0.8386 (tpt) cc_final: 0.7971 (tpt) REVERT: G 292 MET cc_start: 0.8240 (tpt) cc_final: 0.8018 (tpp) REVERT: H 21 VAL cc_start: 0.8157 (m) cc_final: 0.7898 (p) REVERT: I 242 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6474 (m-30) REVERT: I 255 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7840 (mt-10) REVERT: I 303 MET cc_start: 0.8076 (tpt) cc_final: 0.7781 (tpt) REVERT: J 21 VAL cc_start: 0.7692 (m) cc_final: 0.7466 (p) REVERT: J 38 MET cc_start: 0.7455 (mtt) cc_final: 0.7152 (mtt) REVERT: J 40 LYS cc_start: 0.7943 (mmtt) cc_final: 0.7736 (mmtt) REVERT: J 48 LYS cc_start: 0.8408 (tppt) cc_final: 0.8127 (tppt) REVERT: K 207 GLU cc_start: 0.7496 (tt0) cc_final: 0.7190 (tm-30) REVERT: K 298 LYS cc_start: 0.8111 (ptmt) cc_final: 0.7890 (tttp) REVERT: L 21 VAL cc_start: 0.8040 (m) cc_final: 0.7818 (p) REVERT: M 272 ILE cc_start: 0.8179 (tt) cc_final: 0.7934 (tp) REVERT: M 284 LYS cc_start: 0.6787 (mmmt) cc_final: 0.6585 (mmtm) REVERT: N 21 VAL cc_start: 0.7945 (m) cc_final: 0.7707 (p) REVERT: O 226 THR cc_start: 0.6933 (p) cc_final: 0.6660 (p) REVERT: O 272 ILE cc_start: 0.8314 (tt) cc_final: 0.8013 (tp) REVERT: O 284 LYS cc_start: 0.6752 (mmmt) cc_final: 0.6444 (mmtm) REVERT: O 298 LYS cc_start: 0.7431 (ptmt) cc_final: 0.7075 (tttp) REVERT: P 21 VAL cc_start: 0.7697 (m) cc_final: 0.7336 (p) REVERT: Q 237 VAL cc_start: 0.5383 (t) cc_final: 0.4787 (m) REVERT: Q 272 ILE cc_start: 0.8284 (tt) cc_final: 0.8010 (tp) REVERT: Q 298 LYS cc_start: 0.7060 (ptmt) cc_final: 0.6484 (tttp) REVERT: Q 386 THR cc_start: 0.6863 (p) cc_final: 0.6338 (p) REVERT: S 237 VAL cc_start: 0.5713 (t) cc_final: 0.5303 (m) REVERT: S 272 ILE cc_start: 0.7752 (tt) cc_final: 0.7478 (tp) REVERT: S 298 LYS cc_start: 0.6579 (ptmt) cc_final: 0.5906 (tttp) REVERT: U 237 VAL cc_start: 0.5380 (t) cc_final: 0.4868 (m) REVERT: U 319 ASP cc_start: 0.7021 (m-30) cc_final: 0.6687 (m-30) REVERT: U 377 ILE cc_start: 0.8418 (mt) cc_final: 0.8174 (mp) REVERT: V 43 GLN cc_start: 0.6059 (mt0) cc_final: 0.5800 (mt0) REVERT: W 207 GLU cc_start: 0.7041 (tt0) cc_final: 0.6708 (tm-30) REVERT: W 224 LYS cc_start: 0.8172 (mppt) cc_final: 0.7633 (mtmm) REVERT: W 377 ILE cc_start: 0.8218 (mt) cc_final: 0.7971 (mp) REVERT: W 379 ILE cc_start: 0.7817 (mm) cc_final: 0.7549 (mm) REVERT: Y 272 ILE cc_start: 0.6594 (tt) cc_final: 0.6385 (tp) REVERT: a 272 ILE cc_start: 0.6700 (tt) cc_final: 0.6500 (tp) REVERT: c 268 ARG cc_start: 0.7149 (ttm170) cc_final: 0.6745 (ttp80) REVERT: c 279 ASP cc_start: 0.7155 (p0) cc_final: 0.6896 (t0) REVERT: e 255 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6120 (mt-10) REVERT: e 318 LEU cc_start: 0.8061 (tp) cc_final: 0.7851 (tt) REVERT: e 396 GLU cc_start: 0.7033 (pt0) cc_final: 0.6515 (pp20) REVERT: g 284 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8455 (mmtp) REVERT: g 303 MET cc_start: 0.8170 (tpt) cc_final: 0.7781 (tpt) REVERT: h 38 MET cc_start: 0.7267 (mtt) cc_final: 0.7045 (mtt) outliers start: 30 outliers final: 14 residues processed: 1007 average time/residue: 0.4511 time to fit residues: 672.9520 Evaluate side-chains 642 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 627 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain G residue 276 LEU Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain I residue 242 ASP Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain S residue 283 GLN Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain W residue 283 GLN Chi-restraints excluded: chain e residue 283 GLN Chi-restraints excluded: chain g residue 276 LEU Chi-restraints excluded: chain g residue 283 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 2.9990 chunk 270 optimal weight: 7.9990 chunk 150 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 324 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN F 43 GLN G 390 GLN J 52 GLN K 283 GLN K 390 GLN M 283 GLN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 230 GLN U 295 ASN W 230 GLN W 307 GLN W 390 GLN ** a 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 43 GLN c 390 GLN d 43 GLN g 295 ASN h 52 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28441 Z= 0.225 Angle : 0.645 9.318 38233 Z= 0.329 Chirality : 0.044 0.172 4267 Planarity : 0.004 0.032 5015 Dihedral : 6.311 75.266 3985 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 9.06 % Allowed : 28.86 % Favored : 62.07 % 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: -1.99 (0.14), residues: 3655 helix: 2.07 (0.16), residues: 986 sheet: -2.08 (0.16), residues: 1054 loop : -3.04 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 257 HIS 0.005 0.001 HIS E 374 PHE 0.023 0.002 PHE W 205 TYR 0.013 0.001 TYR g 373 ARG 0.006 0.001 ARG K 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 678 time to evaluate : 3.309 Fit side-chains revert: symmetry clash REVERT: A 236 LYS cc_start: 0.8267 (mtmp) cc_final: 0.7923 (mtmt) REVERT: A 303 MET cc_start: 0.8591 (tpt) cc_final: 0.8347 (tpt) REVERT: C 199 TRP cc_start: 0.7467 (OUTLIER) cc_final: 0.6624 (t60) REVERT: C 236 LYS cc_start: 0.8164 (mtmp) cc_final: 0.7861 (mtmt) REVERT: C 279 ASP cc_start: 0.7226 (p0) cc_final: 0.6955 (p0) REVERT: E 199 TRP cc_start: 0.7729 (OUTLIER) cc_final: 0.7367 (t-100) REVERT: E 280 ASP cc_start: 0.7982 (m-30) cc_final: 0.7724 (m-30) REVERT: E 364 ASP cc_start: 0.7992 (p0) cc_final: 0.7370 (t0) REVERT: E 368 LYS cc_start: 0.8318 (ttmm) cc_final: 0.8082 (ttmm) REVERT: G 270 ARG cc_start: 0.7829 (mmm-85) cc_final: 0.7604 (mmm-85) REVERT: H 21 VAL cc_start: 0.7979 (OUTLIER) cc_final: 0.7681 (p) REVERT: H 38 MET cc_start: 0.6770 (mtt) cc_final: 0.6537 (mtt) REVERT: I 199 TRP cc_start: 0.7762 (OUTLIER) cc_final: 0.7303 (t60) REVERT: I 364 ASP cc_start: 0.8485 (t0) cc_final: 0.8240 (p0) REVERT: J 21 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7465 (p) REVERT: J 47 ASP cc_start: 0.8893 (m-30) cc_final: 0.8654 (t0) REVERT: K 292 MET cc_start: 0.8305 (tpp) cc_final: 0.8062 (mtp) REVERT: K 303 MET cc_start: 0.8465 (tpt) cc_final: 0.8162 (tpt) REVERT: K 383 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.7324 (m-40) REVERT: L 21 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7668 (p) REVERT: M 270 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6289 (ttp80) REVERT: M 292 MET cc_start: 0.8247 (mtp) cc_final: 0.7792 (mtp) REVERT: M 399 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7499 (mp0) REVERT: N 21 VAL cc_start: 0.7868 (OUTLIER) cc_final: 0.7597 (p) REVERT: O 268 ARG cc_start: 0.7757 (ptm160) cc_final: 0.7486 (ttp80) REVERT: O 270 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6591 (mtp85) REVERT: O 284 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7637 (mppt) REVERT: O 298 LYS cc_start: 0.7750 (ptmt) cc_final: 0.7533 (tttp) REVERT: O 300 GLU cc_start: 0.7464 (pm20) cc_final: 0.6595 (pt0) REVERT: P 21 VAL cc_start: 0.7944 (OUTLIER) cc_final: 0.7562 (p) REVERT: Q 199 TRP cc_start: 0.6994 (OUTLIER) cc_final: 0.5668 (t60) REVERT: Q 210 VAL cc_start: 0.8143 (t) cc_final: 0.7932 (p) REVERT: Q 268 ARG cc_start: 0.7511 (ptt180) cc_final: 0.7275 (ttp80) REVERT: Q 284 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7193 (mmtm) REVERT: Q 292 MET cc_start: 0.8329 (mtp) cc_final: 0.8093 (mtp) REVERT: Q 300 GLU cc_start: 0.7538 (pm20) cc_final: 0.6823 (pt0) REVERT: Q 311 TYR cc_start: 0.6973 (m-10) cc_final: 0.6508 (m-10) REVERT: Q 368 LYS cc_start: 0.7739 (ptpp) cc_final: 0.7361 (ptpp) REVERT: S 199 TRP cc_start: 0.6960 (OUTLIER) cc_final: 0.5693 (t60) REVERT: S 268 ARG cc_start: 0.7510 (ptt180) cc_final: 0.7125 (ttp80) REVERT: S 284 LYS cc_start: 0.7804 (mmmt) cc_final: 0.7073 (mmtm) REVERT: S 294 LYS cc_start: 0.6805 (mtmt) cc_final: 0.6548 (mtpt) REVERT: T 22 LYS cc_start: 0.8079 (pttt) cc_final: 0.7527 (pttt) REVERT: T 43 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.6992 (mp10) REVERT: U 268 ARG cc_start: 0.7700 (ptt180) cc_final: 0.7149 (ttp80) REVERT: V 21 VAL cc_start: 0.7966 (OUTLIER) cc_final: 0.7665 (p) REVERT: V 38 MET cc_start: 0.5822 (mtt) cc_final: 0.5607 (mtp) REVERT: W 239 MET cc_start: 0.7229 (mmt) cc_final: 0.6913 (mmt) REVERT: W 268 ARG cc_start: 0.7833 (ptt180) cc_final: 0.7500 (ttp80) REVERT: W 319 ASP cc_start: 0.6964 (m-30) cc_final: 0.6514 (m-30) REVERT: W 368 LYS cc_start: 0.7679 (ptpp) cc_final: 0.7159 (ptpp) REVERT: W 396 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7089 (pp20) REVERT: Y 199 TRP cc_start: 0.7685 (OUTLIER) cc_final: 0.7212 (t-100) REVERT: Y 201 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8165 (m) REVERT: Y 294 LYS cc_start: 0.6185 (mtpt) cc_final: 0.5874 (mtpp) REVERT: Y 319 ASP cc_start: 0.6793 (m-30) cc_final: 0.6421 (m-30) REVERT: Y 368 LYS cc_start: 0.7992 (ptpp) cc_final: 0.7486 (ptpp) REVERT: Z 36 MET cc_start: 0.6624 (mtp) cc_final: 0.6382 (mtp) REVERT: Z 43 GLN cc_start: 0.6854 (mt0) cc_final: 0.6422 (mt0) REVERT: a 239 MET cc_start: 0.7554 (mmm) cc_final: 0.7254 (mmt) REVERT: a 242 ASP cc_start: 0.7700 (t70) cc_final: 0.7361 (m-30) REVERT: a 268 ARG cc_start: 0.7769 (ptp90) cc_final: 0.7513 (ttp80) REVERT: a 368 LYS cc_start: 0.8291 (ptpt) cc_final: 0.7927 (ptpp) REVERT: b 47 ASP cc_start: 0.8326 (m-30) cc_final: 0.7918 (m-30) REVERT: c 199 TRP cc_start: 0.7324 (OUTLIER) cc_final: 0.6903 (t60) REVERT: c 255 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8095 (mt-10) REVERT: c 294 LYS cc_start: 0.6665 (mtpt) cc_final: 0.6450 (mtpt) REVERT: c 311 TYR cc_start: 0.7672 (m-10) cc_final: 0.7373 (m-10) REVERT: c 368 LYS cc_start: 0.8177 (ptpp) cc_final: 0.7691 (ptpp) REVERT: d 36 MET cc_start: 0.6685 (mtp) cc_final: 0.6296 (ptp) REVERT: d 48 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7588 (mttm) REVERT: e 255 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8051 (mt-10) REVERT: e 268 ARG cc_start: 0.7847 (ttm170) cc_final: 0.7541 (ttp80) REVERT: e 270 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7497 (mtp85) REVERT: e 294 LYS cc_start: 0.6902 (mtpt) cc_final: 0.6584 (mtpp) REVERT: e 303 MET cc_start: 0.8543 (tpt) cc_final: 0.8180 (tpt) REVERT: f 47 ASP cc_start: 0.8738 (t70) cc_final: 0.8407 (t0) REVERT: g 284 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8568 (mmtp) REVERT: g 292 MET cc_start: 0.7932 (tpp) cc_final: 0.7711 (ttt) REVERT: g 303 MET cc_start: 0.8324 (tpt) cc_final: 0.8070 (tpt) REVERT: h 47 ASP cc_start: 0.8974 (t70) cc_final: 0.8761 (t0) outliers start: 265 outliers final: 122 residues processed: 885 average time/residue: 0.4652 time to fit residues: 607.7563 Evaluate side-chains 694 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 552 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 383 