Starting phenix.real_space_refine on Thu Feb 22 14:09:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fff_31567/02_2024/7fff_31567.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fff_31567/02_2024/7fff_31567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fff_31567/02_2024/7fff_31567.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fff_31567/02_2024/7fff_31567.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fff_31567/02_2024/7fff_31567.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fff_31567/02_2024/7fff_31567.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 268 5.16 5 C 21736 2.51 5 N 5880 2.21 5 O 6468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 21": "NH1" <-> "NH2" Residue "G TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "H ASP 57": "OD1" <-> "OD2" Residue "J ARG -982": "NH1" <-> "NH2" Residue "J ARG -979": "NH1" <-> "NH2" Residue "J TYR -915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG -912": "NH1" <-> "NH2" Residue "J ARG -897": "NH1" <-> "NH2" Residue "J ARG -880": "NH1" <-> "NH2" Residue "J TYR -861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG -839": "NH1" <-> "NH2" Residue "J ARG -719": "NH1" <-> "NH2" Residue "J ARG -581": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 289": "NH1" <-> "NH2" Residue "D PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 88": "NH1" <-> "NH2" Residue "Q ARG 103": "NH1" <-> "NH2" Residue "Q ARG 120": "NH1" <-> "NH2" Residue "Q ARG 281": "NH1" <-> "NH2" Residue "Q ARG 419": "NH1" <-> "NH2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 18": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R ARG 103": "NH1" <-> "NH2" Residue "R ARG 120": "NH1" <-> "NH2" Residue "R TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 281": "NH1" <-> "NH2" Residue "R ARG 407": "NH1" <-> "NH2" Residue "R ARG 419": "NH1" <-> "NH2" Residue "M PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 57": "OD1" <-> "OD2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 21": "NH1" <-> "NH2" Residue "N ARG 103": "NH1" <-> "NH2" Residue "N ARG 120": "NH1" <-> "NH2" Residue "N ARG 281": "NH1" <-> "NH2" Residue "N ARG 362": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34356 Number of models: 1 Model: "" Number of chains: 24 Chain: "K" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "S" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "G" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "H" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "I" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "J" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "B" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "D" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "T" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "Q" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "A" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "F" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "C" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "E" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "P" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "R" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "L" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "M" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "N" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "O" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.76, per 1000 atoms: 0.52 Number of scatterers: 34356 At special positions: 0 Unit cell: (209.88, 158.4, 217.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 268 16.00 O 6468 8.00 N 5880 7.00 C 21736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=65, symmetry=0 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 29 " - pdb=" SG CYS H 42 " distance=2.03 Simple disulfide: pdb=" SG CYS H 37 " - pdb=" SG CYS H 55 " distance=1.25 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 64 " distance=2.03 Simple disulfide: pdb=" SG CYS I 7 " - pdb=" SG CYS I 16 " distance=2.03 Simple disulfide: pdb=" SG CYS J-981 " - pdb=" SG CYS J-877 " distance=2.03 Simple disulfide: pdb=" SG CYS J-978 " - pdb=" SG CYS J-973 " distance=2.03 Simple disulfide: pdb=" SG CYS J-910 " - pdb=" SG CYS J-896 " distance=2.02 Simple disulfide: pdb=" SG CYS J-849 " - pdb=" SG CYS J-734 " distance=2.03 Simple disulfide: pdb=" SG CYS J-800 " - pdb=" SG CYS J-774 " distance=2.03 Simple disulfide: pdb=" SG CYS J-798 " - pdb=" SG CYS J-780 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.04 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.02 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 42 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 55 " distance=2.00 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 64 " distance=2.03 Simple disulfide: pdb=" SG CYS T 7 " - pdb=" SG CYS T 16 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 123 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 27 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 90 " - pdb=" SG CYS Q 104 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 151 " - pdb=" SG CYS Q 266 " distance=1.56 Simple disulfide: pdb=" SG CYS Q 200 " - pdb=" SG CYS Q 226 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 202 " - pdb=" SG CYS Q 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 42 " distance=2.03 Simple disulfide: pdb=" SG CYS E 37 " - pdb=" SG CYS E 55 " distance=1.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 64 " distance=2.03 Simple disulfide: pdb=" SG CYS P 7 " - pdb=" SG CYS P 16 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 123 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 27 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 151 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 200 " - pdb=" SG CYS R 226 " distance=2.03 Simple disulfide: pdb=" SG CYS R 202 " - pdb=" SG CYS R 220 " distance=2.03 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Simple disulfide: pdb=" SG CYS M 29 " - pdb=" SG CYS M 42 " distance=2.03 Simple disulfide: pdb=" SG CYS M 37 " - pdb=" SG CYS M 55 " distance=1.09 Simple disulfide: pdb=" SG CYS M 49 " - pdb=" SG CYS M 64 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 123 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 90 " - pdb=" SG CYS N 104 " distance=2.02 Simple disulfide: pdb=" SG CYS N 151 " - pdb=" SG CYS N 266 " distance=2.03 Simple disulfide: pdb=" SG CYS N 200 " - pdb=" SG CYS N 226 " distance=2.02 Simple disulfide: pdb=" SG CYS N 202 " - pdb=" SG CYS N 220 " distance=2.02 Simple disulfide: pdb=" SG CYS O 62 " - pdb=" SG CYS O 94 " distance=2.04 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 259 " - pdb=" SG CYS O 271 " distance=2.03 Simple disulfide: pdb=" SG CYS O 301 " - pdb=" SG CYS O 376 " distance=2.03 Simple disulfide: pdb=" SG CYS O 306 " - pdb=" SG CYS O 380 " distance=2.03 Simple disulfide: pdb=" SG CYS O 328 " - pdb=" SG CYS O 370 " distance=2.03 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: 14.26 Conformation dependent library (CDL) restraints added in 7.5 seconds 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8264 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 95 sheets defined 16.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'K' and resid 113 through 123 removed outlier: 3.802A pdb=" N ARG K 117 " --> pdb=" O GLY K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 164 removed outlier: 3.874A pdb=" N ALA K 164 " --> pdb=" O ASP K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 185 removed outlier: 3.590A pdb=" N ARG K 185 " --> pdb=" O GLN K 182 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 123 Processing helix chain 'S' and resid 159 through 164 removed outlier: 3.873A pdb=" N ALA S 164 " --> pdb=" O ASP S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 185 removed outlier: 3.591A pdb=" N ARG S 185 " --> pdb=" O GLN S 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 289 through 293 removed outlier: 3.586A pdb=" N GLU G 292 " --> pdb=" O ARG G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 439 removed outlier: 4.758A pdb=" N SER G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA G 418 " --> pdb=" O LEU G 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 55 through 62 removed outlier: 4.434A pdb=" N SER H 59 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP H 60 " --> pdb=" O ASP H 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.968A pdb=" N VAL I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN I 37 " --> pdb=" O MET I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 52 removed outlier: 4.545A pdb=" N LYS I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) Processing helix chain 'J' and resid -998 through -993 Processing helix chain 'J' and resid -920 through -918 No H-bonds generated for 'chain 'J' and resid -920 through -918' Processing helix chain 'J' and resid -825 through -823 No H-bonds generated for 'chain 'J' and resid -825 through -823' Processing helix chain 'J' and resid -778 through -776 No H-bonds generated for 'chain 'J' and resid -778 through -776' Processing helix chain 'J' and resid -649 through -637 removed outlier: 3.785A pdb=" N VAL J-645 " --> pdb=" O LEU J-649 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE J-644 " --> pdb=" O PRO J-648 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR J-643 " --> pdb=" O HIS J-647 " (cutoff:3.500A) Processing helix chain 'J' and resid -637 through -602 removed outlier: 3.863A pdb=" N ILE J-632 " --> pdb=" O PRO J-636 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU J-631 " --> pdb=" O MET J-635 " (cutoff:3.500A) Processing helix chain 'J' and resid -591 through -584 Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 256 through 259 removed outlier: 3.542A pdb=" N CYS B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 259' Processing helix chain 'B' and resid 404 through 438 removed outlier: 4.834A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'T' and resid 28 through 37 removed outlier: 4.098A pdb=" N VAL T 36 " --> pdb=" O ALA T 32 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN T 37 " --> pdb=" O MET T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 52 removed outlier: 3.655A pdb=" N LEU T 46 " --> pdb=" O GLY T 42 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS T 52 " --> pdb=" O GLU T 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 8 through 12 removed outlier: 3.533A pdb=" N THR Q 12 " --> pdb=" O TYR Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 