Starting phenix.real_space_refine on Sun Mar 17 22:17:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eeu_28058/03_2024/8eeu_28058.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eeu_28058/03_2024/8eeu_28058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eeu_28058/03_2024/8eeu_28058.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eeu_28058/03_2024/8eeu_28058.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eeu_28058/03_2024/8eeu_28058.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eeu_28058/03_2024/8eeu_28058.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 12093 2.51 5 N 3265 2.21 5 O 3645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 21": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "D TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 13": "NH1" <-> "NH2" Residue "F TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19127 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3067 Classifications: {'peptide': 402} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 373} Chain: "B" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2685 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 23, 'TRANS': 317} Chain breaks: 1 Chain: "C" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2969 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 359} Chain breaks: 2 Chain: "D" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2794 Classifications: {'peptide': 354} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 327} Chain breaks: 1 Chain: "E" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3025 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 367} Chain: "F" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2799 Classifications: {'peptide': 355} Link IDs: {'CIS': 1, 'PTRANS': 26, 'TRANS': 327} Chain breaks: 1 Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 975 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 98} Time building chain proxies: 9.67, per 1000 atoms: 0.51 Number of scatterers: 19127 At special positions: 0 Unit cell: (160.512, 143.616, 149.952, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 3645 8.00 N 3265 7.00 C 12093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.02 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.04 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.02 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 123 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 104 " distance=2.02 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 200 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 78 " 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 D 19 " - pdb=" SG CYS D 123 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 27 " distance=2.03 Simple disulfide: pdb=" SG CYS D 90 " - pdb=" SG CYS D 104 " distance=2.02 Simple disulfide: pdb=" SG CYS D 151 " - pdb=" SG CYS D 266 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.04 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.02 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 78 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS E 301 " - pdb=" SG CYS E 376 " distance=2.04 Simple disulfide: pdb=" SG CYS E 306 " - pdb=" SG CYS E 380 " distance=2.03 Simple disulfide: pdb=" SG CYS E 328 " - pdb=" SG CYS E 370 " distance=2.02 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 123 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 27 " distance=2.02 Simple disulfide: pdb=" SG CYS F 90 " - pdb=" SG CYS F 104 " distance=2.02 Simple disulfide: pdb=" SG CYS F 151 " - pdb=" SG CYS F 266 " distance=2.03 Simple disulfide: pdb=" SG CYS F 200 " - pdb=" SG CYS F 226 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 100E" distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.69 Conformation dependent library (CDL) restraints added in 3.4 seconds 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 70 sheets defined 3.0% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.518A pdb=" N GLN C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 removed outlier: 4.087A pdb=" N LEU C 286 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.846A 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 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 355 through 362 removed outlier: 3.765A pdb=" N TYR D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 116 removed outlier: 4.511A pdb=" N LEU E 115 " --> pdb=" O ASP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 283 through 287 Processing helix chain 'E' and resid 289 through 293 