ASN Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain I residue 199 TRP Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain K residue 223 ASP Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain K residue 242 ASP Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 383 ASN Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 270 ARG Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain M residue 383 ASN Chi-restraints excluded: chain M residue 388 VAL Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 270 ARG Chi-restraints excluded: chain O residue 271 SER Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 383 ASN Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 211 VAL Chi-restraints excluded: chain Q residue 223 ASP Chi-restraints excluded: chain Q residue 242 ASP Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 383 ASN Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 211 VAL Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 261 SER Chi-restraints excluded: chain S residue 283 GLN Chi-restraints excluded: chain S residue 383 ASN Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain S residue 397 THR Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain U residue 223 ASP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 242 ASP Chi-restraints excluded: chain U residue 276 LEU Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 295 ASN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 223 ASP Chi-restraints excluded: chain W residue 283 GLN Chi-restraints excluded: chain W residue 297 ILE Chi-restraints excluded: chain W residue 309 LEU Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain W residue 396 GLU Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Y residue 201 SER Chi-restraints excluded: chain Y residue 221 THR Chi-restraints excluded: chain Y residue 242 ASP Chi-restraints excluded: chain Y residue 309 LEU Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 32 SER Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 32 SER Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 199 TRP Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain d residue 48 LYS Chi-restraints excluded: chain e residue 237 VAL Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 283 GLN Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 223 ASP Chi-restraints excluded: chain g residue 237 VAL Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 283 GLN Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain h residue 31 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 269 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 89 optimal weight: 0.0370 chunk 324 optimal weight: 0.6980 chunk 350 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 chunk 322 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 260 optimal weight: 0.5980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 52 GLN J 52 GLN ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 225 ASN g 295 ASN h 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.6324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28441 Z= 0.169 Angle : 0.522 7.510 38233 Z= 0.268 Chirality : 0.042 0.161 4267 Planarity : 0.003 0.042 5015 Dihedral : 5.943 76.021 3977 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 7.05 % Allowed : 29.51 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3655 helix: 2.54 (0.17), residues: 1003 sheet: -1.85 (0.17), residues: 1003 loop : -3.04 (0.13), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 199 HIS 0.003 0.001 HIS A 288 PHE 0.015 0.001 PHE W 205 TYR 0.016 0.001 TYR Y 373 ARG 0.009 0.001 ARG c 402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 597 time to evaluate : 3.372 Fit side-chains REVERT: A 303 MET cc_start: 0.8700 (tpt) cc_final: 0.8490 (tpt) REVERT: B 21 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7456 (p) REVERT: C 199 TRP cc_start: 0.7492 (OUTLIER) cc_final: 0.7178 (t-100) REVERT: D 38 MET cc_start: 0.6827 (mtt) cc_final: 0.6443 (mtt) REVERT: E 199 TRP cc_start: 0.7575 (OUTLIER) cc_final: 0.7181 (t-100) REVERT: E 368 LYS cc_start: 0.8573 (ttmm) cc_final: 0.8341 (ttmm) REVERT: H 38 MET cc_start: 0.6828 (mtt) cc_final: 0.6522 (mtt) REVERT: I 199 TRP cc_start: 0.7533 (OUTLIER) cc_final: 0.7265 (t-100) REVERT: I 229 MET cc_start: 0.8313 (mtt) cc_final: 0.8110 (mtp) REVERT: I 303 MET cc_start: 0.8624 (tpt) cc_final: 0.8286 (mmm) REVERT: K 298 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7977 (tttp) REVERT: K 303 MET cc_start: 0.8549 (tpt) cc_final: 0.8243 (tpt) REVERT: M 239 MET cc_start: 0.7348 (mmm) cc_final: 0.7131 (mmt) REVERT: M 292 MET cc_start: 0.8331 (mtp) cc_final: 0.7835 (mtp) REVERT: O 268 ARG cc_start: 0.7604 (ptm160) cc_final: 0.7361 (ttp80) REVERT: O 298 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7714 (tttp) REVERT: O 300 GLU cc_start: 0.7470 (pm20) cc_final: 0.7243 (mp0) REVERT: O 303 MET cc_start: 0.8734 (tpt) cc_final: 0.8532 (tpt) REVERT: O 408 ARG cc_start: 0.6775 (tpm170) cc_final: 0.6461 (tpm170) REVERT: P 43 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7832 (mp10) REVERT: Q 236 LYS cc_start: 0.7331 (mtmp) cc_final: 0.7042 (mtmt) REVERT: Q 268 ARG cc_start: 0.7263 (ptt180) cc_final: 0.7009 (ttp80) REVERT: Q 292 MET cc_start: 0.8262 (mtp) cc_final: 0.8052 (mtp) REVERT: Q 300 GLU cc_start: 0.7312 (pm20) cc_final: 0.6980 (mp0) REVERT: Q 311 TYR cc_start: 0.7007 (m-10) cc_final: 0.6697 (m-10) REVERT: Q 368 LYS cc_start: 0.7984 (ptpp) cc_final: 0.7485 (ptpp) REVERT: S 282 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: S 311 TYR cc_start: 0.7224 (m-10) cc_final: 0.6936 (m-10) REVERT: S 368 LYS cc_start: 0.7876 (ptpp) cc_final: 0.7469 (ptpp) REVERT: T 43 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7092 (mm-40) REVERT: T 47 ASP cc_start: 0.8873 (m-30) cc_final: 0.8592 (m-30) REVERT: U 199 TRP cc_start: 0.7463 (OUTLIER) cc_final: 0.6339 (t60) REVERT: U 243 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.7012 (pm20) REVERT: U 268 ARG cc_start: 0.7332 (ptt180) cc_final: 0.6888 (ttp80) REVERT: U 284 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7912 (mmtm) REVERT: U 319 ASP cc_start: 0.7483 (m-30) cc_final: 0.6916 (m-30) REVERT: U 368 LYS cc_start: 0.8338 (ptpp) cc_final: 0.7871 (ptpp) REVERT: V 21 VAL cc_start: 0.7981 (m) cc_final: 0.7665 (p) REVERT: W 199 TRP cc_start: 0.7630 (OUTLIER) cc_final: 0.6515 (t60) REVERT: W 268 ARG cc_start: 0.7338 (ptt180) cc_final: 0.6864 (ttp80) REVERT: W 368 LYS cc_start: 0.7913 (ptpp) cc_final: 0.7507 (ptpp) REVERT: Y 199 TRP cc_start: 0.7673 (OUTLIER) cc_final: 0.7229 (t-100) REVERT: Y 294 LYS cc_start: 0.6644 (mtpt) cc_final: 0.6228 (mtpp) REVERT: a 239 MET cc_start: 0.7505 (mmm) cc_final: 0.7153 (mmt) REVERT: a 268 ARG cc_start: 0.7490 (ptp90) cc_final: 0.7224 (ttp80) REVERT: a 282 ASP cc_start: 0.8220 (m-30) cc_final: 0.7389 (m-30) REVERT: c 199 TRP cc_start: 0.7542 (OUTLIER) cc_final: 0.6768 (t60) REVERT: c 255 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7727 (mt-10) REVERT: c 298 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7288 (tttp) REVERT: c 368 LYS cc_start: 0.8272 (ptpp) cc_final: 0.7817 (ptpp) REVERT: d 36 MET cc_start: 0.7834 (mtp) cc_final: 0.7199 (ptp) REVERT: e 268 ARG cc_start: 0.7606 (ttm170) cc_final: 0.7377 (ttp80) REVERT: f 36 MET cc_start: 0.7532 (mtp) cc_final: 0.7272 (ptp) REVERT: f 47 ASP cc_start: 0.8869 (t70) cc_final: 0.8545 (t0) REVERT: g 279 ASP cc_start: 0.7763 (p0) cc_final: 0.7542 (p0) REVERT: g 284 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8674 (mmtp) REVERT: h 47 ASP cc_start: 0.9115 (t70) cc_final: 0.8735 (t0) outliers start: 206 outliers final: 129 residues processed: 759 average time/residue: 0.4981 time to fit residues: 563.4433 Evaluate side-chains 673 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 529 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 280 ASP Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain I residue 199 TRP Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain K residue 223 ASP Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 280 ASP Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 242 ASP Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 297 ILE Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain M residue 383 ASN Chi-restraints excluded: chain M residue 388 VAL Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 280 ASP Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 298 LYS Chi-restraints excluded: chain O residue 383 ASN Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 42 ASN Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 271 SER Chi-restraints excluded: chain Q residue 280 ASP Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 261 SER Chi-restraints excluded: chain S residue 282 ASP Chi-restraints excluded: chain S residue 283 GLN Chi-restraints excluded: chain S residue 295 ASN Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain U residue 199 TRP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 243 GLU Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 295 ASN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 383 ASN Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 261 SER Chi-restraints excluded: chain W residue 283 GLN Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Y residue 221 THR Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 237 VAL Chi-restraints excluded: chain Y residue 271 SER Chi-restraints excluded: chain Y residue 276 LEU Chi-restraints excluded: chain Y residue 298 LYS Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 237 VAL Chi-restraints excluded: chain a residue 271 SER Chi-restraints excluded: chain a residue 276 LEU Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 199 TRP Chi-restraints excluded: chain c residue 209 ILE Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 237 VAL Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 308 ILE Chi-restraints excluded: chain c residue 318 LEU Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain e residue 242 ASP Chi-restraints excluded: chain e residue 283 GLN Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain g residue 223 ASP Chi-restraints excluded: chain g residue 225 ASN Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 276 LEU Chi-restraints excluded: chain g residue 283 GLN Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain h residue 31 THR Chi-restraints excluded: chain h residue 37 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 325 optimal weight: 0.3980 chunk 345 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 308 