222 through 224 No H-bonds generated for 'chain 'Q' and resid 222 through 224' Processing helix chain 'Q' and resid 354 through 363 Processing helix chain 'Q' and resid 363 through 402 removed outlier: 3.773A pdb=" N ILE Q 368 " --> pdb=" O PRO Q 364 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU Q 369 " --> pdb=" O MET Q 365 " (cutoff:3.500A) Proline residue: Q 399 - end of helix Processing helix chain 'Q' and resid 409 through 416 Processing helix chain 'A' and resid 114 through 127 removed outlier: 4.094A pdb=" N MET A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASP A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.858A pdb=" N ALA A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 removed outlier: 4.239A pdb=" N ALA A 186 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 126 removed outlier: 4.743A pdb=" N ASP F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.648A pdb=" N ALA F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.566A pdb=" N ARG F 185 " --> pdb=" O GLN F 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 256 through 259 removed outlier: 3.730A pdb=" N CYS C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 259' Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.662A pdb=" N LEU C 286 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE C 287 " --> pdb=" O ASP C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 287' Processing helix chain 'C' and resid 404 through 439 removed outlier: 3.665A pdb=" N LEU C 414 " --> pdb=" O LEU C 410 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N SER C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 55 through 62 removed outlier: 3.901A pdb=" N SER E 59 " --> pdb=" O PHE E 56 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASP E 60 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS E 62 " --> pdb=" O SER E 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 37 removed outlier: 3.592A pdb=" N VAL P 36 " --> pdb=" O ALA P 32 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN P 37 " --> pdb=" O MET P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 52 removed outlier: 4.206A pdb=" N LYS P 52 " --> pdb=" O GLU P 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 7 Processing helix chain 'R' and resid 8 through 12 Processing helix chain 'R' and resid 80 through 82 No H-bonds generated for 'chain 'R' and resid 80 through 82' Processing helix chain 'R' and resid 222 through 224 No H-bonds generated for 'chain 'R' and resid 222 through 224' Processing helix chain 'R' and resid 352 through 363 removed outlier: 3.736A pdb=" N ILE R 356 " --> pdb=" O PRO R 352 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR R 357 " --> pdb=" O HIS R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 363 through 398 removed outlier: 3.862A pdb=" N ILE R 368 " --> pdb=" O PRO R 364 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU R 369 " --> pdb=" O MET R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 401 No H-bonds generated for 'chain 'R' and resid 399 through 401' Processing helix chain 'R' and resid 410 through 416 Processing helix chain 'L' and resid 26 through 37 removed outlier: 3.785A pdb=" N THR L 30 " --> pdb=" O LYS L 26 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU L 31 " --> pdb=" O PRO L 27 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL L 36 " --> pdb=" O ALA L 32 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN L 37 " --> pdb=" O MET L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 52 removed outlier: 4.141A pdb=" N LYS L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 48 No H-bonds generated for 'chain 'M' and resid 46 through 48' Processing helix chain 'M' and resid 55 through 59 removed outlier: 3.973A pdb=" N SER M 59 " --> pdb=" O PHE M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 5 Processing helix chain 'N' and resid 6 through 11 Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'N' and resid 351 through 363 removed outlier: 3.805A pdb=" N VAL N 355 " --> pdb=" O LEU N 351 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE N 356 " --> pdb=" O PRO N 352 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR N 357 " --> pdb=" O HIS N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 402 removed outlier: 3.515A pdb=" N THR N 367 " --> pdb=" O TYR N 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE N 368 " --> pdb=" O PRO N 364 " (cutoff:3.500A) Proline residue: N 399 - end of helix removed outlier: 3.616A pdb=" N LEU N 402 " --> pdb=" O THR N 398 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 415 removed outlier: 4.118A pdb=" N VAL N 414 " --> pdb=" O PHE N 410 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 246 Processing helix chain 'O' and resid 250 through 255 Processing helix chain 'O' and resid 256 through 259 removed outlier: 3.502A pdb=" N CYS O 259 " --> pdb=" O PRO O 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 256 through 259' Processing helix chain 'O' and resid 283 through 287 removed outlier: 3.572A pdb=" N LEU O 286 " --> pdb=" O PRO O 283 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE O 287 " --> pdb=" O ASP O 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 283 through 287' Processing helix chain 'O' and resid 289 through 293 removed outlier: 3.582A pdb=" N GLU O 292 " --> pdb=" O ARG O 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 403 through 415 removed outlier: 3.900A pdb=" N LEU O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 439 Processing sheet with id=AA1, first strand: chain 'K' and resid 135 through 139 removed outlier: 5.658A pdb=" N ILE K 136 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU K 132 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY K 138 " --> pdb=" O ILE K 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 141 through 143 Processing sheet with id=AA3, first strand: chain 'K' and resid 168 through 170 Processing sheet with id=AA4, first strand: chain 'K' and resid 190 through 191 removed outlier: 6.705A pdb=" N LYS K 190 " --> pdb=" O VAL K 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 198 through 202 removed outlier: 8.494A pdb=" N ALA K 206 " --> pdb=" O PRO K 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 213 through 217 current: chain 'K' and resid 239 through 245 removed outlier: 6.157A pdb=" N VAL K 241 " --> pdb=" O VAL K 256 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL K 256 " --> pdb=" O VAL K 241 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.656A pdb=" N ILE S 136 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU S 132 " --> pdb=" O ILE S 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY S 138 " --> pdb=" O ILE S 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 141 through 143 Processing sheet with id=AA8, first strand: chain 'S' and resid 168 through 170 Processing sheet with id=AA9, first strand: chain 'S' and resid 190 through 191 removed outlier: 6.706A pdb=" N LYS S 190 " --> pdb=" O VAL S 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'S' and resid 198 through 202 removed outlier: 8.495A pdb=" N ALA S 206 " --> pdb=" O PRO S 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 213 through 217 current: chain 'S' and resid 239 through 245 removed outlier: 6.157A pdb=" N VAL S 241 " --> pdb=" O VAL S 256 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL S 256 " --> pdb=" O VAL S 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AB3, first strand: chain 'G' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 27 through 31 current: chain 'G' and resid 119 through 137 removed outlier: 3.505A pdb=" N THR G 144 " --> pdb=" O LEU G 133 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 141 through 147 current: chain 'G' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 183 through 186 current: chain 'G' and resid 267 through 269 Processing sheet with id=AB4, first strand: chain 'G' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 55 current: chain 'G' and resid 101 through 110 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AB6, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AB7, first strand: chain 'G' and resid 296 through 306 removed outlier: 5.337A pdb=" N ALA G 298 " --> pdb=" O SER G 321 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER G 321 " --> pdb=" O ALA G 298 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE G 315 " --> pdb=" O ASN G 304 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 327 through 329 Processing sheet with id=AB9, first strand: chain 'G' and resid 364 through 367 Processing sheet with id=AC1, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AC2, first strand: chain 'H' and resid 34 through 36 Processing sheet with id=AC3, first strand: chain 'I' and resid 6 through 8 removed outlier: 3.616A pdb=" N PHE I 14 " --> pdb=" O CYS I 7 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid -983 through -981 Processing sheet with id=AC5, first strand: chain 'J' and resid -967 through -963 removed outlier: 6.587A pdb=" N GLN J-952 " --> pdb=" O GLU J-966 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL J-964 " --> pdb=" O ARG J-954 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG J-954 " --> pdb=" O VAL J-964 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N SER J-950 " --> pdb=" O ASP J-931 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASP J-931 " --> pdb=" O SER J-950 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR J-935 " --> pdb=" O GLY J-946 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid -917 through -915 removed outlier: 3.504A pdb=" N ILE J-890 " --> pdb=" O VAL J-875 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid -853 through -851 Processing sheet with id=AC8, first strand: chain 'J' and resid -848 through -846 Processing sheet with id=AC9, first strand: chain 'J' and resid -763 through -762 removed outlier: 3.534A pdb=" N VAL J-763 " --> pdb=" O HIS J-832 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY J-747 " --> pdb=" O MET J-833 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid -821 through -819 Processing sheet with id=AD2, first strand: chain 'J' and resid -804 through -800 removed outlier: 3.983A pdb=" N LEU J-803 " --> pdb=" O TYR J-771 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid -725 through -721 Processing sheet with id=AD4, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AD5, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AD6, first