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.643A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 5.402A pdb=" N ILE A 31 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A 134 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 35 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER A 128 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 48 removed outlier: 7.006A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA A 119 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 155 removed outlier: 3.591A pdb=" N LYS A 160 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 281 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA8, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AB1, first strand: chain 'A' and resid 338 through 339 removed outlier: 6.390A pdb=" N THR A 317 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU A 303 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LYS A 319 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N CYS A 301 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A 301 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS A 377 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 303 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AB3, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB4, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AB5, first strand: chain 'B' and resid 33 through 37 removed outlier: 6.136A pdb=" N ARG B 103 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE B 92 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 52 through 55 removed outlier: 6.471A pdb=" N THR B 65 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AB8, first strand: chain 'B' and resid 147 through 154 Processing sheet with id=AB9, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AC1, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.776A pdb=" N SER B 195 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS B 206 " --> pdb=" O CYS B 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AC3, first strand: chain 'B' and resid 275 through 279 Processing sheet with id=AC4, first strand: chain 'C' and resid 3 through 8 removed outlier: 4.019A pdb=" N THR C 5 " --> pdb=" O LEU C 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 15 through 17 Processing sheet with id=AC6, first strand: chain 'C' and resid 35 through 48 removed outlier: 4.015A pdb=" N LYS C 35 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR C 41 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR C 126 " --> pdb=" O THR C 41 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASN C 43 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ALA C 124 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU C 45 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR C 122 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 47 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU C 120 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 35 through 48 removed outlier: 4.015A pdb=" N LYS C 35 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR C 41 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR C 126 " --> pdb=" O THR C 41 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASN C 43 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ALA C 124 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU C 45 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR C 122 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 47 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU C 120 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.659A pdb=" N ALA C 59 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AD1, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AD2, first strand: chain 'C' and resid 154 through 155 removed outlier: 3.699A pdb=" N VAL C 154 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 203 through 205 Processing sheet with id=AD4, first strand: chain 'C' and resid 260 through 262 Processing sheet with id=AD5, first strand: chain 'C' and resid 302 through 306 removed outlier: 6.367A pdb=" N ILE C 315 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 364 through 368 Processing sheet with id=AD7, first strand: chain 'D' and resid 17 through 19 removed outlier: 3.902A pdb=" N CYS D 19 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS D 27 " --> pdb=" O CYS D 19 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 33 through 37 removed outlier: 7.705A pdb=" N ILE D 33 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER D 50 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N SER D 50 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASP D 69 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR D 65 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR D 68 " --> pdb=" O LYS D 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 33 through 37 removed outlier: 7.705A pdb=" N ILE D 33 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER D 50 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N TYR D 98 " --> pdb=" O THR D 49 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N SER D 51 " --> pdb=" O HIS D 96 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N HIS D 96 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N TYR D 53 " --> pdb=" O ASP D 94 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N ASP D 94 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 15.009A pdb=" N LEU D 55 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 16.913A pdb=" N ILE D 92 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 83 through 85 Processing sheet with id=AE2, first strand: chain 'D' and resid 147 through 154 Processing sheet with id=AE3, first strand: chain 'D' and resid 164 through 166 Processing sheet with id=AE4, first strand: chain 'D' and resid 173 through 175 removed outlier: 3.652A pdb=" N GLU D 173 " --> pdb=" O ARG D 230 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 228 " --> pdb=" O ASP D 175 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 179 through 180 Processing sheet with id=AE6, first strand: chain 'D' and resid 275 through 279 removed outlier: 3.643A pdb=" N VAL D 283 " --> pdb=" O PHE D 319 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA D 315 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 307 through 311 Processing sheet with id=AE8, first strand: chain 'E' and resid 2 through 8 removed outlier: 3.785A pdb=" N THR E 5 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 278 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 15 through 19 removed outlier: 5.480A pdb=" N ILE E 31 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR E 136 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN E 134 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS E 35 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 39 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR E 41 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR E 126 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN E 43 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ALA E 124 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU E 45 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR E 122 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL E 47 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU E 120 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 15 through 19 removed outlier: 5.480A pdb=" N ILE E 31 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR E 136 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN E 134 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS E 35 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 39 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR E 41 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR E 126 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ASN E 43 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ALA E 124 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU E 45 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR E 122 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL E 47 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU E 120 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 51 through 55 Processing sheet with id=AF3, first strand: chain 'E' and resid 51 through 55 Processing sheet with id=AF4, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AF5, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AF6, first strand: chain 'E' and resid 260 through 262 removed outlier: 3.928A pdb=" N ARG E 267 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 300 through 306 removed outlier: 6.661A pdb=" N ILE E 315 " --> pdb=" O ASN E 304 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 326 through 328 Processing sheet with id=AF9, first strand: chain 'E' and resid 364 through 368 Processing sheet with id=AG1, first strand: chain 'E' and resid 387 through 388 Processing sheet with id=AG2, first strand: chain 'F' and resid 33 through 37 removed outlier: 8.402A pdb=" N ILE F 33 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER F 50 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 35 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N SER F 50 