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 52 GLN ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 390 GLN V 42 ASN W 307 GLN Y 288 HIS a 288 HIS c 394 GLN e 394 GLN f 52 GLN g 390 GLN h 52 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.7754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28441 Z= 0.352 Angle : 0.625 7.803 38233 Z= 0.317 Chirality : 0.045 0.184 4267 Planarity : 0.004 0.052 5015 Dihedral : 6.321 63.404 3977 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 8.76 % Allowed : 28.45 % Favored : 62.79 % 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: -1.67 (0.14), residues: 3655 helix: 2.53 (0.17), residues: 1020 sheet: -1.86 (0.16), residues: 1054 loop : -3.15 (0.13), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 199 HIS 0.003 0.001 HIS W 374 PHE 0.012 0.002 PHE e 251 TYR 0.018 0.002 TYR Y 373 ARG 0.012 0.001 ARG e 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 602 time to evaluate : 3.226 Fit side-chains REVERT: A 242 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: A 282 ASP cc_start: 0.8293 (m-30) cc_final: 0.7628 (m-30) REVERT: A 303 MET cc_start: 0.8721 (tpt) cc_final: 0.8474 (tpt) REVERT: B 51 LYS cc_start: 0.8843 (mmpt) cc_final: 0.8593 (tmmt) REVERT: C 199 TRP cc_start: 0.7909 (OUTLIER) cc_final: 0.6681 (t60) REVERT: C 282 ASP cc_start: 0.8025 (m-30) cc_final: 0.7382 (m-30) REVERT: C 387 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8104 (tp) REVERT: E 199 TRP cc_start: 0.7985 (OUTLIER) cc_final: 0.7019 (t60) REVERT: E 298 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7670 (tttp) REVERT: E 303 MET cc_start: 0.8615 (tpt) cc_final: 0.8188 (tpt) REVERT: E 387 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8166 (tp) REVERT: G 199 TRP cc_start: 0.7943 (OUTLIER) cc_final: 0.6705 (t60) REVERT: G 282 ASP cc_start: 0.8014 (m-30) cc_final: 0.7351 (m-30) REVERT: H 38 MET cc_start: 0.7017 (mtt) cc_final: 0.6798 (mtt) REVERT: I 199 TRP cc_start: 0.7934 (OUTLIER) cc_final: 0.7147 (t60) REVERT: I 298 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7420 (ptmt) REVERT: K 199 TRP cc_start: 0.7766 (OUTLIER) cc_final: 0.6163 (t60) REVERT: K 298 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7688 (tttp) REVERT: K 303 MET cc_start: 0.8667 (tpt) cc_final: 0.8007 (tpt) REVERT: M 292 MET cc_start: 0.8430 (mtp) cc_final: 0.7905 (mtp) REVERT: N 21 VAL cc_start: 0.7633 (OUTLIER) cc_final: 0.7322 (p) REVERT: O 199 TRP cc_start: 0.7939 (OUTLIER) cc_final: 0.6776 (t60) REVERT: O 268 ARG cc_start: 0.7778 (ptm160) cc_final: 0.7566 (ttp80) REVERT: O 408 ARG cc_start: 0.6844 (tpm170) cc_final: 0.6545 (tpm170) REVERT: Q 199 TRP cc_start: 0.7825 (OUTLIER) cc_final: 0.6627 (t60) REVERT: Q 268 ARG cc_start: 0.7562 (ptt180) cc_final: 0.7204 (ttp80) REVERT: Q 300 GLU cc_start: 0.7671 (pm20) cc_final: 0.7442 (mp0) REVERT: Q 379 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7715 (mp) REVERT: R 43 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7450 (mm-40) REVERT: S 199 TRP cc_start: 0.7773 (OUTLIER) cc_final: 0.6946 (t60) REVERT: S 282 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7788 (m-30) REVERT: S 303 MET cc_start: 0.8822 (tpt) cc_final: 0.8259 (tpt) REVERT: S 311 TYR cc_start: 0.7413 (m-10) cc_final: 0.7182 (m-10) REVERT: T 43 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7654 (mm-40) REVERT: T 47 ASP cc_start: 0.8846 (m-30) cc_final: 0.8517 (m-30) REVERT: U 199 TRP cc_start: 0.7673 (OUTLIER) cc_final: 0.6748 (t60) REVERT: U 311 TYR cc_start: 0.7316 (m-10) cc_final: 0.7104 (m-10) REVERT: W 199 TRP cc_start: 0.7796 (OUTLIER) cc_final: 0.6974 (t60) REVERT: W 268 ARG cc_start: 0.7393 (ptt180) cc_final: 0.7096 (ttp80) REVERT: W 284 LYS cc_start: 0.8810 (mmtm) cc_final: 0.8495 (mmtm) REVERT: W 368 LYS cc_start: 0.8019 (ptpp) cc_final: 0.7644 (ptpp) REVERT: X 43 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: Y 199 TRP cc_start: 0.7565 (OUTLIER) cc_final: 0.6703 (t60) REVERT: Y 284 LYS cc_start: 0.8935 (mmtp) cc_final: 0.8663 (mmtp) REVERT: a 279 ASP cc_start: 0.6489 (t0) cc_final: 0.6071 (t0) REVERT: a 280 ASP cc_start: 0.7507 (m-30) cc_final: 0.6606 (p0) REVERT: b 23 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8466 (t) REVERT: c 199 TRP cc_start: 0.7996 (OUTLIER) cc_final: 0.7105 (t60) REVERT: c 231 LEU cc_start: 0.8307 (pp) cc_final: 0.8079 (pp) REVERT: c 268 ARG cc_start: 0.7474 (ttp80) cc_final: 0.7237 (ttp80) REVERT: c 283 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6533 (mp10) REVERT: c 298 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7791 (tttp) REVERT: e 270 ARG cc_start: 0.7891 (mtp85) cc_final: 0.7541 (mtp85) REVERT: f 51 LYS cc_start: 0.9036 (tppt) cc_final: 0.8435 (tmmt) REVERT: g 279 ASP cc_start: 0.7745 (p0) cc_final: 0.7541 (p0) REVERT: g 292 MET cc_start: 0.8347 (ttm) cc_final: 0.8095 (ttt) REVERT: h 21 VAL cc_start: 0.7757 (OUTLIER) cc_final: 0.7365 (p) REVERT: h 47 ASP cc_start: 0.9099 (t70) cc_final: 0.8855 (t0) REVERT: h 51 LYS cc_start: 0.9122 (tppt) cc_final: 0.8501 (tmmt) outliers start: 256 outliers final: 163 residues processed: 786 average time/residue: 0.4749 time to fit residues: 544.3674 Evaluate side-chains 740 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 549 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 383 ASN Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain G residue 199 TRP Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 242 ASP Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 273 SER Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain I residue 199 TRP Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 199 TRP Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 223 ASP Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 280 ASP Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain M residue 388 VAL Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain O residue 199 TRP Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 280 ASP Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 298 LYS Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 223 ASP Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 280 ASP Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 379 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain Q residue 408 ARG Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 242 ASP Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 261 SER Chi-restraints excluded: chain S residue 282 ASP Chi-restraints excluded: chain S residue 283 GLN Chi-restraints excluded: chain S residue 295 ASN Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 43 GLN Chi-restraints excluded: chain U residue 199 TRP Chi-restraints excluded: chain U residue 223 ASP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 276 LEU Chi-restraints excluded: chain U residue 282 ASP Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 223 ASP Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 261 SER Chi-restraints excluded: chain W residue 276 LEU Chi-restraints excluded: chain W residue 283 GLN Chi-restraints excluded: chain W residue 298 LYS Chi-restraints excluded: chain W residue 361 THR Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 43 GLN Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 231 LEU Chi-restraints excluded: chain Y residue 237 VAL Chi-restraints excluded: chain Y residue 242 ASP Chi-restraints excluded: chain Y residue 261 SER Chi-restraints excluded: chain Y residue 276 LEU Chi-restraints excluded: chain Y residue 297 ILE Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 237 VAL Chi-restraints excluded: chain a residue 261 SER Chi-restraints excluded: chain a residue 276 LEU Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 36 MET Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 199 TRP Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 237 VAL Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 302 VAL Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain e residue 196 ARG Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 283 GLN Chi-restraints excluded: chain e residue 292 MET Chi-restraints excluded: chain e residue 297 ILE Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 223 ASP Chi-restraints excluded: chain g residue 225 ASN Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 276 LEU Chi-restraints excluded: chain g residue 280 ASP Chi-restraints excluded: chain g residue 283 GLN Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain h residue 21 VAL Chi-restraints excluded: chain h residue 31 THR Chi-restraints excluded: chain h residue 37 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 294 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 309 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 390 GLN J 52 GLN ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 372 GLN ** M 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 52 GLN Z 52 GLN f 52 GLN h 52 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.8025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 28441 Z= 0.243 Angle : 0.554 7.773 38233 Z= 0.280 Chirality : 0.043 0.194 4267 Planarity : 0.003 0.050 5015 Dihedral : 6.093 61.846 3977 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 8.65 % Allowed : 29.41 % Favored : 61.94 % 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: -1.50 (0.14), residues: 3655 helix: 2.68 (0.17), residues: 1020 sheet: -1.74 (0.17), residues: 1054 loop : -3.07 (0.13), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 199 HIS 0.003 0.001 HIS Y 374 PHE 0.008 0.001 PHE a 205 TYR 0.015 0.001 TYR M 373 ARG 0.011 0.001 ARG e 402 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 552 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 ASP cc_start: 0.8201 (m-30) cc_final: 0.7536 (m-30) REVERT: A 303 MET cc_start: 0.8765 (tpt) cc_final: 0.8356 (tpt) REVERT: B 21 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7417 (p) REVERT: B 51 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8573 (tmmt) REVERT: C 199 TRP cc_start: 0.7730 (OUTLIER) cc_final: 0.6540 (t60) REVERT: E 199 TRP cc_start: 0.7903 (OUTLIER) cc_final: 0.7026 (t60) REVERT: E 298 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7640 (tttp) REVERT: G 199 TRP cc_start: 0.7877 (OUTLIER) cc_final: 0.6369 (t60) REVERT: H 38 MET cc_start: 0.6988 (mtt) cc_final: 0.6768 (mtt) REVERT: I 298 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7251 (ptmt) REVERT: K 298 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7684 (tttp) REVERT: K 303 MET cc_start: 0.8641 (tpt) cc_final: 0.8163 (tpt) REVERT: M 292 MET cc_start: 0.8351 (mtp) cc_final: 0.7809 (mtp) REVERT: N 21 VAL