strand: chain 'B' and resid 16 through 19 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 27 through 31 current: chain 'B' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 141 through 147 current: chain 'B' and resid 183 through 185 Processing sheet with id=AD7, first strand: chain 'B' and resid 51 through 61 removed outlier: 4.751A pdb=" N LYS B 105 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL B 103 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE B 60 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR B 101 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AD9, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AE1, first strand: chain 'B' and resid 260 through 262 Processing sheet with id=AE2, first strand: chain 'B' and resid 300 through 306 removed outlier: 6.306A pdb=" N ILE B 315 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 343 through 344 removed outlier: 3.647A pdb=" N CYS B 328 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AE5, first strand: chain 'D' and resid 34 through 36 Processing sheet with id=AE6, first strand: chain 'T' and resid 6 through 8 removed outlier: 3.516A pdb=" N PHE T 14 " --> pdb=" O CYS T 7 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 17 through 19 Processing sheet with id=AE8, first strand: chain 'Q' and resid 33 through 37 removed outlier: 6.624A pdb=" N GLN Q 48 " --> pdb=" O GLU Q 34 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL Q 36 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG Q 46 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N SER Q 50 " --> pdb=" O ASP Q 69 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP Q 69 " --> pdb=" O SER Q 50 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR Q 65 " --> pdb=" O GLY Q 54 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 82 through 85 Processing sheet with id=AF1, first strand: chain 'Q' and resid 148 through 151 Processing sheet with id=AF2, first strand: chain 'Q' and resid 237 through 238 removed outlier: 3.786A pdb=" N GLY Q 253 " --> pdb=" O MET Q 167 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Q' and resid 179 through 181 removed outlier: 4.120A pdb=" N VAL Q 186 " --> pdb=" O PHE Q 217 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 206 through 208 Processing sheet with id=AF5, first strand: chain 'Q' and resid 275 through 279 Processing sheet with id=AF6, first strand: chain 'A' and resid 128 through 129 removed outlier: 7.733A pdb=" N TYR A 139 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 143 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 198 through 202 removed outlier: 8.099A pdb=" N ALA A 206 " --> pdb=" O PRO A 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 214 through 217 current: chain 'A' and resid 239 through 247 removed outlier: 7.859A pdb=" N ALA A 239 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N TRP A 258 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL A 241 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 256 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 243 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 250 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 146 through 148 removed outlier: 3.640A pdb=" N VAL F 143 " --> pdb=" O LYS F 146 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU F 132 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY F 138 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 190 through 191 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 190 through 191 current: chain 'F' and resid 205 through 209 removed outlier: 8.538A pdb=" N ALA F 206 " --> pdb=" O PRO F 217 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 214 through 217 current: chain 'F' and resid 236 through 246 removed outlier: 5.774A pdb=" N VAL F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL F 256 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 2 through 8 Processing sheet with id=AG2, first strand: chain 'C' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 27 through 31 current: chain 'C' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 141 through 147 current: chain 'C' and resid 183 through 185 Processing sheet with id=AG3, first strand: chain 'C' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 55 current: chain 'C' and resid 101 through 110 No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.698A pdb=" N GLY C 91 " --> pdb=" O MET C 88 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AG6, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AG7, first strand: chain 'C' and resid 300 through 306 removed outlier: 6.405A pdb=" N ILE C 315 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AG9, first strand: chain 'C' and resid 364 through 369 Processing sheet with id=AH1, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AH2, first strand: chain 'E' and resid 34 through 36 Processing sheet with id=AH3, first strand: chain 'P' and resid 6 through 7 Processing sheet with id=AH4, first strand: chain 'R' and resid 17 through 19 Processing sheet with id=AH5, first strand: chain 'R' and resid 33 through 37 removed outlier: 6.795A pdb=" N GLN R 48 " --> pdb=" O GLU R 34 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL R 36 " --> pdb=" O ARG R 46 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG R 46 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N SER R 50 " --> pdb=" O ASP R 69 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ASP R 69 " --> pdb=" O SER R 50 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'R' and resid 83 through 85 Processing sheet with id=AH7, first strand: chain 'R' and resid 147 through 154 Processing sheet with id=AH8, first strand: chain 'R' and resid 237 through 238 removed outlier: 3.629A pdb=" N GLY R 253 " --> pdb=" O MET R 167 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'R' and resid 179 through 181 removed outlier: 3.879A pdb=" N VAL R 186 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL R 188 " --> pdb=" O LYS R 215 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'R' and resid 206 through 211 removed outlier: 3.563A pdb=" N LYS R 206 " --> pdb=" O CYS R 200 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU R 197 " --> pdb=" O TYR R 229 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'R' and resid 275 through 279 Processing sheet with id=AI3, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AI4, first strand: chain 'M' and resid 34 through 36 Processing sheet with id=AI5, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.928A pdb=" N CYS N 27 " --> pdb=" O CYS N 19 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 35 through 37 removed outlier: 9.536A pdb=" N SER N 50 " --> pdb=" O ASP N 69 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP N 69 " --> pdb=" O SER N 50 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'N' and resid 83 through 85 Processing sheet with id=AI8, first strand: chain 'N' and resid 147 through 154 Processing sheet with id=AI9, first strand: chain 'N' and resid 237 through 238 Processing sheet with id=AJ1, first strand: chain 'N' and resid 173 through 174 removed outlier: 3.714A pdb=" N GLU N 173 " --> pdb=" O ARG N 230 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU N 197 " --> pdb=" O TYR N 229 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 179 through 181 removed outlier: 3.684A pdb=" N VAL N 186 " --> pdb=" O PHE N 217 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'N' and resid 275 through 279 Processing sheet with id=AJ4, first strand: chain 'N' and resid 307 through 311 Processing sheet with id=AJ5, first strand: chain 'O' and resid 2 through 8 Processing sheet with id=AJ6, first strand: chain 'O' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 27 through 42 current: chain 'O' and resid 119 through 137 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 141 through 147 current: chain 'O' and resid 183 through 185 Processing sheet with id=AJ7, first strand: chain 'O' and resid 51 through 55 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 51 through 55 current: chain 'O' and resid 101 through 110 No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'O' and resid 87 through 88 removed outlier: 3.889A pdb=" N GLY O 91 " --> pdb=" O MET O 88 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'O' and resid 203 through 205 Processing sheet with id=AK1, first strand: chain 'O' and resid 220 through 221 Processing sheet with id=AK2, first strand: chain 'O' and resid 260 through 262 Processing sheet with id=AK3, first strand: chain 'O' and resid 296 through 306 removed outlier: 5.012A pdb=" N ALA O 298 " --> pdb=" O SER O 321 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER O 321 " --> pdb=" O ALA O 298 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE O 315 " --> pdb=" O ASN O 304 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY O 350 " --> pdb=" O TYR O 320 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'O' and resid 326 through 328 Processing sheet with id=AK5, first strand: chain 'O' and resid 364 through 369 1017 hydrogen bonds defined for protein. 2625 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: 13.77 Time building geometry restraints manager: 15.