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP F 69 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR F 68 " --> pdb=" O LYS F 75 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 33 through 37 removed outlier: 8.402A pdb=" N ILE F 33 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER F 50 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 35 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR F 98 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N SER F 51 " --> pdb=" O HIS F 96 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N HIS F 96 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N TYR F 53 " --> pdb=" O ASP F 94 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N ASP F 94 " --> pdb=" O TYR F 53 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 83 through 85 removed outlier: 3.696A pdb=" N SER F 109 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TYR F 127 " --> pdb=" O SER F 109 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N THR F 111 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL F 125 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLU F 113 " --> pdb=" O CYS F 123 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS F 123 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LYS F 115 " --> pdb=" O HIS F 121 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS F 121 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 147 through 154 Processing sheet with id=AG6, first strand: chain 'F' and resid 237 through 238 Processing sheet with id=AG7, first strand: chain 'F' and resid 173 through 174 removed outlier: 3.503A pdb=" N GLU F 173 " --> pdb=" O ARG F 230 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 179 through 181 Processing sheet with id=AG9, first strand: chain 'F' and resid 275 through 279 Processing sheet with id=AH1, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AH2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.218A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'H' and resid 57 through 58 removed outlier: 6.544A pdb=" N LEU H 45 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N SER H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TRP H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 97 through 100 removed outlier: 7.161A pdb=" N TYR H 100F" --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.506A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.562A pdb=" N ARG L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN L 37 " --> pdb=" O ARG L 46 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 62 through 67 removed outlier: 4.240A pdb=" N SER L 65 " --> pdb=" O THR L 72 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 7.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6199 1.34 - 1.47: 5207 1.47 - 1.59: 8082 1.59 - 1.71: 0 1.71 - 1.84: 159 Bond restraints: 19647 Sorted by residual: bond pdb=" C HIS B 28 " pdb=" N SER B 29 " ideal model delta sigma weight residual 1.329 1.256 0.073 1.86e-02 2.89e+03 1.54e+01 bond pdb=" N ARG B 13 " pdb=" CA ARG B 13 " ideal model delta sigma weight residual 1.456 1.427 0.030 1.04e-02 9.25e+03 8.13e+00 bond pdb=" CB PRO F 142 " pdb=" CG PRO F 142 " ideal model delta sigma weight residual 1.492 1.352 0.140 5.00e-02 4.00e+02 7.82e+00 bond pdb=" C VAL E 231 " pdb=" N PRO E 232 " ideal model delta sigma weight residual 1.335 1.311 0.024 8.70e-03 1.32e+04 7.57e+00 bond pdb=" N GLN C 196 " pdb=" CA GLN C 196 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.41e-02 5.03e+03 6.80e+00 ... (remaining 19642 not shown) Histogram of bond angle deviations from ideal: 98.33 - 105.53: 569 105.53 - 112.73: 10242 112.73 - 119.93: 6535 119.93 - 127.14: 9077 127.14 - 134.34: 319 Bond angle restraints: 26742 Sorted by residual: angle pdb=" N TYR F 360 " pdb=" CA TYR F 360 " pdb=" C TYR F 360 " ideal model delta sigma weight residual 113.88 107.87 6.01 1.23e+00 6.61e-01 2.39e+01 angle pdb=" N GLY D 325 " pdb=" CA GLY D 325 " pdb=" C GLY D 325 " ideal model delta sigma weight residual 110.88 117.59 -6.71 1.48e+00 4.57e-01 2.06e+01 angle pdb=" C TYR E 262 " pdb=" N THR E 263 " pdb=" CA THR E 263 " ideal model delta sigma weight residual 122.15 129.54 -7.39 1.74e+00 3.30e-01 1.81e+01 angle pdb=" C ILE A 369 " pdb=" N CYS A 370 " pdb=" CA CYS A 370 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" CA TYR F 9 " pdb=" CB TYR F 9 " pdb=" CG TYR F 9 " ideal model delta sigma weight residual 113.90 120.77 -6.87 1.80e+00 3.09e-01 1.46e+01 ... (remaining 26737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 11353 17.56 - 35.12: 386 35.12 - 52.69: 67 