cc_start: 0.7614 (OUTLIER) cc_final: 0.7294 (p) REVERT: O 199 TRP cc_start: 0.7890 (OUTLIER) cc_final: 0.6806 (t60) REVERT: O 266 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7885 (mp) REVERT: O 268 ARG cc_start: 0.7865 (ptm160) cc_final: 0.7377 (ptt180) REVERT: O 408 ARG cc_start: 0.6840 (tpm170) cc_final: 0.6599 (tpm170) REVERT: Q 268 ARG cc_start: 0.7512 (ptt180) cc_final: 0.7123 (ttp80) REVERT: Q 379 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7816 (mp) REVERT: R 47 ASP cc_start: 0.8704 (m-30) cc_final: 0.8346 (m-30) REVERT: S 199 TRP cc_start: 0.7680 (OUTLIER) cc_final: 0.6831 (t60) REVERT: S 282 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: S 303 MET cc_start: 0.8816 (tpt) cc_final: 0.8400 (tpt) REVERT: T 47 ASP cc_start: 0.8804 (m-30) cc_final: 0.8404 (t70) REVERT: U 199 TRP cc_start: 0.7738 (OUTLIER) cc_final: 0.6649 (t60) REVERT: U 298 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7552 (tttp) REVERT: W 199 TRP cc_start: 0.7810 (OUTLIER) cc_final: 0.6759 (t60) REVERT: W 268 ARG cc_start: 0.7397 (ptt180) cc_final: 0.7096 (ttp80) REVERT: W 284 LYS cc_start: 0.8795 (mmtm) cc_final: 0.8485 (mmtm) REVERT: X 43 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7330 (mp10) REVERT: X 47 ASP cc_start: 0.8737 (m-30) cc_final: 0.8499 (m-30) REVERT: Y 199 TRP cc_start: 0.7508 (OUTLIER) cc_final: 0.6437 (t60) REVERT: Y 283 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.6542 (mp10) REVERT: Z 51 LYS cc_start: 0.8711 (mptt) cc_final: 0.8285 (tmmt) REVERT: a 279 ASP cc_start: 0.6506 (t0) cc_final: 0.6126 (t0) REVERT: a 280 ASP cc_start: 0.7304 (m-30) cc_final: 0.6795 (p0) REVERT: b 51 LYS cc_start: 0.8789 (mptt) cc_final: 0.8448 (tmmt) REVERT: c 199 TRP cc_start: 0.7944 (OUTLIER) cc_final: 0.6981 (t60) REVERT: c 283 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6370 (mp10) REVERT: c 298 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7740 (tttp) REVERT: d 51 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8333 (tmmt) REVERT: e 270 ARG cc_start: 0.7978 (mtp85) cc_final: 0.7676 (mtp85) REVERT: f 51 LYS cc_start: 0.9006 (tppt) cc_final: 0.8461 (tmmt) REVERT: g 292 MET cc_start: 0.8447 (ttm) cc_final: 0.8044 (ttt) REVERT: h 21 VAL cc_start: 0.7753 (OUTLIER) cc_final: 0.7334 (p) REVERT: h 47 ASP cc_start: 0.9107 (t70) cc_final: 0.8863 (t0) REVERT: h 48 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7887 (ttmt) REVERT: h 51 LYS cc_start: 0.9110 (tppt) cc_final: 0.8517 (tmmt) outliers start: 253 outliers final: 176 residues processed: 733 average time/residue: 0.4753 time to fit residues: 509.1623 Evaluate side-chains 746 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 546 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain G residue 199 TRP Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 273 SER Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain I residue 199 TRP Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 223 ASP Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 242 ASP Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain M residue 387 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain O residue 199 TRP Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 237 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 266 ILE Chi-restraints excluded: chain O residue 280 ASP Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 292 MET Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 298 LYS Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 223 ASP Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 280 ASP Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 379 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 242 ASP Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 261 SER Chi-restraints excluded: chain S residue 282 ASP Chi-restraints excluded: chain S residue 283 GLN Chi-restraints excluded: chain S residue 292 MET Chi-restraints excluded: chain S residue 295 ASN Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain U residue 199 TRP Chi-restraints excluded: chain U residue 223 ASP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 242 ASP Chi-restraints excluded: chain U residue 276 LEU Chi-restraints excluded: chain U residue 282 ASP Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 223 ASP Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 261 SER Chi-restraints excluded: chain W residue 276 LEU Chi-restraints excluded: chain W residue 283 GLN Chi-restraints excluded: chain W residue 298 LYS Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 43 GLN Chi-restraints excluded: chain Y residue 196 ARG Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 237 VAL Chi-restraints excluded: chain Y residue 242 ASP Chi-restraints excluded: chain Y residue 261 SER Chi-restraints excluded: chain Y residue 276 LEU Chi-restraints excluded: chain Y residue 283 GLN Chi-restraints excluded: chain Y residue 298 LYS Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 261 SER Chi-restraints excluded: chain a residue 276 LEU Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 36 MET Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 199 TRP Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 237 VAL Chi-restraints excluded: chain c residue 242 ASP Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 280 ASP Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 302 VAL Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 36 MET Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain e residue 196 ARG Chi-restraints excluded: chain e residue 210 VAL Chi-restraints excluded: chain e residue 231 LEU Chi-restraints excluded: chain e residue 253 THR Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 283 GLN Chi-restraints excluded: chain e residue 292 MET Chi-restraints excluded: chain e residue 318 LEU Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain g residue 221 THR Chi-restraints excluded: chain g residue 223 ASP Chi-restraints excluded: chain g residue 225 ASN Chi-restraints excluded: chain g residue 237 VAL Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 276 LEU Chi-restraints excluded: chain g residue 280 ASP Chi-restraints excluded: chain g residue 283 GLN Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain h residue 21 VAL Chi-restraints excluded: chain h residue 31 THR Chi-restraints excluded: chain h residue 37 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 5.9990 chunk 310 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 345 optimal weight: 1.9990 chunk 286 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 181 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 ASN Y 390 GLN f 52 GLN g 394 GLN h 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.8396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 28441 Z= 0.555 Angle : 0.739 9.100 38233 Z= 0.373 Chirality : 0.048 0.218 4267 Planarity : 0.004 0.057 5015 Dihedral : 6.671 60.583 3977 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 10.12 % Allowed : 29.24 % Favored : 60.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.14), residues: 3655 helix: 2.34 (0.17), residues: 1020 sheet: -2.11 (0.17), residues: 901 loop : -3.14 (0.12), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 199 HIS 0.004 0.002 HIS Y 288 PHE 0.012 0.002 PHE e 251 TYR 0.021 0.002 TYR e 373 ARG 0.011 0.001 ARG g 402 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 546 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8707 (tpt) cc_final: 0.8276 (tpt) REVERT: B 46 ARG cc_start: 0.7144 (mtm110) cc_final: 0.6791 (ttp-170) REVERT: B 48 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8185 (ttpt) REVERT: B 51 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8720 (tmmt) REVERT: C 199 TRP cc_start: 0.7970 (OUTLIER) cc_final: 0.6825 (t60) REVERT: C 282 ASP cc_start: 0.8117 (m-30) cc_final: 0.7537 (m-30) REVERT: C 408 ARG cc_start: 0.7356 (mmp-170) cc_final: 0.6933 (mmp-170) REVERT: E 199 TRP cc_start: 0.8047 (OUTLIER) cc_final: 0.7008 (t60) REVERT: E 268 ARG cc_start: 0.7578 (ttm170) cc_final: 0.7329 (ttp80) REVERT: E 298 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7683 (tttp) REVERT: E 303 MET cc_start: 0.8592 (tpt) cc_final: 0.8091 (tpt) REVERT: F 51 LYS cc_start: 0.8891 (mmtm) cc_final: 0.8473 (tmmt) REVERT: G 199 TRP cc_start: 0.7973 (OUTLIER) cc_final: 0.6815 (t60) REVERT: I 199 TRP cc_start: 0.8014 (OUTLIER) cc_final: 0.7096 (t60) REVERT: I 298 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7713 (ptmt) REVERT: J 51 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8512 (tmmt) REVERT: K 199 TRP cc_start: 0.7847 (OUTLIER) cc_final: 0.6286 (t60) REVERT: K 282 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.6713 (m-30) REVERT: K 303 MET cc_start: 0.8595 (tpt) cc_final: 0.8142 (tpt) REVERT: M 199 TRP cc_start: 0.7958 (OUTLIER) cc_final: 0.6376 (t60) REVERT: M 292 MET cc_start: 0.8478 (mtp) cc_final: 0.7874 (mtp) REVERT: N 21 VAL cc_start: 0.7662 (OUTLIER) cc_final: 0.7322 (p) REVERT: O 199 TRP cc_start: 0.8046 (OUTLIER) cc_final: 0.6925 (t60) REVERT: O 266 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7772 (mp) REVERT: O 268 ARG cc_start: 0.8097 (ptm160) cc_final: 0.7564 (ptt180) REVERT: O 408 ARG cc_start: 0.6643 (tpm170) cc_final: 0.6319 (tpm170) REVERT: P 46 ARG cc_start: 0.6867 (mtm110) cc_final: 0.6562 (mtm110) REVERT: Q 199 TRP cc_start: 0.7870 (OUTLIER) cc_final: 0.6884 (t60) REVERT: Q 268 ARG cc_start: 0.7645 (ptt180) cc_final: 0.7332 (ttp80) REVERT: Q 379 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7871 (mp) REVERT: S 282 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: S 303 MET cc_start: 0.8786 (tpt) cc_final: 0.8291 (tpt) REVERT: T 33 ASP cc_start: 0.7729 (t0) cc_final: 0.7208 (t0) REVERT: T 47 ASP cc_start: 0.8824 (m-30) cc_final: 0.8402 (t70) REVERT: U 199 TRP cc_start: 0.7846 (OUTLIER) cc_final: 0.6730 (t60) REVERT: U 298 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7634 (tttp) REVERT: U 379 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7874 (mp) REVERT: V 21 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7482 (p) REVERT: V 47 ASP cc_start: 0.8708 (m-30) cc_final: 0.8397 (t0) REVERT: W 199 TRP cc_start: 0.7899 (OUTLIER) cc_final: 0.6838 (t60) REVERT: W 284 LYS cc_start: 0.8849 (mmtm) cc_final: 0.8597 (mmtm) REVERT: Y 199 TRP cc_start: 0.7686 (OUTLIER) cc_final: 0.6604 (t60) REVERT: Y 283 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.6612 (mp10) REVERT: Z 51 LYS cc_start: 0.8914 (mptt) cc_final: 0.8561 (tmmt) REVERT: a 199 TRP cc_start: 0.7973 (OUTLIER) cc_final: 0.6594 (t60) REVERT: a 239 MET cc_start: 