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11020 1.34 - 1.46: 8594 1.46 - 1.59: 15277 1.59 - 1.72: 1 1.72 - 1.84: 352 Bond restraints: 35244 Sorted by residual: bond pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 1.526 1.614 -0.089 1.08e-02 8.57e+03 6.74e+01 bond pdb=" C ASP N 175 " pdb=" O ASP N 175 " ideal model delta sigma weight residual 1.235 1.310 -0.076 1.21e-02 6.83e+03 3.90e+01 bond pdb=" N VAL N 179 " pdb=" CA VAL N 179 " ideal model delta sigma weight residual 1.457 1.528 -0.071 1.32e-02 5.74e+03 2.89e+01 bond pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 1.525 1.589 -0.065 1.22e-02 6.72e+03 2.81e+01 bond pdb=" N ASP N 175 " pdb=" CA ASP N 175 " ideal model delta sigma weight residual 1.464 1.505 -0.041 1.25e-02 6.40e+03 1.09e+01 ... (remaining 35239 not shown) Histogram of bond angle deviations from ideal: 96.91 - 107.50: 2032 107.50 - 118.10: 24998 118.10 - 128.69: 20633 128.69 - 139.29: 304 139.29 - 149.89: 1 Bond angle restraints: 47968 Sorted by residual: angle pdb=" N PRO R 409 " pdb=" CA PRO R 409 " pdb=" C PRO R 409 " ideal model delta sigma weight residual 112.47 149.89 -37.42 2.06e+00 2.36e-01 3.30e+02 angle pdb=" N PHE R 410 " pdb=" CA PHE R 410 " pdb=" CB PHE R 410 " ideal model delta sigma weight residual 110.49 132.06 -21.57 1.69e+00 3.50e-01 1.63e+02 angle pdb=" N LYS D 58 " pdb=" CA LYS D 58 " pdb=" C LYS D 58 " ideal model delta sigma weight residual 111.39 123.03 -11.64 1.38e+00 5.25e-01 7.12e+01 angle pdb=" N ASP N 175 " pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 107.44 123.32 -15.88 1.93e+00 2.68e-01 6.77e+01 angle pdb=" N LYS H 58 " pdb=" CA LYS H 58 " pdb=" C LYS H 58 " ideal model delta sigma weight residual 111.54 120.31 -8.77 1.36e+00 5.41e-01 4.16e+01 ... (remaining 47963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 20397 17.61 - 35.22: 671 35.22 - 52.82: 141 52.82 - 70.43: 30 70.43 - 88.04: 8 Dihedral angle restraints: 21247 sinusoidal: 8347 harmonic: 12900 Sorted by residual: dihedral pdb=" N PRO R 409 " pdb=" C PRO R 409 " pdb=" CA PRO R 409 " pdb=" CB PRO R 409 " ideal model delta harmonic sigma weight residual 115.10 155.01 -39.91 0 2.50e+00 1.60e-01 2.55e+02 dihedral pdb=" C PRO R 409 " pdb=" N PRO R 409 " pdb=" CA PRO R 409 " pdb=" CB PRO R 409 " ideal model delta harmonic sigma weight residual -120.70 -155.06 34.36 0 2.50e+00 1.60e-01 1.89e+02 dihedral pdb=" N PHE R 410 " pdb=" C PHE R 410 " pdb=" CA PHE R 410 " pdb=" CB PHE R 410 " ideal model delta harmonic sigma weight residual 122.80 157.11 -34.31 0 2.50e+00 1.60e-01 1.88e+02 ... (remaining 21244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.403: 5310 0.403 - 0.806: 4 0.806 - 1.209: 0 1.209 - 1.612: 1 1.612 - 2.015: 1 Chirality restraints: 5316 Sorted by residual: chirality pdb=" CA PRO R 409 " pdb=" N PRO R 409 " pdb=" C PRO R 409 " pdb=" CB PRO R 409 " both_signs ideal model delta sigma weight residual False 2.72 0.70 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CA PHE R 410 " pdb=" N PHE R 410 " pdb=" C PHE R 410 " pdb=" CB PHE R 410 " both_signs ideal model delta sigma weight residual False 2.51 1.15 1.36 2.00e-01 2.50e+01 4.63e+01 chirality pdb=" CA LYS D 58 " pdb=" N LYS D 58 " pdb=" C LYS D 58 " pdb=" CB LYS D 58 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 5313 not shown) Planarity restraints: 6196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 264 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO C 265 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 265 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 265 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN O 264 " 0.066 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO O 265 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO O 265 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO O 265 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J-764 " 0.039 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP J-764 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP J-764 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP J-764 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J-764 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP J-764 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J-764 " -0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP J-764 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP J-764 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP J-764 " 0.018 2.00e-02 2.50e+03 ... (remaining 6193 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 146 2.52 - 3.11: 23006 3.11 - 3.71: 49451 3.71 - 4.30: 70655 4.30 - 4.90: 120782 Nonbonded interactions: 264040 Sorted by model distance: nonbonded pdb=" OH TYR K 173 " pdb=" NE2 GLN O 439 " model vdw 1.924 2.520 nonbonded pdb=" NZ LYS K 156 " pdb=" OE2 GLU A 133 " model vdw 2.002 2.520 nonbonded pdb=" OG SER J-823 " pdb=" OD1 ASP D 57 " model vdw 2.091 2.440 nonbonded pdb=" O ASN O 442 " pdb=" ND2 ASN O 442 " model vdw 2.111 2.520 nonbonded pdb=" O HIS G 441 " pdb=" OXT ASN G 442 " model vdw 2.236 3.040 ... (remaining 264035 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 'F' selection = chain 'K' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'P' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'N' selection = chain 'Q' selection = chain 'R' } 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: 2.760 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: 11.890 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 93.310 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 35244 Z= 0.491 Angle : 0.959 37.415 47968 Z= 0.529 Chirality : 0.068 2.015 5316 Planarity : 0.008 0.102 6196 Dihedral : 9.593 88.037 12788 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.65 % Favored : 93.22 % Rotamer: Outliers : 0.40 % Allowed : 2.52 % Favored : 97.08 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.11), residues: 4408 helix: -2.14 (0.17), residues: 548 sheet: -1.70 (0.13), residues: 1429 loop : -2.51 (0.10), residues: 2431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP J-764 HIS 0.011 0.002 HIS N 28 PHE 0.032 0.004 PHE Q 328 TYR 0.039 0.003 TYR C 308 ARG 0.015 0.001 ARG Q 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 801 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 159 ASN cc_start: 0.4531 (t0) cc_final: 0.4241 (t160) REVERT: K 193 HIS cc_start: 0.6886 (p-80) cc_final: 0.6531 (p90) REVERT: K 215 THR cc_start: 0.6433 (p) cc_final: 0.6000 (p) REVERT: K 270 GLU cc_start: 0.6727 (tt0) cc_final: 0.6342 (pm20) REVERT: S 256 VAL cc_start: 0.5820 (m) cc_final: 0.5526 (m) REVERT: S 261 LYS cc_start: 0.6548 (mmtt) cc_final: 0.6270 (mtmm) REVERT: S 266 LYS cc_start: 0.6495 (tttm) cc_final: 0.5909 (tmtp) REVERT: G 212 ASP cc_start: 0.7539 (t0) cc_final: 0.7314 (p0) REVERT: B 29 ILE cc_start: 0.7555 (mt) cc_final: 0.7203 (mm) REVERT: B 369 ILE cc_start: 0.8473 (tt) cc_final: 0.8267 (tt) REVERT: T 23 TYR cc_start: 0.6250 (t80) cc_final: 0.5677 (t80) REVERT: Q 112 MET cc_start: 0.8772 (ttm) cc_final: 0.8383 (ttm) REVERT: A 148 PHE cc_start: 0.8275 (m-10) cc_final: 0.8072 (m-80) REVERT: R 360 TYR cc_start: 0.8474 (t80) cc_final: 0.8181 (t80) REVERT: N 9 TYR cc_start: 0.8366 (m-80) cc_final: 0.8107 (m-80) REVERT: N 42 ASP cc_start: 0.7649 (m-30) cc_final: 0.7348 (m-30) REVERT: N 112 MET cc_start: 0.9013 (ttm) cc_final: 0.8793 (ttp) REVERT: N 365 MET cc_start: 0.7668 (ttt) cc_final: 0.7355 (pmt) REVERT: O 115 LEU cc_start: 0.8481 (tm) cc_final: 0.8263 (mm) REVERT: O 442 ASN cc_start: 0.6350 (OUTLIER) cc_final: 0.6017 (t0) outliers start: 15 outliers final: 4 residues processed: 809 average time/residue: 1.4967 time to fit residues: 1436.6992 Evaluate side-chains 416 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 411 time to evaluate : 4.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 442 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 368 optimal weight: 5.9990 chunk 330 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 222 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 341 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 254 optimal weight: 3.9990 chunk 395 optimal weight: 0.9980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 HIS G 235 GLN G 264 ASN G 304 ASN G 394 HIS G 396 GLN G 439 GLN H 27 ASN H 30 ASN J-848 GLN J-744 HIS J-647 HIS J-639 HIS B 10 GLN B 43 ASN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN D 27 ASN D 30 ASN ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 160 ASN Q 212 ASN Q 225 GLN Q 232 GLN Q 239 ASN ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 353 HIS F 203 HIS C 130 GLN C 235 GLN C 360 ASN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN C 439 GLN C 442 ASN E 27 ASN ** R 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 159 GLN ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 347 ASN R 361 HIS R 405 ASN M 27 ASN M 30 ASN N 7 ASN N 52 GLN N 96 HIS N 353 HIS O 3 HIS ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 386 HIS O 392 GLN O 394 HIS O 439 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35244 Z= 0.273 Angle : 0.640 11.230 47968 Z= 0.334 Chirality : 0.046 0.266 5316 Planarity : 0.006 0.090 6196 Dihedral : 6.402 160.178 4819 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 3.48 % Allowed : 11.26 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.05 % 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: -2.02 (0.12), residues: 4408 helix: 0.04 (0.22), residues: 538 sheet: -1.08 (0.13), residues: 1443 loop : -1.85 (0.12), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP J-764 HIS 0.008 0.001 HIS N 256 PHE 0.024 0.002 PHE A 189 TYR 0.023 0.002 TYR O 308 ARG 0.006 0.001 ARG J-912 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 463 time to evaluate : 3.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 118 MET cc_start: 0.6002 (ptt) cc_final: 0.5091 (tpp) REVERT: K 193 HIS cc_start: 0.6751 (p-80) cc_final: 0.6493 (p90) REVERT: K 270 GLU cc_start: 0.6682 (tt0) cc_final: 0.6317 (pm20) REVERT: S 131 MET cc_start: 0.6113 (mmm) cc_final: 0.5636 (mpt) REVERT: G 10 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: G 52 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8370 (tttp) REVERT: G 305 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6782 (mt-10) REVERT: H 57 ASP cc_start: 0.6724 (p0) cc_final: 0.6474 (p0) REVERT: J -775 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8435 (mt0) REVERT: J -687 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6936 (mm-30) REVERT: J -609 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7161 (ttm170) REVERT: B 97 ASP cc_start: 0.7644 (m-30) cc_final: 0.7376 (m-30) REVERT: B 207 THR cc_start: 0.7950 (m) cc_final: 0.7692 (t) REVERT: B 433 MET cc_start: 0.6457 (pp-130) cc_final: 0.5710 (ptp) REVERT: T 23 TYR cc_start: 0.6247 (t80) cc_final: 0.5480 (t80) REVERT: Q 130 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8579 (pttp) REVERT: Q 213 LYS cc_start: 0.7136 (mttt) cc_final: 0.6926 (mmtp) REVERT: A 118 MET cc_start: 0.6065 (pmt) cc_final: 0.5643 (pmt) REVERT: C 140 HIS cc_start: 0.7234 (m90) cc_final: 0.7000 (m90) REVERT: C 188 ASP cc_start: 0.8365 (t0) cc_final: 0.8030 (t70) REVERT: C 300 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7096 (pt0) REVERT: R 79 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7584 (tp) REVERT: R 360 TYR cc_start: 0.8588 (t80) cc_final: 0.8240 (t80) REVERT: R 377 ILE cc_start: 0.8783 (mt) cc_final: 0.8477 (mm) REVERT: N 66 MET cc_start: 0.9150 (ttt) cc_final: 0.8886 (ttt) REVERT: N 365 MET cc_start: 0.7828 (ttt) cc_final: 0.7591 (pmt) REVERT: O 2 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8066 (mm-30) REVERT: O 24 TYR cc_start: 0.8350 (m-80) cc_final: 0.8070 (m-80) REVERT: O 73 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7459 (mtp180) REVERT: O 175 ARG cc_start: 0.7734 (ttt-90) cc_final: 0.7350 (ttp-110) REVERT: O 246 ASP cc_start: 0.8204 (m-30) cc_final: 0.7919 (m-30) REVERT: O 442 ASN cc_start: 0.6714 (OUTLIER) cc_final: 0.6444 (t0) outliers start: 131 outliers final: 43 residues processed: 534 average time/residue: 1.3529 time to fit residues: 872.8635 Evaluate side-chains 430 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 375 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain J residue -826 VAL Chi-restraints excluded: chain J residue -775 GLN Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 302 ASP Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 73 ARG Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 433 MET Chi-restraints excluded: chain O residue 442 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 220 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 329 optimal weight: 7.9990 chunk 269 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 396 optimal weight: 4.9990 chunk 428 optimal weight: 2.9990 chunk 353 optimal weight: 5.9990 chunk 393 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 318 optimal weight: 6.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN C 394 HIS C 396 GLN C 439 GLN R 96 HIS ** R 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN N 152 GLN ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 35244 Z= 0.328 Angle : 0.647 13.600 47968 Z= 0.334 Chirality : 0.047 0.459 5316 Planarity : 0.006 0.092 6196 Dihedral : 5.722 74.266 4813 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.49 % Favored : 94.35 % Rotamer: Outliers : 4.30 % Allowed : 12.73 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.07 % 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: -1.54 (0.12), residues: 4408 helix: 0.55 (0.23), residues: 569 sheet: -0.75 (0.13), residues: 1455 loop : -1.61 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP J-764 HIS 0.009 0.002 HIS O 386 PHE 0.022 0.002 PHE R 6 TYR 0.028 0.002 TYR O 308 ARG 0.008 0.001 ARG Q 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 399 time to evaluate : 4.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 226 SER cc_start: 0.4890 (t) cc_final: 0.4590 (m) REVERT: K 270 GLU cc_start: 0.6645 (tt0) cc_final: 0.6296 (pm20) REVERT: G 52 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8309 (tttp) REVERT: H 57 ASP cc_start: 0.6690 (p0) cc_final: 0.6387 (p0) REVERT: J -687 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6880 (mm-30) REVERT: J -609 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7033 (ttm170) REVERT: B 282 ILE cc_start: 0.7044 (OUTLIER) cc_final: 0.6693 (tp) REVERT: D 61 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7025 (mm-30) REVERT: T 23 TYR cc_start: 0.6296 (t80) cc_final: 0.5572 (t80) REVERT: Q 74 ILE cc_start: 0.8622 (mt) cc_final: 0.8368 (mp) REVERT: Q 130 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8591 (pttp) REVERT: Q 137 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7197 (mt-10) REVERT: Q 213 LYS cc_start: 0.7380 (mttt) cc_final: 0.7170 (mmtp) REVERT: Q 255 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8487 (mt) REVERT: A 118 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5343 (pmt) REVERT: A 184 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6540 (mpt) REVERT: F 119 VAL cc_start: 0.7155 (t) cc_final: 0.6878 (p) REVERT: F 257 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6616 (ptm) REVERT: C 115 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8208 (tp) REVERT: C 160 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7569 (mttm) REVERT: C 188 ASP cc_start: 0.8422 (t0) cc_final: 0.8139 (t70) REVERT: C 206 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8083 (tpt170) REVERT: R 79 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7701 (tp) REVERT: R 323 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: R 360 TYR cc_start: 0.8557 (t80) cc_final: 0.8231 (t80) REVERT: R 377 ILE cc_start: 0.8780 (mt) cc_final: 0.8552 (mm) REVERT: N 66 MET cc_start: 0.9156 (ttt) cc_final: 0.8891 (ttt) REVERT: N 365 MET cc_start: 0.7923 (ttt) cc_final: 0.7547 (pmt) REVERT: O 2 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: O 18 ILE cc_start: 0.8644 (pt) cc_final: 0.8263 (pp) REVERT: O 24 TYR cc_start: 0.8640 (m-80) cc_final: 0.8343 (m-80) REVERT: O 175 ARG cc_start: 0.7956 (ttt-90) cc_final: 0.7544 (ttp-110) REVERT: O 442 ASN cc_start: 0.6726 (OUTLIER) cc_final: 0.6439 (t0) outliers start: 162 outliers final: 63 residues processed: 506 average time/residue: 1.3199 time to fit residues: 814.5513 Evaluate side-chains 442 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 362 time to evaluate : 4.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 184 MET Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain S residue 126 LYS Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 LYS Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 207 ILE Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain R residue 382 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 442 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 391 optimal weight: 0.9990 chunk 298 optimal weight: 20.0000 chunk 205 optimal weight: 4.9990 chunk 43 optimal weight: 0.0270 chunk 189 optimal weight: 0.7980 chunk 266 optimal weight: 1.9990 chunk 398 optimal weight: 3.9990 chunk 421 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 377 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 203 HIS ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 360 ASN B 394 HIS Q 60 ASN ** Q 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 121 HIS O 130 GLN O 235 GLN ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35244 Z= 0.175 Angle : 0.569 9.959 47968 Z= 0.293 Chirality : 0.044 0.403 5316 Planarity : 0.005 0.071 6196 Dihedral : 5.333 75.542 4813 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.76 % Favored : 95.12 % Rotamer: Outliers : 3.43 % Allowed : 14.19 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.02 % 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: -1.15 (0.13), residues: 4408 helix: 0.94 (0.23), residues: 575 sheet: -0.46 (0.13), residues: 1439 loop : -1.40 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.001 TRP J-764 HIS 0.004 0.001 HIS R 156 PHE 0.015 0.001 PHE A 148 TYR 0.024 0.001 TYR R 363 ARG 0.004 0.000 ARG G 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 405 time to evaluate : 3.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 118 MET cc_start: 0.5736 (ptt) cc_final: 0.5468 (ppp) REVERT: K 226 SER cc_start: 0.4888 (t) cc_final: 0.4284 (m) REVERT: K 270 GLU cc_start: 0.6631 (tt0) cc_final: 0.6275 (pm20) REVERT: G 52 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8231 (tttp) REVERT: G 305 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6991 (mt-10) REVERT: H 57 ASP cc_start: 0.6594 (p0) cc_final: 0.6301 (p0) REVERT: I 33 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6893 (ttp) REVERT: J -687 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6822 (mm-30) REVERT: J -609 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7062 (ttm170) REVERT: B 433 MET cc_start: 0.6730 (pp-130) cc_final: 0.5872 (ptm) REVERT: T 23 TYR cc_start: 0.6233 (t80) cc_final: 0.5477 (t80) REVERT: Q 4 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6864 (tm-30) REVERT: Q 74 ILE cc_start: 0.8553 (mt) cc_final: 0.8251 (mp) REVERT: Q 130 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8500 (mtmm) REVERT: Q 255 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8481 (mt) REVERT: A 118 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.5806 (pmm) REVERT: A 184 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6503 (mpt) REVERT: A 265 VAL cc_start: 0.8045 (t) cc_final: 0.7833 (p) REVERT: C 115 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7929 (tp) REVERT: C 160 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7658 (mttm) REVERT: C 188 ASP cc_start: 0.8397 (t0) cc_final: 0.8099 (t70) REVERT: C 206 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7999 (tpt170) REVERT: C 289 ARG cc_start: 0.7536 (mtm110) cc_final: 0.7317 (mtm110) REVERT: R 6 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.7156 (t80) REVERT: R 79 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7635 (tp) REVERT: R 197 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7605 (pt) REVERT: R 360 TYR cc_start: 0.8479 (t80) cc_final: 0.8160 (t80) REVERT: R 377 ILE cc_start: 0.8746 (mt) cc_final: 0.8510 (mm) REVERT: R 398 THR cc_start: 0.6073 (m) cc_final: 0.5733 (m) REVERT: N 66 MET cc_start: 0.9092 (ttt) cc_final: 0.8783 (ttt) REVERT: N 365 MET cc_start: 0.7807 (ttt) cc_final: 0.7494 (pmt) REVERT: O 2 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7676 (mm-30) REVERT: O 24 TYR cc_start: 0.8597 (m-80) cc_final: 0.8286 (m-80) REVERT: O 175 ARG cc_start: 0.7989 (ttt-90) cc_final: 0.7563 (ttp-110) outliers start: 129 outliers final: 52 residues processed: 489 average time/residue: 1.3445 time to fit residues: 802.4567 Evaluate side-chains 429 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 361 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 168 LYS Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 257 MET Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain J residue -826 VAL Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 233 ASN Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 365 MET Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 167 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 350 optimal weight: 0.0570 chunk 239 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 313 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 359 optimal weight: 0.6980 chunk 291 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 215 optimal weight: 4.9990 chunk 378 optimal weight: 0.0470 chunk 106 optimal weight: 3.