0.7221 (mmm) cc_final: 0.6856 (mtt) REVERT: a 279 ASP cc_start: 0.6785 (t0) cc_final: 0.6565 (t0) REVERT: a 280 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7184 (p0) REVERT: a 282 ASP cc_start: 0.8066 (m-30) cc_final: 0.7364 (m-30) REVERT: a 283 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.6209 (mp10) REVERT: b 51 LYS cc_start: 0.8951 (mptt) cc_final: 0.8646 (tmmt) REVERT: c 199 TRP cc_start: 0.8004 (OUTLIER) cc_final: 0.7007 (t60) REVERT: c 283 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.6514 (mp10) REVERT: c 298 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7785 (tttp) REVERT: d 51 LYS cc_start: 0.8890 (mmtm) cc_final: 0.8682 (tmmt) REVERT: e 303 MET cc_start: 0.8396 (tpt) cc_final: 0.8107 (tpt) REVERT: f 51 LYS cc_start: 0.9119 (tppt) cc_final: 0.8672 (tmmt) REVERT: h 21 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7448 (p) REVERT: h 51 LYS cc_start: 0.9169 (tppt) cc_final: 0.8681 (tmmt) outliers start: 296 outliers final: 194 residues processed: 764 average time/residue: 0.4713 time to fit residues: 526.9648 Evaluate side-chains 743 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 518 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 48 LYS Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain G residue 199 TRP Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 280 ASP Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain I residue 199 TRP Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 199 TRP Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 223 ASP Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 282 ASP Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 199 TRP Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain M residue 383 ASN Chi-restraints excluded: chain M residue 388 VAL Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 199 TRP Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 237 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 266 ILE Chi-restraints excluded: chain O residue 280 ASP Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 298 LYS Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 210 VAL Chi-restraints excluded: chain Q residue 223 ASP Chi-restraints excluded: chain Q residue 237 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 280 ASP Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 379 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 242 ASP Chi-restraints excluded: chain S residue 244 GLU Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 261 SER Chi-restraints excluded: chain S residue 280 ASP Chi-restraints excluded: chain S residue 282 ASP Chi-restraints excluded: chain S residue 283 GLN Chi-restraints excluded: chain S residue 292 MET Chi-restraints excluded: chain S residue 295 ASN Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain U residue 199 TRP Chi-restraints excluded: chain U residue 223 ASP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 261 SER Chi-restraints excluded: chain U residue 282 ASP Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 379 ILE Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 42 ASN Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 223 ASP Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 261 SER Chi-restraints excluded: chain W residue 282 ASP Chi-restraints excluded: chain W residue 283 GLN Chi-restraints excluded: chain W residue 297 ILE Chi-restraints excluded: chain W residue 298 LYS Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain Y residue 196 ARG Chi-restraints excluded: chain Y residue 199 TRP Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 231 LEU Chi-restraints excluded: chain Y residue 237 VAL Chi-restraints excluded: chain Y residue 261 SER Chi-restraints excluded: chain Y residue 283 GLN Chi-restraints excluded: chain Y residue 298 LYS Chi-restraints excluded: chain Y residue 388 VAL Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain a residue 199 TRP Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 237 VAL Chi-restraints excluded: chain a residue 261 SER Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 283 GLN Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain a residue 302 VAL Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 36 MET Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 199 TRP Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain c residue 209 ILE Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 237 VAL Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 280 ASP Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 302 VAL Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 36 MET Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain e residue 196 ARG Chi-restraints excluded: chain e residue 210 VAL Chi-restraints excluded: chain e residue 221 THR Chi-restraints excluded: chain e residue 231 LEU Chi-restraints excluded: chain e residue 253 THR Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 283 GLN Chi-restraints excluded: chain e residue 292 MET Chi-restraints excluded: chain e residue 297 ILE Chi-restraints excluded: chain e residue 318 LEU Chi-restraints excluded: chain f residue 21 VAL Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 221 THR Chi-restraints excluded: chain g residue 223 ASP Chi-restraints excluded: chain g residue 225 ASN Chi-restraints excluded: chain g residue 237 VAL Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 280 ASP Chi-restraints excluded: chain g residue 283 GLN Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 396 GLU Chi-restraints excluded: chain h residue 21 VAL Chi-restraints excluded: chain h residue 31 THR Chi-restraints excluded: chain h residue 37 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 290 optimal weight: 0.8980 chunk 192 optimal weight: 0.6980 chunk 344 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 390 GLN J 52 GLN ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 305 ASN ** M 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 390 GLN V 42 ASN V 52 GLN a 390 GLN f 52 GLN h 52 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.8480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28441 Z= 0.197 Angle : 0.554 7.222 38233 Z= 0.279 Chirality : 0.042 0.184 4267 Planarity : 0.003 0.053 5015 Dihedral : 6.099 62.783 3977 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 7.59 % Allowed : 31.84 % Favored : 60.57 % 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: -1.56 (0.14), residues: 3655 helix: 2.66 (0.17), residues: 1003 sheet: -1.91 (0.17), residues: 901 loop : -2.92 (0.12), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 199 HIS 0.003 0.001 HIS U 374 PHE 0.008 0.001 PHE E 317 TYR 0.013 0.001 TYR e 373 ARG 0.012 0.001 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 552 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7674 (tttp) REVERT: A 303 MET cc_start: 0.8656 (tpt) cc_final: 0.8284 (tpt) REVERT: B 51 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8604 (tmmt) REVERT: C 199 TRP cc_start: 0.7689 (OUTLIER) cc_final: 0.6722 (t60) REVERT: C 408 ARG cc_start: 0.7324 (mmp-170) cc_final: 0.6951 (mmp-170) REVERT: D 21 VAL cc_start: 0.7798 (m) cc_final: 0.7462 (p) REVERT: E 199 TRP cc_start: 0.7876 (OUTLIER) cc_final: 0.7037 (t60) REVERT: E 298 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7635 (tttp) REVERT: E 303 MET cc_start: 0.8624 (tpt) cc_final: 0.8049 (tpt) REVERT: G 199 TRP cc_start: 0.7732 (OUTLIER) cc_final: 0.6167 (t60) REVERT: I 199 TRP cc_start: 0.7635 (OUTLIER) cc_final: 0.7000 (t60) REVERT: I 368 LYS cc_start: 0.8563 (ttmm) cc_final: 0.8346 (ttmm) REVERT: J 51 LYS cc_start: 0.8702 (mmtm) cc_final: 0.8356 (tmmt) REVERT: K 199 TRP cc_start: 0.7768 (OUTLIER) cc_final: 0.6191 (t60) REVERT: K 298 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7732 (tttp) REVERT: K 303 MET cc_start: 0.8583 (tpt) cc_final: 0.8121 (tpt) REVERT: N 21 VAL cc_start: 0.7609 (OUTLIER) cc_final: 0.7293 (p) REVERT: N 33 ASP cc_start: 0.7494 (t0) cc_final: 0.7104 (t0) REVERT: O 199 TRP cc_start: 0.7887 (OUTLIER) cc_final: 0.6783 (t60) REVERT: O 268 ARG cc_start: 0.7846 (ptm160) cc_final: 0.7348 (ptt180) REVERT: P 33 ASP cc_start: 0.7643 (t0) cc_final: 0.7207 (t0) REVERT: P 38 MET cc_start: 0.6912 (mtt) cc_final: 0.6672 (mtt) REVERT: P 46 ARG cc_start: 0.7074 (mtm110) cc_final: 0.6803 (mtm110) REVERT: Q 268 ARG cc_start: 0.7566 (ptt180) cc_final: 0.7180 (ttp80) REVERT: R 33 ASP cc_start: 0.7560 (t0) cc_final: 0.6967 (t0) REVERT: S 244 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: S 303 MET cc_start: 0.8764 (tpt) cc_final: 0.8187 (tpt) REVERT: T 47 ASP cc_start: 0.8787 (m-30) cc_final: 0.8412 (t70) REVERT: U 298 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7572 (tttp) REVERT: U 379 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7877 (mp) REVERT: V 21 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7374 (p) REVERT: W 199 TRP cc_start: 0.7832 (OUTLIER) cc_final: 0.6790 (t60) REVERT: W 284 LYS cc_start: 0.8827 (mmtm) cc_final: 0.8582 (mmtm) REVERT: Y 283 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.6432 (mp10) REVERT: Z 51 LYS cc_start: 0.8777 (mptt) cc_final: 0.8509 (tmmt) REVERT: a 279 ASP cc_start: 0.6901 (t0) cc_final: 0.6140 (t0) REVERT: a 280 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.7087 (p0) REVERT: a 282 ASP cc_start: 0.8195 (m-30) cc_final: 0.7268 (m-30) REVERT: a 283 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.5939 (mp10) REVERT: b 46 ARG cc_start: 0.7576 (ttp-170) cc_final: 0.7373 (ttp-170) REVERT: b 48 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7891 (ttmt) REVERT: b 51 LYS cc_start: 0.8812 (mptt) cc_final: 0.8590 (tmmt) REVERT: c 196 ARG cc_start: 0.8215 (tmm-80) cc_final: 0.7806 (tmm-80) REVERT: c 199 TRP cc_start: 0.7937 (OUTLIER) cc_final: 0.6960 (t60) REVERT: c 283 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6994 (mt0) REVERT: c 298 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7753 (tttp) REVERT: e 196 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7931 (ptt90) REVERT: e 270 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7703 (mtp85) REVERT: f 51 LYS cc_start: 0.9021 (tppt) cc_final: 0.8576 (tmmt) REVERT: g 255 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7708 (mt-10) REVERT: h 21 VAL cc_start: 0.7635 (OUTLIER) cc_final: 0.7194 (p) REVERT: h 51 LYS cc_start: 0.9070 (tppt) cc_final: 0.8598 (tmmt) outliers start: 222 outliers final: 164 residues processed: 712 average time/residue: 0.4839 time to fit residues: 500.4013 Evaluate side-chains 725 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 537 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain G residue 199 TRP Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain I residue 199 TRP Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 199 TRP Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 223 ASP Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 408 ARG Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 199 TRP Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 298 LYS Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 210 VAL Chi-restraints excluded: chain Q residue 223 ASP Chi-restraints excluded: chain Q residue 231 LEU Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 244 GLU Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 283 GLN Chi-restraints excluded: chain S residue 292 MET Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 242 ASP Chi-restraints excluded: chain U residue 261 SER Chi-restraints excluded: chain U residue 276 LEU Chi-restraints excluded: chain U residue 282 ASP Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 379 ILE Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 223 ASP Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 261 SER Chi-restraints excluded: chain W residue 276 LEU Chi-restraints excluded: chain W residue 282 ASP Chi-restraints excluded: chain W residue 283 GLN Chi-restraints excluded: chain W residue 298 LYS Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain Y residue 196 ARG Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 231 LEU Chi-restraints excluded: chain Y residue 261 SER Chi-restraints excluded: chain Y residue 283 GLN Chi-restraints excluded: chain Y residue 388 VAL Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 237 VAL Chi-restraints excluded: chain a residue 261 SER Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 283 GLN Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 36 MET Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 199 TRP Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain c residue 209 ILE Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 280 ASP Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain c residue 297 ILE Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 36 MET Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain e residue 196 ARG Chi-restraints excluded: chain e residue 221 THR Chi-restraints excluded: chain e residue 253 THR Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 283 GLN Chi-restraints excluded: chain e residue 292 MET Chi-restraints excluded: chain e residue 318 LEU Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain g residue 221 THR Chi-restraints excluded: chain g residue 223 ASP Chi-restraints excluded: chain g residue 225 ASN Chi-restraints excluded: chain g residue 237 VAL Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 276 LEU Chi-restraints excluded: chain g residue 280 ASP Chi-restraints excluded: chain g residue 283 GLN Chi-restraints excluded: chain g residue 292 MET Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain h residue 21 VAL Chi-restraints excluded: chain h residue 31 THR Chi-restraints excluded: chain h residue 37 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 218 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 270 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 52 GLN ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.8581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 28441 Z= 0.496 Angle : 0.725 9.225 38233 Z= 0.362 Chirality : 0.047 0.225 4267 Planarity : 0.004 0.058 5015 Dihedral : 6.527 61.409 3977 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 9.03 % Allowed : 31.22 % Favored : 59.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.14), residues: 3655 helix: 2.46 (0.16), residues: 1020 sheet: -2.07 (0.17), residues: 901 loop : -3.07 (0.12), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 199 HIS 0.003 0.001 HIS U 374 PHE 0.011 0.002 PHE S 245 TYR 0.020 0.002 TYR M 373 ARG 0.013 0.001 ARG g 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 551 time to evaluate : 3.201 Fit side-chains revert: symmetry clash REVERT: A 303 MET cc_start: 0.8751 (tpt) cc_final: 0.8330 (tpt) REVERT: B 46 ARG cc_start: 0.7199 (mtm110) cc_final: 0.6791 (ttp-170) REVERT: C 199 TRP cc_start: 0.7945 (OUTLIER) cc_final: 0.6881 (t60) REVERT: C 282 ASP cc_start: 0.8244 (m-30) cc_final: 0.7534 (m-30) REVERT: C 408 ARG cc_start: 0.7313 (mmp-170) cc_final: 0.6960 (mmp-170) REVERT: D 51 LYS cc_start: 0.8712 (mmpt) cc_final: 0.8500 (tptt) REVERT: E 199 TRP cc_start: 0.8081 (OUTLIER) cc_final: 0.7078 (t60) REVERT: E 298 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7844 (tttp) REVERT: E 303 MET cc_start: 0.8589 (tpt) cc_final: 0.8055 (tpt) REVERT: F 51 LYS cc_start: 0.8858 (mmtm) cc_final: 0.8510 (tmmt) REVERT: G 199 TRP cc_start: 0.7960 (OUTLIER) cc_final: 0.6545 (t60) REVERT: H 38 MET cc_start: 0.7025 (mtt) cc_final: 0.6796 (mtt) REVERT: I 199 TRP cc_start: 0.7868 (OUTLIER) cc_final: 0.7049 (t60) REVERT: I 298 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7483 (ptmt) REVERT: J 51 LYS cc_start: 0.8856 (mmtm) cc_final: 0.8544 (tmmt) REVERT: K 199 TRP cc_start: 0.7832 (OUTLIER) cc_final: 0.6317 (t60) REVERT: K 303 MET cc_start: 0.8666 (tpt) cc_final: 0.8249 (tpt) REVERT: N 21 VAL cc_start: 0.7659 (OUTLIER) cc_final: 0.7331 (p) REVERT: O 199 TRP cc_start: 0.8025 (OUTLIER) cc_final: 0.6873 (t60) REVERT: O 266 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7773 (mp) REVERT: O 268 ARG cc_start: 0.8080 (ptm160) cc_final: 0.7615 (ptt180) REVERT: P 51 LYS cc_start: 0.8963 (mmtm) cc_final: 0.8551 (tmmt) REVERT: Q 199 TRP cc_start: 0.7866 (OUTLIER) cc_final: 0.6821 (t60) REVERT: Q 268 ARG cc_start: 0.7630 (ptt180) cc_final: 0.7320 (ttp80) REVERT: Q 282 ASP cc_start: 0.7951 (m-30) cc_final: 0.7028 (m-30) REVERT: Q 379 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7818 (mp) REVERT: S 199 TRP cc_start: 0.7903 (OUTLIER) cc_final: 0.6779 (t60) REVERT: S 244 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: S 303 MET cc_start: 0.8756 (tpt) cc_final: 0.8090 (tpt) REVERT: T 47 ASP cc_start: 0.8815 (m-30) cc_final: 0.8467 (t70) REVERT: U 199 TRP cc_start: 0.7862 (OUTLIER) cc_final: 0.6661 (t60) REVERT: U 239 MET cc_start: 0.7526 (mmt) cc_final: 0.7310 (mmm) REVERT: U 298 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7666 (tttp) REVERT: U 379 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7902 (mp) REVERT: V 21 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7484 (p) REVERT: V 47 ASP cc_start: 0.8930 (t70) cc_final: 0.8625 (t70) REVERT: W 199 TRP cc_start: 0.7824 (OUTLIER) cc_final: 0.6764 (t60) REVERT: W 284 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8620 (mmtm) REVERT: X 51 LYS cc_start: 0.8916 (mmtm) cc_final: 0.8479 (tmmt) REVERT: Y 283 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.6580 (mp10) REVERT: a 199 TRP cc_start: 0.7909 (OUTLIER) cc_final: 0.6586 (t60) REVERT: a 239 MET cc_start: 0.7192 (mmm) cc_final: 0.6727 (mtt) REVERT: a 279 ASP cc_start: 0.6851 (t0) cc_final: 0.6474 (t70) REVERT: a 280 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7339 (p0) REVERT: a 282 ASP cc_start: 0.8099 (m-30) cc_final: 0.7336 (m-30) REVERT: a 283 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.6093 (mp10) REVERT: b 51 LYS cc_start: 0.8907 (mptt) cc_final: 0.8676 (tmmt) REVERT: c 196 ARG cc_start: 0.8237 (tmm-80) cc_final: 0.7835 (tmm-80) REVERT: c 199 TRP cc_start: 0.7995 (OUTLIER) cc_final: 0.6927 (t60) REVERT: c 283 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.6504 (mp10) REVERT: c 298 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7806 (tttp) REVERT: e 196 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7971 (ptt90) REVERT: e 242 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7385 (m-30) REVERT: f 51 LYS cc_start: 0.9150 (tppt) cc_final: 0.8716 (tmmt) REVERT: h 51 LYS cc_start: 0.9126 (tppt) cc_final: 0.8703 (tmmt) outliers start: 264 outliers final: 199 residues processed: 742 average time/residue: 0.4671 time to fit residues: 506.1585 Evaluate side-chains 757 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 530 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain G residue 199 TRP Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 280 ASP Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain I residue 199 TRP Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 199 TRP Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 223 ASP Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 280 ASP Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 408 ARG Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 199 TRP Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 237 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 266 ILE Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 298 LYS Chi-restraints excluded: chain O residue 318 LEU Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 27 CYS Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 210 VAL Chi-restraints excluded: chain Q residue 223 ASP Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 379 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 244 GLU Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 261 SER Chi-restraints excluded: chain S residue 280 ASP Chi-restraints excluded: chain S residue 283 GLN Chi-restraints excluded: chain S residue 292 MET Chi-restraints excluded: chain S residue 295 ASN Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain T residue 27 CYS Chi-restraints excluded: chain U residue 199 TRP Chi-restraints excluded: chain U residue 223 ASP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 237 VAL Chi-restraints excluded: chain U residue 242 ASP Chi-restraints excluded: chain U residue 261 SER Chi-restraints excluded: chain U residue 282 ASP Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 295 ASN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 379 ILE Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 220 VAL Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 223 ASP Chi-restraints excluded: chain W residue 237 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 261 SER Chi-restraints excluded: chain W residue 282 ASP Chi-restraints excluded: chain W residue 283 GLN Chi-restraints excluded: chain W residue 297 ILE Chi-restraints excluded: chain W residue 298 LYS Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain Y residue 196 ARG Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 231 LEU Chi-restraints excluded: chain Y residue 237 VAL Chi-restraints excluded: chain Y