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 439 GLN Q 60 ASN ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 358 HIS O 235 GLN O 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35244 Z= 0.206 Angle : 0.575 9.572 47968 Z= 0.295 Chirality : 0.045 0.460 5316 Planarity : 0.005 0.068 6196 Dihedral : 5.238 76.724 4811 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.08 % Favored : 94.80 % Rotamer: Outliers : 3.96 % Allowed : 14.93 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 4408 helix: 1.15 (0.24), residues: 579 sheet: -0.36 (0.14), residues: 1439 loop : -1.30 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP J-764 HIS 0.005 0.001 HIS R 156 PHE 0.015 0.001 PHE R 217 TYR 0.022 0.001 TYR O 308 ARG 0.009 0.000 ARG Q 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 366 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 118 MET cc_start: 0.5944 (ptt) cc_final: 0.5636 (ppp) REVERT: K 226 SER cc_start: 0.4715 (t) cc_final: 0.4420 (m) REVERT: K 270 GLU cc_start: 0.6355 (tt0) cc_final: 0.6056 (pm20) REVERT: G 52 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8199 (ttpt) REVERT: G 370 CYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6406 (m) REVERT: H 57 ASP cc_start: 0.6534 (p0) cc_final: 0.6237 (p0) REVERT: J -709 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8100 (p0) REVERT: J -687 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6733 (mm-30) REVERT: J -609 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.7033 (ttm170) REVERT: J -588 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7471 (mp) REVERT: B 305 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.5963 (mt-10) REVERT: B 433 MET cc_start: 0.6714 (pp-130) cc_final: 0.6496 (ppp) REVERT: T 23 TYR cc_start: 0.6229 (t80) cc_final: 0.5646 (t80) REVERT: Q 4 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: Q 74 ILE cc_start: 0.8562 (mt) cc_final: 0.8267 (mp) REVERT: Q 130 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8506 (mtmm) REVERT: Q 137 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7169 (mt-10) REVERT: Q 255 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8448 (mt) REVERT: A 118 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6230 (pmm) REVERT: A 184 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.6255 (mpt) REVERT: A 265 VAL cc_start: 0.8049 (t) cc_final: 0.7833 (p) REVERT: C 115 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7965 (tp) REVERT: C 188 ASP cc_start: 0.8413 (t0) cc_final: 0.8106 (t70) REVERT: C 206 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8018 (tpt170) REVERT: R 6 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7337 (t80) REVERT: R 8 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6676 (mt-10) REVERT: R 79 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7826 (tp) REVERT: R 197 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7554 (pt) REVERT: R 323 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: R 360 TYR cc_start: 0.8513 (t80) cc_final: 0.8227 (t80) REVERT: R 377 ILE cc_start: 0.8760 (mt) cc_final: 0.8541 (mm) REVERT: R 397 LEU cc_start: 0.7805 (mt) cc_final: 0.7428 (mp) REVERT: R 398 THR cc_start: 0.6232 (m) cc_final: 0.5870 (m) REVERT: N 20 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7176 (mp) REVERT: N 66 MET cc_start: 0.9141 (ttt) cc_final: 0.8878 (ttt) REVERT: N 160 ASN cc_start: 0.6904 (t0) cc_final: 0.6672 (t0) REVERT: N 365 MET cc_start: 0.7816 (ttt) cc_final: 0.7498 (pmt) REVERT: O 2 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: O 18 ILE cc_start: 0.8637 (pt) cc_final: 0.8345 (pp) REVERT: O 24 TYR cc_start: 0.8642 (m-80) cc_final: 0.8267 (m-80) REVERT: O 144 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8581 (p) REVERT: O 175 ARG cc_start: 0.7970 (ttt-90) cc_final: 0.7550 (ttp-110) outliers start: 149 outliers final: 65 residues processed: 466 average time/residue: 1.3115 time to fit residues: 747.9454 Evaluate side-chains 436 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 348 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 168 LYS Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -826 VAL Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -709 ASN Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain J residue -588 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 365 MET Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 400 TYR Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 304 ASN Chi-restraints excluded: chain O residue 327 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 141 optimal weight: 20.0000 chunk 379 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 247 optimal weight: 30.0000 chunk 104 optimal weight: 6.9990 chunk 421 optimal weight: 0.0020 chunk 350 optimal weight: 0.0170 chunk 195 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 221 optimal weight: 8.9990 overall best weight: 1.4032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 60 ASN Q 233 ASN ** Q 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 225 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35244 Z= 0.190 Angle : 0.570 10.710 47968 Z= 0.291 Chirality : 0.044 0.466 5316 Planarity : 0.005 0.068 6196 Dihedral : 5.168 77.698 4811 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.69 % Rotamer: Outliers : 3.75 % Allowed : 15.28 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4408 helix: 1.55 (0.24), residues: 551 sheet: -0.22 (0.14), residues: 1424 loop : -1.17 (0.12), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP J-764 HIS 0.004 0.001 HIS R 156 PHE 0.021 0.001 PHE R 217 TYR 0.024 0.001 TYR R 363 ARG 0.007 0.000 ARG Q 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 364 time to evaluate : 3.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 118 MET cc_start: 0.6068 (ptt) cc_final: 0.5787 (ppp) REVERT: K 226 SER cc_start: 0.4713 (t) cc_final: 0.4460 (m) REVERT: K 270 GLU cc_start: 0.6341 (tt0) cc_final: 0.6049 (pm20) REVERT: G 10 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7533 (tt0) REVERT: G 52 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8192 (ttpt) REVERT: G 319 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7972 (ttmt) REVERT: G 370 CYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6442 (m) REVERT: H 57 ASP cc_start: 0.6790 (p0) cc_final: 0.6469 (p0) REVERT: J -775 GLN cc_start: 0.8634 (mt0) cc_final: 0.8402 (mt0) REVERT: J -709 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8104 (p0) REVERT: J -687 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6576 (mm-30) REVERT: J -609 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.7025 (ttm170) REVERT: B 29 ILE cc_start: 0.7771 (mt) cc_final: 0.7546 (mm) REVERT: B 282 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7032 (tp) REVERT: B 305 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.5901 (mt-10) REVERT: T 23 TYR cc_start: 0.6276 (t80) cc_final: 0.5679 (t80) REVERT: Q 4 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: Q 74 ILE cc_start: 0.8560 (mt) cc_final: 0.8277 (mp) REVERT: Q 108 ASP cc_start: 0.8004 (p0) cc_final: 0.7736 (p0) REVERT: Q 130 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8508 (mtmm) REVERT: Q 137 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: Q 255 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8508 (mt) REVERT: Q 291 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7427 (p0) REVERT: A 118 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6336 (pmm) REVERT: A 120 MET cc_start: 0.6220 (pmm) cc_final: 0.5681 (pmm) REVERT: A 184 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.6274 (mpt) REVERT: A 265 VAL cc_start: 0.8044 (t) cc_final: 0.7832 (p) REVERT: C 72 TYR cc_start: 0.8332 (m-80) cc_final: 0.8022 (m-80) REVERT: C 115 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7956 (tp) REVERT: C 160 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7830 (mtmt) REVERT: C 188 ASP cc_start: 0.8405 (t0) cc_final: 0.8104 (t70) REVERT: C 206 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7990 (tpt170) REVERT: R 8 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6932 (mt-10) REVERT: R 197 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7545 (pt) REVERT: R 323 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: R 360 TYR cc_start: 0.8517 (t80) cc_final: 0.8215 (t80) REVERT: R 377 ILE cc_start: 0.8754 (mt) cc_final: 0.8546 (mm) REVERT: R 397 LEU cc_start: 0.7877 (mt) cc_final: 0.7467 (mp) REVERT: R 398 THR cc_start: 0.6334 (m) cc_final: 0.5950 (m) REVERT: N 66 MET cc_start: 0.9142 (ttt) cc_final: 0.8893 (ttt) REVERT: N 365 MET cc_start: 0.7934 (ttt) cc_final: 0.7574 (pmt) REVERT: O 2 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: O 18 ILE cc_start: 0.8612 (pt) cc_final: 0.8341 (pp) REVERT: O 24 TYR cc_start: 0.8669 (m-80) cc_final: 0.8309 (m-80) REVERT: O 175 ARG cc_start: 0.7965 (ttt-90) cc_final: 0.7558 (ttp-110) REVERT: O 247 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7582 (mtmp) outliers start: 141 outliers final: 80 residues processed: 462 average time/residue: 1.2961 time to fit residues: 732.6265 Evaluate side-chains 442 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 340 time to evaluate : 4.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 LYS Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 257 MET Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -875 VAL Chi-restraints excluded: chain J residue -826 VAL Chi-restraints excluded: chain J residue -759 ASP Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -709 ASN Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 130 LYS Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 365 MET Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 302 ASP Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 400 TYR Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 247 LYS Chi-restraints excluded: chain O residue 304 ASN Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 406 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 308 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 chunk 355 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 420 optimal weight: 0.9990 chunk 262 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 349 GLN J-920 HIS J-919 GLN J-642 HIS ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 HIS B 392 GLN B 396 GLN Q 60 ASN Q 233 ASN Q 288 HIS A 203 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35244 Z= 0.277 Angle : 0.607 10.988 47968 Z= 0.311 Chirality : 0.046 0.474 5316 Planarity : 0.005 0.067 6196 Dihedral : 5.281 80.055 4811 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.63 % Favored : 94.26 % Rotamer: Outliers : 3.85 % Allowed : 15.73 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 4408 helix: 1.58 (0.24), residues: 556 sheet: -0.26 (0.14), residues: 1362 loop : -1.11 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP J-764 HIS 0.011 0.001 HIS C 441 PHE 0.023 0.002 PHE R 217 TYR 0.024 0.002 TYR C 373 ARG 0.007 0.001 ARG N 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 344 time to evaluate : 3.