residue 261 SER Chi-restraints excluded: chain Y residue 283 GLN Chi-restraints excluded: chain Y residue 298 LYS Chi-restraints excluded: chain Y residue 388 VAL Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain a residue 199 TRP Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 237 VAL Chi-restraints excluded: chain a residue 261 SER Chi-restraints excluded: chain a residue 280 ASP Chi-restraints excluded: chain a residue 283 GLN Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 36 MET Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 199 TRP Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 237 VAL Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 280 ASP Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 302 VAL Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 36 MET Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain e residue 196 ARG Chi-restraints excluded: chain e residue 221 THR Chi-restraints excluded: chain e residue 231 LEU Chi-restraints excluded: chain e residue 242 ASP Chi-restraints excluded: chain e residue 253 THR Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 283 GLN Chi-restraints excluded: chain e residue 292 MET Chi-restraints excluded: chain e residue 297 ILE Chi-restraints excluded: chain e residue 318 LEU Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain g residue 221 THR Chi-restraints excluded: chain g residue 223 ASP Chi-restraints excluded: chain g residue 225 ASN Chi-restraints excluded: chain g residue 237 VAL Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 276 LEU Chi-restraints excluded: chain g residue 280 ASP Chi-restraints excluded: chain g residue 283 GLN Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain g residue 388 VAL Chi-restraints excluded: chain h residue 31 THR Chi-restraints excluded: chain h residue 37 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 5.9990 chunk 329 optimal weight: 0.7980 chunk 300 optimal weight: 0.9980 chunk 320 optimal weight: 0.9990 chunk 192 optimal weight: 0.6980 chunk 139 optimal weight: 10.0000 chunk 251 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 303 optimal weight: 0.8980 chunk 319 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 383 ASN ** M 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 390 GLN V 52 GLN h 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.8666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28441 Z= 0.195 Angle : 0.573 7.656 38233 Z= 0.286 Chirality : 0.042 0.196 4267 Planarity : 0.003 0.059 5015 Dihedral : 6.075 63.188 3977 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 6.91 % Allowed : 32.93 % Favored : 60.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3655 helix: 2.82 (0.16), residues: 1020 sheet: -1.88 (0.17), residues: 901 loop : -2.92 (0.12), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 199 HIS 0.003 0.001 HIS C 288 PHE 0.010 0.001 PHE Q 291 TYR 0.012 0.001 TYR W 373 ARG 0.014 0.001 ARG T 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 549 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8664 (tpt) cc_final: 0.8293 (tpt) REVERT: B 33 ASP cc_start: 0.7342 (t0) cc_final: 0.7132 (t0) REVERT: B 51 LYS cc_start: 0.8680 (tmmt) cc_final: 0.8412 (tmmt) REVERT: C 199 TRP cc_start: 0.7676 (OUTLIER) cc_final: 0.6713 (t60) REVERT: C 408 ARG cc_start: 0.7316 (mmp-170) cc_final: 0.6970 (mmp-170) REVERT: D 21 VAL cc_start: 0.7835 (m) cc_final: 0.7446 (p) REVERT: E 199 TRP cc_start: 0.7820 (OUTLIER) cc_final: 0.6994 (t60) REVERT: E 298 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7645 (tttp) REVERT: E 303 MET cc_start: 0.8633 (tpt) cc_final: 0.8019 (tpt) REVERT: G 199 TRP cc_start: 0.7738 (OUTLIER) cc_final: 0.6170 (t60) REVERT: I 199 TRP cc_start: 0.7620 (OUTLIER) cc_final: 0.6973 (t60) REVERT: I 292 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7946 (ttm) REVERT: J 51 LYS cc_start: 0.8705 (mmtm) cc_final: 0.8406 (tmmt) REVERT: K 298 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7777 (tttp) REVERT: K 303 MET cc_start: 0.8593 (tpt) cc_final: 0.8133 (tpt) REVERT: K 408 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6813 (mmp-170) REVERT: M 199 TRP cc_start: 0.7757 (OUTLIER) cc_final: 0.6647 (t60) REVERT: M 292 MET cc_start: 0.8098 (mtp) cc_final: 0.7684 (mtp) REVERT: N 21 VAL cc_start: 0.7586 (OUTLIER) cc_final: 0.7232 (p) REVERT: O 268 ARG cc_start: 0.7845 (ptm160) cc_final: 0.7338 (ptt180) REVERT: Q 268 ARG cc_start: 0.7421 (ptt180) cc_final: 0.7052 (ttp80) REVERT: Q 379 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7839 (mp) REVERT: S 303 MET cc_start: 0.8744 (tpt) cc_final: 0.8121 (tpt) REVERT: T 47 ASP cc_start: 0.8791 (m-30) cc_final: 0.8424 (t70) REVERT: U 298 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7628 (tttp) REVERT: U 379 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7917 (mp) REVERT: V 21 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7514 (p) REVERT: W 199 TRP cc_start: 0.7763 (OUTLIER) cc_final: 0.6704 (t60) REVERT: W 284 LYS cc_start: 0.8835 (mmtm) cc_final: 0.8570 (mmtm) REVERT: Y 283 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6327 (mp10) REVERT: a 196 ARG cc_start: 0.8306 (tmm-80) cc_final: 0.7970 (ptm-80) REVERT: a 282 ASP cc_start: 0.8161 (m-30) cc_final: 0.7211 (m-30) REVERT: a 283 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.5922 (mp10) REVERT: c 196 ARG cc_start: 0.8272 (tmm-80) cc_final: 0.7921 (tmm-80) REVERT: c 199 TRP cc_start: 0.7922 (OUTLIER) cc_final: 0.6858 (t60) REVERT: c 283 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7122 (mt0) REVERT: c 298 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7839 (tttp) REVERT: e 196 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8004 (ptt90) REVERT: f 51 LYS cc_start: 0.9057 (tppt) cc_final: 0.8627 (tmmt) REVERT: g 196 ARG cc_start: 0.7897 (ptt90) cc_final: 0.7664 (ptt-90) REVERT: g 255 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7680 (mt-10) REVERT: g 292 MET cc_start: 0.8328 (ttt) cc_final: 0.8068 (mtp) REVERT: h 51 LYS cc_start: 0.9084 (tppt) cc_final: 0.8701 (tmmt) outliers start: 202 outliers final: 169 residues processed: 694 average time/residue: 0.5377 time to fit residues: 546.6332 Evaluate side-chains 740 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 550 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain G residue 199 TRP Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain I residue 199 TRP Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain I residue 292 MET Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 223 ASP Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 408 ARG Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 199 TRP Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 298 LYS Chi-restraints excluded: chain O residue 318 LEU Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 27 CYS Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 223 ASP Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 379 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 261 SER Chi-restraints excluded: chain S residue 283 GLN Chi-restraints excluded: chain S residue 292 MET Chi-restraints excluded: chain S residue 295 ASN Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain U residue 223 ASP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 242 ASP Chi-restraints excluded: chain U residue 261 SER Chi-restraints excluded: chain U residue 282 ASP Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 379 ILE Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 223 ASP Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 261 SER Chi-restraints excluded: chain W residue 282 ASP Chi-restraints excluded: chain W residue 283 GLN Chi-restraints excluded: chain W residue 298 LYS Chi-restraints excluded: chain W residue 318 LEU Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain Y residue 196 ARG Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 261 SER Chi-restraints excluded: chain Y residue 283 GLN Chi-restraints excluded: chain Y residue 298 LYS Chi-restraints excluded: chain Y residue 388 VAL Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 237 VAL Chi-restraints excluded: chain a residue 261 SER Chi-restraints excluded: chain a residue 283 GLN Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 36 MET Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 199 TRP Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 237 VAL Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 283 GLN Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 36 MET Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain e residue 196 ARG Chi-restraints excluded: chain e residue 221 THR Chi-restraints excluded: chain e residue 223 ASP Chi-restraints excluded: chain e residue 253 THR Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 283 GLN Chi-restraints excluded: chain e residue 297 ILE Chi-restraints excluded: chain e residue 318 LEU Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain g residue 221 THR Chi-restraints excluded: chain g residue 223 ASP Chi-restraints excluded: chain g residue 225 ASN Chi-restraints excluded: chain g residue 237 VAL Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 276 LEU Chi-restraints excluded: chain g residue 280 ASP Chi-restraints excluded: chain g residue 283 GLN Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain h residue 31 THR Chi-restraints excluded: chain h residue 37 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 0.7980 chunk 339 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 355 optimal weight: 0.9990 chunk 327 optimal weight: 9.9990 chunk 283 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 218 optimal weight: 0.0670 chunk 173 optimal weight: 2.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.8688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28441 Z= 0.233 Angle : 0.593 8.644 38233 Z= 0.296 Chirality : 0.043 0.201 4267 Planarity : 0.004 0.060 5015 Dihedral : 6.040 63.417 3977 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 6.98 % Allowed : 32.73 % Favored : 60.