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 118 MET cc_start: 0.6294 (ptt) cc_final: 0.5946 (ppp) REVERT: K 270 GLU cc_start: 0.6294 (tt0) cc_final: 0.6022 (pm20) REVERT: G 10 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7575 (tt0) REVERT: G 52 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8175 (ttpt) REVERT: G 370 CYS cc_start: 0.6781 (OUTLIER) cc_final: 0.6265 (m) REVERT: H 57 ASP cc_start: 0.6899 (p0) cc_final: 0.6569 (p0) REVERT: J -709 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8114 (p0) REVERT: J -687 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6619 (mm-30) REVERT: J -609 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.7028 (ttm170) REVERT: J -588 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7476 (mp) REVERT: B 282 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.6981 (tp) REVERT: B 433 MET cc_start: 0.6433 (ppp) cc_final: 0.5348 (ptm) REVERT: T 23 TYR cc_start: 0.6252 (t80) cc_final: 0.5732 (t80) REVERT: Q 4 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: Q 74 ILE cc_start: 0.8384 (mt) cc_final: 0.8095 (mp) REVERT: Q 108 ASP cc_start: 0.8044 (p0) cc_final: 0.7748 (p0) REVERT: Q 137 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: Q 255 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8556 (mt) REVERT: Q 291 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.7551 (p0) REVERT: A 118 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6316 (pmm) REVERT: A 120 MET cc_start: 0.6324 (OUTLIER) cc_final: 0.5883 (pmm) REVERT: A 168 LYS cc_start: 0.7263 (mtmm) cc_final: 0.6755 (mtmm) REVERT: A 184 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.6330 (mpt) REVERT: A 265 VAL cc_start: 0.8048 (t) cc_final: 0.7816 (p) REVERT: C 72 TYR cc_start: 0.8350 (m-80) cc_final: 0.8042 (m-80) REVERT: C 115 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7981 (tp) REVERT: C 160 LYS cc_start: 0.8089 (ttmt) cc_final: 0.7645 (mttm) REVERT: C 188 ASP cc_start: 0.8365 (t0) cc_final: 0.8056 (t70) REVERT: C 206 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8044 (tpt170) REVERT: C 289 ARG cc_start: 0.7642 (ttp80) cc_final: 0.7187 (ttp80) REVERT: R 8 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: R 323 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: R 360 TYR cc_start: 0.8478 (t80) cc_final: 0.8240 (t80) REVERT: R 377 ILE cc_start: 0.8766 (mt) cc_final: 0.8559 (mm) REVERT: R 388 LEU cc_start: 0.7681 (tp) cc_final: 0.7420 (tp) REVERT: R 397 LEU cc_start: 0.7975 (mt) cc_final: 0.7554 (mp) REVERT: R 398 THR cc_start: 0.6455 (m) cc_final: 0.6129 (m) REVERT: N 66 MET cc_start: 0.9172 (ttp) cc_final: 0.8929 (ttt) REVERT: N 187 THR cc_start: 0.8238 (m) cc_final: 0.7912 (p) REVERT: N 365 MET cc_start: 0.7976 (ttt) cc_final: 0.7595 (pmt) REVERT: O 2 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: O 18 ILE cc_start: 0.8666 (pt) cc_final: 0.8391 (pp) REVERT: O 24 TYR cc_start: 0.8722 (m-80) cc_final: 0.8355 (m-80) REVERT: O 175 ARG cc_start: 0.7917 (ttt-90) cc_final: 0.7586 (ttp-110) REVERT: O 246 ASP cc_start: 0.7864 (m-30) cc_final: 0.7610 (m-30) REVERT: O 247 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7673 (mtmp) outliers start: 145 outliers final: 83 residues processed: 448 average time/residue: 1.2509 time to fit residues: 689.1800 Evaluate side-chains 431 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 327 time to evaluate : 4.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain S residue 126 LYS Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 LYS Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain S residue 257 MET Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 52 LYS Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -875 VAL Chi-restraints excluded: chain J residue -759 ASP Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -709 ASN Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain J residue -588 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 365 MET Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 247 LYS Chi-restraints excluded: chain O residue 304 ASN Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 259 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 267 optimal weight: 7.9990 chunk 286 optimal weight: 6.9990 chunk 207 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 330 optimal weight: 6.9990 overall best weight: 3.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J-919 GLN J-840 ASN ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 ASN B 386 HIS Q 60 ASN A 159 ASN R 232 GLN O 130 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 35244 Z= 0.338 Angle : 0.635 11.880 47968 Z= 0.326 Chirality : 0.047 0.454 5316 Planarity : 0.005 0.074 6196 Dihedral : 5.455 80.992 4811 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.76 % Favored : 94.12 % Rotamer: Outliers : 3.35 % Allowed : 16.74 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4408 helix: 1.58 (0.24), residues: 553 sheet: -0.30 (0.14), residues: 1389 loop : -1.12 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP J-764 HIS 0.007 0.001 HIS O 386 PHE 0.021 0.002 PHE R 217 TYR 0.029 0.002 TYR C 373 ARG 0.006 0.001 ARG N 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 344 time to evaluate : 4.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 118 MET cc_start: 0.6289 (ptt) cc_final: 0.5944 (ppp) REVERT: K 270 GLU cc_start: 0.6216 (tt0) cc_final: 0.5951 (pm20) REVERT: S 131 MET cc_start: 0.6107 (mmm) cc_final: 0.5571 (mpt) REVERT: G 10 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: G 370 CYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6351 (m) REVERT: H 57 ASP cc_start: 0.6981 (p0) cc_final: 0.6675 (p0) REVERT: J -709 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.7919 (p0) REVERT: J -687 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6634 (mm-30) REVERT: J -609 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7061 (ttm170) REVERT: J -588 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7603 (mp) REVERT: B 7 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7803 (ptt) REVERT: B 282 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.6994 (tp) REVERT: D 63 GLU cc_start: 0.7157 (mp0) cc_final: 0.6904 (tp30) REVERT: Q 4 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: Q 74 ILE cc_start: 0.8455 (mt) cc_final: 0.8194 (mp) REVERT: Q 137 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: Q 255 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8556 (mt) REVERT: Q 291 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.7661 (p0) REVERT: A 118 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6475 (pmm) REVERT: A 120 MET cc_start: 0.6360 (OUTLIER) cc_final: 0.5862 (pmm) REVERT: A 168 LYS cc_start: 0.7332 (mtmm) cc_final: 0.6838 (mtmm) REVERT: A 265 VAL cc_start: 0.8101 (t) cc_final: 0.7822 (p) REVERT: F 151 MET cc_start: 0.6066 (mpm) cc_final: 0.5815 (mmt) REVERT: C 72 TYR cc_start: 0.8375 (m-80) cc_final: 0.8065 (m-80) REVERT: C 115 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8021 (tp) REVERT: C 160 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7677 (mttm) REVERT: C 188 ASP cc_start: 0.8384 (t0) cc_final: 0.8075 (t70) REVERT: C 206 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8104 (tpt170) REVERT: C 411 THR cc_start: 0.8670 (m) cc_final: 0.8334 (p) REVERT: R 6 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7822 (t80) REVERT: R 8 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: R 323 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: R 360 TYR cc_start: 0.8544 (t80) cc_final: 0.8223 (t80) REVERT: R 377 ILE cc_start: 0.8763 (mt) cc_final: 0.8554 (mm) REVERT: R 397 LEU cc_start: 0.7891 (mt) cc_final: 0.7496 (mp) REVERT: N 20 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8065 (mp) REVERT: N 66 MET cc_start: 0.9189 (ttp) cc_final: 0.8926 (ttt) REVERT: N 187 THR cc_start: 0.8219 (m) cc_final: 0.7871 (p) REVERT: N 365 MET cc_start: 0.7983 (ttt) cc_final: 0.7554 (pmt) REVERT: O 2 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: O 18 ILE cc_start: 0.8681 (pt) cc_final: 0.8405 (pp) REVERT: O 175 ARG cc_start: 0.7917 (ttt-90) cc_final: 0.7591 (ttp-110) REVERT: O 247 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7779 (mtmp) outliers start: 126 outliers final: 81 residues processed: 433 average time/residue: 1.2781 time to fit residues: 681.3397 Evaluate side-chains 426 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 323 time to evaluate : 3.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 LYS Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -875 VAL Chi-restraints excluded: chain J residue -759 ASP Chi-restraints excluded: chain J residue -745 LEU Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -709 ASN Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -609 ARG Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain J residue -588 LEU Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 365 MET Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 247 LYS Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 382 optimal weight: 3.9990 chunk 402 optimal weight: 0.7980 chunk 367 optimal weight: 7.9990 chunk 391 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 chunk 307 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 353 optimal weight: 7.9990 chunk 370 optimal weight: 5.9990 chunk 390 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J-647 HIS ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 60 ASN C 396 GLN R 159 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35244 Z= 0.310 Angle : 0.629 11.478 47968 Z= 0.322 Chirality : 0.046 0.446 5316 Planarity : 0.005 0.070 6196 Dihedral : 5.418 80.054 4811 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.74 % Favored : 94.17 % Rotamer: Outliers : 3.32 % Allowed : 16.92 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.13), residues: 4408 helix: 1.57 (0.24), residues: 559 sheet: -0.22 (0.14), residues: 1367 loop : -1.16 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP J-764 HIS 0.007 0.001 HIS O 386 PHE 0.020 0.002 PHE R 217 TYR 0.028 0.002 TYR C 373 ARG 0.006 0.001 ARG N 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 344 time to evaluate : 4.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 118 MET cc_start: 0.6295 (ptt) cc_final: 0.5954 (ppp) REVERT: S 131 MET cc_start: 0.6190 (mmm) cc_final: 0.5572 (mpt) REVERT: G 10 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: G 370 CYS cc_start: 0.6813 (OUTLIER) cc_final: 0.6348 (m) REVERT: H 57 ASP cc_start: 0.6989 (p0) cc_final: 0.6694 (p0) REVERT: J -709 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.7907 (p0) REVERT: J -687 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6600 (mm-30) REVERT: J -588 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7763 (mp) REVERT: B 7 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7716 (ptt) REVERT: B 282 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.6912 (tp) REVERT: B 433 MET cc_start: 0.6549 (ppp) cc_final: 0.5774 (ptm) REVERT: Q 4 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: Q 137 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: Q 255 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8543 (mt) REVERT: Q 291 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.7707 (p0) REVERT: A 118 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6466 (pmm) REVERT: A 120 MET cc_start: 0.6425 (OUTLIER) cc_final: 0.5929 (pmm) REVERT: A 131 MET cc_start: 0.7110 (tpt) cc_final: 0.6709 (tpt) REVERT: A 168 LYS cc_start: 0.7324 (mtmm) cc_final: 0.6831 (mtmm) REVERT: F 151 MET cc_start: 0.6569 (mpm) cc_final: 0.6326 (mmt) REVERT: C 72 TYR cc_start: 0.8345 (m-80) cc_final: 0.7992 (m-80) REVERT: C 115 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7993 (tp) REVERT: C 160 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7642 (mttm) REVERT: C 188 ASP cc_start: 0.8497 (t0) cc_final: 0.8198 (t70) REVERT: C 206 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8106 (tpt170) REVERT: C 411 THR cc_start: 0.8700 (m) cc_final: 0.8407 (p) REVERT: R 6 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7781 (t80) REVERT: R 8 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6614 (mt-10) REVERT: R 323 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7623 (pm20) REVERT: R 360 TYR cc_start: 0.8564 (t80) cc_final: 0.8231 (t80) REVERT: R 377 ILE cc_start: 0.8762 (mt) cc_final: 0.8558 (mm) REVERT: R 397 LEU cc_start: 0.8118 (mt) cc_final: 0.7719 (mp) REVERT: N 20 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8003 (mp) REVERT: N 66 MET cc_start: 0.9184 (ttp) cc_final: 0.8852 (ttt) REVERT: N 187 THR cc_start: 0.8216 (m) cc_final: 0.7897 (p) REVERT: N 365 MET cc_start: 0.8024 (ttt) cc_final: 0.7552 (pmt) REVERT: O 2 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: O 18 ILE cc_start: 0.8679 (pt) cc_final: 0.8402 (pp) REVERT: O 175 ARG cc_start: 0.7916 (ttt-90) cc_final: 0.7602 (ttp-110) REVERT: O 247 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7865 (mtmp) outliers start: 125 outliers final: 83 residues processed: 433 average time/residue: 1.2879 time to fit residues: 685.6326 Evaluate side-chains 432 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 328 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 ARG Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain S residue 167 THR Chi-restraints excluded: chain S residue 168 LYS Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 257 MET Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain H residue 62 LYS Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -875 VAL Chi-restraints excluded: chain J residue -759 ASP Chi-restraints excluded: chain J residue -733 THR Chi-restraints excluded: chain J residue -709 ASN Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain J residue -604 CYS Chi-restraints excluded: chain J residue -588 LEU Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 137 GLU Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain Q residue 263 ASP Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 303 GLU Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 365 MET Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 291 ASN Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 82 THR Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 247 LYS Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 257 optimal weight: 0.9990 chunk 414 optimal weight: 2.9990 chunk 252 optimal weight: 0.5980 chunk 196 optimal weight: 0.0470 chunk 287 optimal weight: 7.9990 chunk 434 optimal weight: 1.9990 chunk 399 optimal weight: 4.9990 chunk 345 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 212 optimal weight: 9.9990 overall best weight: 0.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN ** K 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J-647 HIS B 3 HIS ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 60 ASN Q 132 ASN C 368 GLN C 441 HIS O 130 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 35244 Z= 0.164 Angle : 0.579 13.316 47968 Z= 0.294 Chirality : 0.044 0.444 5316 Planarity : 0.005 0.073 6196 Dihedral : 5.129 77.868 4811 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.01 % Favored : 94.87 % Rotamer: Outliers : 2.52 % Allowed : 17.96 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 4408 helix: 1.55 (0.24), residues: 572 sheet: -0.10 (0.14), residues: 1353 loop : -1.09 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP J-764 HIS 0.007 0.001 HIS R 168 PHE 0.017 0.001 PHE K 214 TYR 0.036 0.001 TYR C 373 ARG 0.006 0.000 ARG Q 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8816 Ramachandran restraints generated. 4408 Oldfield, 0 Emsley, 4408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 353 time to evaluate : 4.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 118 MET cc_start: 0.6266 (ptt) cc_final: 0.5923 (ppp) REVERT: S 131 MET cc_start: 0.6202 (mmm) cc_final: 0.5582 (mpt) REVERT: G 370 CYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6248 (m) REVERT: H 57 ASP cc_start: 0.6894 (p0) cc_final: 0.6594 (p0) REVERT: J -687 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6566 (mm-30) REVERT: B 7 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7752 (ptt) REVERT: B 282 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7028 (tp) REVERT: Q 4 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: Q 74 ILE cc_start: 0.8401 (mt) cc_final: 0.8107 (mp) REVERT: Q 108 ASP cc_start: 0.7993 (p0) cc_final: 0.7728 (p0) REVERT: Q 255 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8513 (mt) REVERT: Q 291 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7482 (p0) REVERT: A 118 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6491 (pmm) REVERT: A 120 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.5933 (pmm) REVERT: A 168 LYS cc_start: 0.7186 (mtmm) cc_final: 0.6721 (mtmm) REVERT: C 115 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7973 (tp) REVERT: C 160 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7778 (mtmt) REVERT: C 188 ASP cc_start: 0.8342 (t0) cc_final: 0.8025 (t70) REVERT: C 206 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8021 (tpt170) REVERT: E 43 ILE cc_start: 0.9203 (pt) cc_final: 0.8992 (pt) REVERT: R 6 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7670 (t80) REVERT: R 197 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7507 (pt) REVERT: R 360 TYR cc_start: 0.8530 (t80) cc_final: 0.8189 (t80) REVERT: R 377 ILE cc_start: 0.8752 (mt) cc_final: 0.8551 (mm) REVERT: R 397 LEU cc_start: 0.7925 (mt) cc_final: 0.7532 (mp) REVERT: R 398 THR cc_start: 0.7420 (m) cc_final: 0.7095 (m) REVERT: N 66 MET cc_start: 0.9187 (ttp) cc_final: 0.8943 (ttt) REVERT: N 187 THR cc_start: 0.8327 (m) cc_final: 0.7987 (p) REVERT: N 365 MET cc_start: 0.8024 (ttt) cc_final: 0.7570 (pmt) REVERT: O 2 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: O 18 ILE cc_start: 0.8585 (pt) cc_final: 0.8325 (pp) REVERT: O 24 TYR cc_start: 0.8696 (m-80) cc_final: 0.8353 (m-80) REVERT: O 175 ARG cc_start: 0.7893 (ttt-90) cc_final: 0.7578 (ttp-110) outliers start: 95 outliers final: 62 residues processed: 424 average time/residue: 1.2899 time to fit residues: 674.4687 Evaluate side-chains 409 residues out of total 3764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 333 time to evaluate : 4.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 161 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 63 CYS Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain J residue -934 MET Chi-restraints excluded: chain J residue -875 VAL Chi-restraints excluded: chain J residue -687 GLU Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 407 TRP Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain Q residue 4 GLU Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 148 GLU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 194 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain Q residue 208 SER Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain Q residue 255 LEU Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 357 THR Chi-restraints excluded: chain Q residue 365 MET Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain F residue 256 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 6 PHE Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 213 LYS Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 233 ASN Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 2 GLU Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 274 optimal weight: 4.9990 chunk 368 optimal weight: 8.9990 chunk 105 optimal weight: 0.0370 chunk 318 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 346 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 355 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 208 GLN S 116 GLN J-647 HIS B 3 HIS ** B 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN Q 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.174593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118635 restraints weight = 46009.244| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.33 r_work: 0.3197 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35244 Z= 0.178 Angle : 0.577 12.821 47968 Z= 0.292 Chirality : 0.044 0.443 5316 Planarity : 0.005 0.072 6196 Dihedral : 5.056 77.396 4811 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.69 % Rotamer: Outliers : 2.39 % Allowed : 18.52 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.71 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4408 helix: 1.65 (0.24), residues: 571 sheet: -0.03 (0.14), residues: 1368 loop : -1.04 (0.12), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP J-764 HIS 0.008 0.001 HIS R 168 PHE 0.014 0.001 PHE B 365 TYR 0.030 0.001 TYR C 373 ARG 0.007 0.000 ARG C 366 =============================================================================== Job complete usr+sys time: 13302.70 seconds wall clock time: 236 minutes 49.46 seconds (14209.46 seconds total)