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.14), residues: 3655 helix: 2.85 (0.16), residues: 1020 sheet: -2.16 (0.16), residues: 1071 loop : -2.73 (0.14), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 199 HIS 0.003 0.001 HIS C 288 PHE 0.008 0.001 PHE g 251 TYR 0.014 0.001 TYR M 373 ARG 0.018 0.001 ARG L 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 550 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 MET cc_start: 0.8683 (tpt) cc_final: 0.8331 (tpt) REVERT: B 33 ASP cc_start: 0.7438 (t0) cc_final: 0.7215 (t0) REVERT: B 51 LYS cc_start: 0.8714 (tmmt) cc_final: 0.8446 (tmmt) REVERT: C 199 TRP cc_start: 0.7707 (OUTLIER) cc_final: 0.6719 (t60) REVERT: C 282 ASP cc_start: 0.8300 (m-30) cc_final: 0.7629 (m-30) REVERT: C 408 ARG cc_start: 0.7377 (mmp-170) cc_final: 0.7049 (mmp-170) REVERT: D 21 VAL cc_start: 0.7873 (m) cc_final: 0.7499 (p) REVERT: E 199 TRP cc_start: 0.7825 (OUTLIER) cc_final: 0.6983 (t60) REVERT: E 298 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7882 (tttp) REVERT: E 303 MET cc_start: 0.8591 (tpt) cc_final: 0.8051 (tpt) REVERT: G 199 TRP cc_start: 0.7731 (OUTLIER) cc_final: 0.6160 (t60) REVERT: H 38 MET cc_start: 0.6989 (mtt) cc_final: 0.6759 (mtt) REVERT: I 199 TRP cc_start: 0.7685 (OUTLIER) cc_final: 0.6956 (t60) REVERT: I 292 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7819 (ttm) REVERT: J 51 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8446 (tmmt) REVERT: K 298 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7701 (tttp) REVERT: K 303 MET cc_start: 0.8615 (tpt) cc_final: 0.8108 (tpt) REVERT: K 408 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6809 (mmp-170) REVERT: M 199 TRP cc_start: 0.7803 (OUTLIER) cc_final: 0.6587 (t60) REVERT: M 292 MET cc_start: 0.8144 (mtp) cc_final: 0.7652 (mtp) REVERT: N 21 VAL cc_start: 0.7595 (OUTLIER) cc_final: 0.7261 (p) REVERT: O 266 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7810 (mp) REVERT: O 268 ARG cc_start: 0.7834 (ptm160) cc_final: 0.7505 (ptt-90) REVERT: Q 268 ARG cc_start: 0.7427 (ptt180) cc_final: 0.7051 (ttp80) REVERT: Q 379 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7845 (mp) REVERT: S 244 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: S 303 MET cc_start: 0.8703 (tpt) cc_final: 0.8051 (tpt) REVERT: T 47 ASP cc_start: 0.8791 (m-30) cc_final: 0.8432 (t70) REVERT: U 244 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7584 (mp0) REVERT: U 298 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7730 (tttp) REVERT: U 379 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7917 (mp) REVERT: V 21 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7500 (p) REVERT: W 199 TRP cc_start: 0.7797 (OUTLIER) cc_final: 0.6720 (t60) REVERT: W 284 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8568 (mmtm) REVERT: Y 283 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6311 (mp10) REVERT: a 196 ARG cc_start: 0.8313 (tmm-80) cc_final: 0.7982 (ptm-80) REVERT: a 282 ASP cc_start: 0.8062 (m-30) cc_final: 0.7090 (m-30) REVERT: a 283 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.5938 (mp10) REVERT: c 196 ARG cc_start: 0.8268 (tmm-80) cc_final: 0.7949 (tmm-80) REVERT: c 199 TRP cc_start: 0.7973 (OUTLIER) cc_final: 0.6841 (t60) REVERT: c 298 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7875 (tttp) REVERT: e 196 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7953 (ptt90) REVERT: f 51 LYS cc_start: 0.9094 (tppt) cc_final: 0.8663 (tmmt) REVERT: g 255 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7671 (mt-10) REVERT: h 51 LYS cc_start: 0.9098 (tppt) cc_final: 0.8719 (tmmt) outliers start: 204 outliers final: 172 residues processed: 702 average time/residue: 0.4940 time to fit residues: 503.1111 Evaluate side-chains 732 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 538 time to evaluate : 3.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain C residue 199 TRP Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 298 LYS Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 199 TRP Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 34 THR Chi-restraints excluded: chain G residue 199 TRP Chi-restraints excluded: chain G residue 223 ASP Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 237 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 292 MET Chi-restraints excluded: chain G residue 298 LYS Chi-restraints excluded: chain G residue 303 MET Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 388 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 51 LYS Chi-restraints excluded: chain I residue 199 TRP Chi-restraints excluded: chain I residue 276 LEU Chi-restraints excluded: chain I residue 280 ASP Chi-restraints excluded: chain I residue 283 GLN Chi-restraints excluded: chain I residue 292 MET Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 221 THR Chi-restraints excluded: chain K residue 223 ASP Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 242 ASP Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 276 LEU Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 298 LYS Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 408 ARG Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 199 TRP Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 276 LEU Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 211 VAL Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain O residue 234 THR Chi-restraints excluded: chain O residue 237 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 266 ILE Chi-restraints excluded: chain O residue 280 ASP Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain O residue 298 LYS Chi-restraints excluded: chain O residue 387 LEU Chi-restraints excluded: chain O residue 388 VAL Chi-restraints excluded: chain P residue 27 CYS Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 34 THR Chi-restraints excluded: chain Q residue 199 TRP Chi-restraints excluded: chain Q residue 223 ASP Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 280 ASP Chi-restraints excluded: chain Q residue 283 GLN Chi-restraints excluded: chain Q residue 297 ILE Chi-restraints excluded: chain Q residue 379 ILE Chi-restraints excluded: chain Q residue 387 LEU Chi-restraints excluded: chain Q residue 388 VAL Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain S residue 199 TRP Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 244 GLU Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 261 SER Chi-restraints excluded: chain S residue 283 GLN Chi-restraints excluded: chain S residue 292 MET Chi-restraints excluded: chain S residue 295 ASN Chi-restraints excluded: chain S residue 298 LYS Chi-restraints excluded: chain S residue 388 VAL Chi-restraints excluded: chain U residue 223 ASP Chi-restraints excluded: chain U residue 234 THR Chi-restraints excluded: chain U residue 242 ASP Chi-restraints excluded: chain U residue 261 SER Chi-restraints excluded: chain U residue 269 SER Chi-restraints excluded: chain U residue 282 ASP Chi-restraints excluded: chain U residue 283 GLN Chi-restraints excluded: chain U residue 297 ILE Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 379 ILE Chi-restraints excluded: chain U residue 388 VAL Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 31 THR Chi-restraints excluded: chain W residue 199 TRP Chi-restraints excluded: chain W residue 221 THR Chi-restraints excluded: chain W residue 223 ASP Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 261 SER Chi-restraints excluded: chain W residue 282 ASP Chi-restraints excluded: chain W residue 283 GLN Chi-restraints excluded: chain W residue 298 LYS Chi-restraints excluded: chain W residue 318 LEU Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 32 SER Chi-restraints excluded: chain X residue 36 MET Chi-restraints excluded: chain Y residue 196 ARG Chi-restraints excluded: chain Y residue 223 ASP Chi-restraints excluded: chain Y residue 231 LEU Chi-restraints excluded: chain Y residue 261 SER Chi-restraints excluded: chain Y residue 283 GLN Chi-restraints excluded: chain Y residue 298 LYS Chi-restraints excluded: chain Y residue 388 VAL Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain a residue 223 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain a residue 237 VAL Chi-restraints excluded: chain a residue 261 SER Chi-restraints excluded: chain a residue 283 GLN Chi-restraints excluded: chain a residue 298 LYS Chi-restraints excluded: chain b residue 31 THR Chi-restraints excluded: chain b residue 36 MET Chi-restraints excluded: chain b residue 37 THR Chi-restraints excluded: chain c residue 199 TRP Chi-restraints excluded: chain c residue 206 VAL Chi-restraints excluded: chain c residue 223 ASP Chi-restraints excluded: chain c residue 237 VAL Chi-restraints excluded: chain c residue 276 LEU Chi-restraints excluded: chain c residue 298 LYS Chi-restraints excluded: chain c residue 367 ILE Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 36 MET Chi-restraints excluded: chain d residue 37 THR Chi-restraints excluded: chain e residue 196 ARG Chi-restraints excluded: chain e residue 223 ASP Chi-restraints excluded: chain e residue 276 LEU Chi-restraints excluded: chain e residue 280 ASP Chi-restraints excluded: chain e residue 283 GLN Chi-restraints excluded: chain e residue 292 MET Chi-restraints excluded: chain e residue 297 ILE Chi-restraints excluded: chain e residue 318 LEU Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain g residue 209 ILE Chi-restraints excluded: chain g residue 221 THR Chi-restraints excluded: chain g residue 223 ASP Chi-restraints excluded: chain g residue 225 ASN Chi-restraints excluded: chain g residue 237 VAL Chi-restraints excluded: chain g residue 252 VAL Chi-restraints excluded: chain g residue 253 THR Chi-restraints excluded: chain g residue 276 LEU Chi-restraints excluded: chain g residue 280 ASP Chi-restraints excluded: chain g residue 283 GLN Chi-restraints excluded: chain g residue 297 ILE Chi-restraints excluded: chain h residue 31 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 283 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 chunk 291 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.119179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.090812 restraints weight = 46538.184| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.95 r_work: 0.3028 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.8740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28441 Z= 0.210 Angle : 0.578 8.768 38233 Z= 0.287 Chirality : 0.042 0.213 4267 Planarity : 0.004 0.061 5015 Dihedral : 5.966 63.497 3977 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 6.98 % Allowed : 32.76 % Favored : 60.26 % 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: -1.21 (0.14), residues: 3655 helix: 3.00 (0.16), residues: 1020 sheet: -1.72 (0.17), residues: 901 loop : -2.79 (0.12), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 199 HIS 0.003 0.001 HIS C 288 PHE 0.008 0.001 PHE Y 205 TYR 0.012 0.001 TYR S 373 ARG 0.016 0.001 ARG g 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9015.40 seconds wall clock time: 162 minutes 31.93 seconds (9751.93 seconds total)