52.69 - 70.25: 6 70.25 - 87.81: 9 Dihedral angle restraints: 11821 sinusoidal: 4637 harmonic: 7184 Sorted by residual: dihedral pdb=" CB CYS D 19 " pdb=" SG CYS D 19 " pdb=" SG CYS D 123 " pdb=" CB CYS D 123 " ideal model delta sinusoidal sigma weight residual -86.00 -173.81 87.81 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS B 19 " pdb=" SG CYS B 19 " pdb=" SG CYS B 123 " pdb=" CB CYS B 123 " ideal model delta sinusoidal sigma weight residual -86.00 -170.94 84.94 1 1.00e+01 1.00e-02 8.75e+01 dihedral pdb=" CB CYS C 62 " pdb=" SG CYS C 62 " pdb=" SG CYS C 94 " pdb=" CB CYS C 94 " ideal model delta sinusoidal sigma weight residual -86.00 -162.15 76.15 1 1.00e+01 1.00e-02 7.30e+01 ... (remaining 11818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1615 0.040 - 0.079: 869 0.079 - 0.119: 360 0.119 - 0.158: 83 0.158 - 0.198: 8 Chirality restraints: 2935 Sorted by residual: chirality pdb=" CB ILE A 369 " pdb=" CA ILE A 369 " pdb=" CG1 ILE A 369 " pdb=" CG2 ILE A 369 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" CB VAL E 148 " pdb=" CA VAL E 148 " pdb=" CG1 VAL E 148 " pdb=" CG2 VAL E 148 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.67e-01 chirality pdb=" CB ILE F 31 " pdb=" CA ILE F 31 " pdb=" CG1 ILE F 31 " pdb=" CG2 ILE F 31 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.27e-01 ... (remaining 2932 not shown) Planarity restraints: 3462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 57 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.17e+00 pdb=" N PRO A 58 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 39 " -0.045 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO C 40 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 40 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 40 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 9 " -0.031 2.00e-02 2.50e+03 1.80e-02 6.45e+00 pdb=" CG TYR F 9 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR F 9 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR F 9 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR F 9 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 9 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR F 9 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR F 9 " -0.007 2.00e-02 2.50e+03 ... (remaining 3459 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 179 2.58 - 3.16: 15668 3.16 - 3.74: 26997 3.74 - 4.32: 38718 4.32 - 4.90: 66294 Nonbonded interactions: 147856 Sorted by model distance: nonbonded pdb=" OG1 THR D 297 " pdb=" OG1 THR D 307 " model vdw 1.997 2.440 nonbonded pdb=" O CYS B 22 " pdb=" OG SER B 122 " model vdw 2.005 2.440 nonbonded pdb=" OG SER E 309 " pdb=" OD1 ASP E 311 " model vdw 2.051 2.440 nonbonded pdb=" OG SER F 185 " pdb=" O PHE F 217 " model vdw 2.082 2.440 nonbonded pdb=" OG SER E 205 " pdb=" OG SER E 210 " model vdw 2.082 2.440 ... (remaining 147851 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 320 or resid 324 through 344 or resid 352 throug \ h 396)) selection = (chain 'C' and resid 2 through 396) selection = (chain 'E' and (resid 2 through 320 or resid 324 through 344 or resid 352 throug \ h 396)) } ncs_group { reference = (chain 'B' and resid 6 through 344) selection = (chain 'D' and (resid 6 through 201 or resid 205 through 344)) selection = (chain 'F' and (resid 6 through 201 or resid 205 through 344)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.440 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 47.720 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 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 : 0.012 0.140 19647 Z= 0.772 Angle : 0.935 8.408 26742 Z= 0.519 Chirality : 0.054 0.198 2935 Planarity : 0.008 0.067 3462 Dihedral : 9.271 75.806 7101 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.92 % Favored : 88.92 % Rotamer: Outliers : 0.05 % Allowed : 1.00 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.71 (0.14), residues: 2445 helix: -4.63 (0.24), residues: 60 sheet: -2.45 (0.15), residues: 915 loop : -3.68 (0.12), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 236 HIS 0.018 0.003 HIS D 168 PHE 0.030 0.003 PHE F 328 TYR 0.038 0.003 TYR F 9 ARG 0.014 0.002 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 824 time to evaluate : 2.214 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: A 9 SER cc_start: 0.7754 (t) cc_final: 0.7526 (t) REVERT: A 29 ILE cc_start: 0.8507 (mt) cc_final: 0.8250 (mm) REVERT: A 30 SER cc_start: 0.8029 (m) cc_final: 0.7408 (p) REVERT: A 35 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7620 (ttmm) REVERT: A 37 LYS cc_start: 0.8302 (mttt) cc_final: 0.7979 (mtmm) REVERT: A 45 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6627 (mm-30) REVERT: A 51 TYR cc_start: 0.7251 (p90) cc_final: 0.6668 (p90) REVERT: A 52 LYS cc_start: 0.8445 (ttpt) cc_final: 0.8139 (ttpp) REVERT: A 105 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7853 (mtpp) REVERT: A 111 SER cc_start: 0.7953 (t) cc_final: 0.7731 (p) REVERT: A 136 THR cc_start: 0.7292 (m) cc_final: 0.6849 (p) REVERT: A 137 VAL cc_start: 0.8122 (t) cc_final: 0.7732 (p) REVERT: A 145 THR cc_start: 0.8367 (m) cc_final: 0.8063 (t) REVERT: A 147 TYR cc_start: 0.7575 (m-10) cc_final: 0.7001 (m-80) REVERT: A 176 LYS cc_start: 0.8132 (mttt) cc_final: 0.7894 (mtpp) REVERT: A 179 GLN cc_start: 0.7775 (tt0) cc_final: 0.7412 (tt0) REVERT: A 189 PHE cc_start: 0.7878 (p90) cc_final: 0.7673 (p90) REVERT: A 238 SER cc_start: 0.7327 (t) cc_final: 0.6853 (p) REVERT: A 252 LYS cc_start: 0.8758 (tttt) cc_final: 0.8450 (ttmm) REVERT: A 269 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6838 (mt-10) REVERT: A 281 ASP cc_start: 0.7881 (t0) cc_final: 0.7545 (t0) REVERT: A 284 ASP cc_start: 0.7037 (m-30) cc_final: 0.6829 (m-30) REVERT: A 291 SER cc_start: 0.8305 (p) cc_final: 0.8031 (t) REVERT: A 308 TYR cc_start: 0.7645 (p90) cc_final: 0.7440 (p90) REVERT: A 340 LYS cc_start: 0.8151 (tttt) cc_final: 0.7928 (ttmt) REVERT: B 42 ASP cc_start: 0.5781 (p0) cc_final: 0.5510 (p0) REVERT: B 62 LYS cc_start: 0.7105 (tttt) cc_final: 0.6747 (ttmm) REVERT: B 108 ASP cc_start: 0.7311 (p0) cc_final: 0.6917 (p0) REVERT: B 115 LYS cc_start: 0.7516 (mtpt) cc_final: 0.7163 (mtpp) REVERT: B 130 LYS cc_start: 0.7694 (mtmm) cc_final: 0.7130 (mtmm) REVERT: B 164 TYR cc_start: 0.7949 (m-80) cc_final: 0.7463 (m-80) REVERT: B 192 ASP cc_start: 0.7117 (t70) cc_final: 0.6853 (t70) REVERT: B 235 LYS cc_start: 0.8338 (mmtt) cc_final: 0.8115 (mmtp) REVERT: B 254 LYS cc_start: 0.7415 (mmmt) cc_final: 0.7194 (mmmt) REVERT: B 324 LYS cc_start: 0.7698 (mtmm) cc_final: 0.7474 (mtmm) REVERT: B 336 LYS cc_start: 0.8077 (ttmt) cc_final: 0.7826 (ttmm) REVERT: C 19 VAL cc_start: 0.7959 (t) cc_final: 0.7709 (m) REVERT: C 29 ILE cc_start: 0.7984 (mt) cc_final: 0.7769 (mm) REVERT: C 35 LYS cc_start: 0.8470 (tttt) cc_final: 0.8031 (tmtt) REVERT: C 76 GLU cc_start: 0.7458 (tp30) cc_final: 0.6943 (tp30) REVERT: C 79 LYS cc_start: 0.8101 (tmtm) cc_final: 0.7424 (tmtm) REVERT: C 105 LYS cc_start: 0.7706 (ttpt) cc_final: 0.7440 (tttp) REVERT: C 107 TYR cc_start: 0.7506 (p90) cc_final: 0.7302 (p90) REVERT: C 120 GLU cc_start: 0.7540 (pt0) cc_final: 0.7273 (pt0) REVERT: C 128 SER cc_start: 0.7797 (m) cc_final: 0.6964 (p) REVERT: C 130 GLN cc_start: 0.7817 (tt0) cc_final: 0.7467 (mt0) REVERT: C 185 TYR cc_start: 0.6479 (OUTLIER) cc_final: 0.5562 (m-10) REVERT: C 220 VAL cc_start: 0.8325 (t) cc_final: 0.8073 (m) REVERT: C 244 LYS cc_start: 0.8033 (mtpm) cc_final: 0.7800 (mttm) REVERT: C 245 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7436 (mtpt) REVERT: C 246 ASP cc_start: 0.6700 (m-30) cc_final: 0.6291 (m-30) REVERT: C 254 THR cc_start: 0.8393 (p) cc_final: 0.8170 (t) REVERT: C 261 ILE cc_start: 0.8034 (mm) cc_final: 0.7791 (mm) REVERT: C 340 LYS cc_start: 0.4836 (tttt) cc_final: 0.3924 (tttp) REVERT: C 355 HIS cc_start: 0.7011 (m-70) cc_final: 0.6737 (m-70) REVERT: C 392 GLN cc_start: 0.7776 (mt0) cc_final: 0.7558 (mt0) REVERT: D 31 ILE cc_start: 0.7777 (tt) cc_final: 0.7546 (tt) REVERT: D 74 ILE cc_start: 0.8059 (mt) cc_final: 0.7859 (mt) REVERT: D 75 LYS cc_start: 0.8522 (mmtt) cc_final: 0.8183 (mttm) REVERT: D 77 ILE cc_start: 0.8299 (mt) cc_final: 0.7887 (tt) REVERT: D 83 SER cc_start: 0.7954 (m) cc_final: 0.7686 (p) REVERT: D 94 ASP cc_start: 0.6972 (t0) cc_final: 0.6645 (t0) REVERT: D 100 LEU cc_start: 0.8476 (tp) cc_final: 0.8111 (tp) REVERT: D 108 ASP cc_start: 0.7282 (m-30) cc_final: 0.7070 (m-30) REVERT: D 130 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7558 (mtmm) REVERT: D 134 VAL cc_start: 0.8444 (t) cc_final: 0.8221 (t) REVERT: D 173 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6988 (mm-30) REVERT: D 180 SER cc_start: 0.7634 (p) cc_final: 0.7312 (m) REVERT: D 254 LYS cc_start: 0.8598 (mtmp) cc_final: 0.8194 (mtpp) REVERT: D 277 THR cc_start: 0.8113 (m) cc_final: 0.7723 (p) REVERT: D 309 GLU cc_start: 0.7337 (tt0) cc_final: 0.7051 (tt0) REVERT: E 6 THR cc_start: 0.8113 (m) cc_final: 0.7788 (p) REVERT: E 9 SER cc_start: 0.8377 (t) cc_final: 0.8172 (t) REVERT: E 17 THR cc_start: 0.7900 (t) cc_final: 0.7104 (m) REVERT: E 18 ILE cc_start: 0.8600 (pt) cc_final: 0.8388 (mm) REVERT: E 35 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7656 (mtpp) REVERT: E 69 THR cc_start: 0.7375 (p) cc_final: 0.7002 (t) REVERT: E 79 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7584 (ttmm) REVERT: E 202 ASP cc_start: 0.7856 (p0) cc_final: 0.7598 (p0) REVERT: E 246 ASP cc_start: 0.6914 (m-30) cc_final: 0.6700 (m-30) REVERT: E 252 LYS cc_start: 0.7962 (tttt) cc_final: 0.7610 (ptmm) REVERT: E 262 TYR cc_start: 0.7467 (m-80) cc_final: 0.5802 (m-80) REVERT: E 269 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6996 (mt-10) REVERT: E 300 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6988 (tm-30) REVERT: E 304 ASN cc_start: 0.8016 (m110) cc_final: 0.7606 (m-40) REVERT: E 324 LYS cc_start: 0.8122 (mtmp) cc_final: 0.7674 (mtmm) REVERT: E 340 LYS cc_start: 0.7583 (tttt) cc_final: 0.7265 (ttmt) REVERT: E 349 GLN cc_start: 0.7153 (tp40) cc_final: 0.6694 (tp40) REVERT: E 392 GLN cc_start: 0.7583 (mp10) cc_final: 0.7298 (mp10) REVERT: F 8 GLU cc_start: 0.7427 (tp30) cc_final: 0.7117 (tp30) REVERT: F 12 THR cc_start: 0.8053 (m) cc_final: 0.7824 (m) REVERT: F 57 SER cc_start: 0.8409 (p) cc_final: 0.8065 (t) REVERT: F 60 ASN cc_start: 0.7877 (m-40) cc_final: 0.7413 (m-40) REVERT: F 75 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7692 (mmtp) REVERT: F 100 LEU cc_start: 0.8177 (tp) cc_final: 0.7973 (tt) REVERT: F 130 LYS cc_start: 0.7873 (pttm) cc_final: 0.7535 (ptpp) REVERT: F 210 THR cc_start: 0.6934 (m) cc_final: 0.6612 (p) REVERT: F 222 LYS cc_start: 0.7870 (mtpp) cc_final: 0.7410 (mtpp) REVERT: F 235 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7738 (mtpp) REVERT: F 245 LYS cc_start: 0.8246 (ptmt) cc_final: 0.7885 (ptmt) REVERT: F 290 LYS cc_start: 0.7564 (mttt) cc_final: 0.7285 (mttt) REVERT: F 347 ASN cc_start: 0.8194 (t0) cc_final: 0.7867 (t0) REVERT: L 7 SER cc_start: 0.7339 (t) cc_final: 0.6916 (p) REVERT: L 20 THR cc_start: 0.8610 (t) cc_final: 0.8324 (p) REVERT: L 42 LYS cc_start: 0.8302 (mmmt) cc_final: 0.8070 (mmmt) REVERT: L 77 SER cc_start: 0.7576 (t) cc_final: 0.7140 (m) REVERT: L 82 ASP cc_start: 0.7502 (m-30) cc_final: 0.7261 (m-30) REVERT: L 104 VAL cc_start: 0.7899 (t) cc_final: 0.7512 (p) outliers start: 1 outliers final: 0 residues processed: 824 average time/residue: 0.3461 time to fit residues: 414.4384 Evaluate side-chains 714 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 713 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 220 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 77 GLN A 100 ASN A 216 ASN A 222 GLN A 360 ASN B 81 GLN B 256 HIS B 332 ASN ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN C 222 GLN D 71 HIS D 160 ASN D 288 HIS E 157 ASN E 362 HIS ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 ASN F 305 HIS F 318 ASN L 37 GLN L 38 GLN L 90 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19647 Z= 0.228 Angle : 0.630 8.146 26742 Z= 0.329 Chirality : 0.046 0.206 2935 Planarity : 0.006 0.048 3462 Dihedral : 5.837 30.310 2676 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.28 % Favored : 92.68 % Rotamer: Outliers : 1.90 % Allowed : 8.76 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.59 (0.15), residues: 2445 helix: -3.47 (0.44), residues: 54 sheet: -1.78 (0.16), residues: 923 loop : -2.87 (0.14), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 236 HIS 0.008 0.001 HIS C 394 PHE 0.020 0.002 PHE C 287 TYR 0.023 0.001 TYR A 122 ARG 0.005 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 722 time to evaluate : 2.026 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: A 9 SER cc_start: 0.7723 (t) cc_final: 0.7437 (t) REVERT: A 29 ILE cc_start: 0.8614 (mt) cc_final: 0.8406 (mp) REVERT: A 30 SER cc_start: 0.8275 (m) cc_final: 0.7628 (p) REVERT: A 35 LYS cc_start: 0.8382 (ttmt) cc_final: 0.7599 (ttmm) REVERT: A 37 LYS cc_start: 0.8210 (mttt) cc_final: 0.7968 (mtmm) REVERT: A 42 VAL cc_start: 0.8403 (t) cc_final: 0.7905 (m) REVERT: A 45 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6717 (mm-30) REVERT: A 52 LYS cc_start: 0.8339 (ttpt) cc_final: 0.8026 (ttpp) REVERT: A 76 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6130 (tm-30) REVERT: A 82 THR cc_start: 0.7571 (m) cc_final: 0.7275 (p) REVERT: A 105 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7745 (mtpp) REVERT: A 123 LYS cc_start: 0.7704 (mtmt) cc_final: 0.7394 (mtmt) REVERT: A 130 GLN cc_start: 0.7536 (tt0) cc_final: 0.7181 (tt0) REVERT: A 147 TYR cc_start: 0.7671 (m-10) cc_final: 0.7209 (m-80) REVERT: A 176 LYS cc_start: 0.8220 (mttt) cc_final: 0.7912 (mtpp) REVERT: A 251 LEU cc_start: 0.8316 (tp) cc_final: 0.8106 (tp) REVERT: A 252 LYS cc_start: 0.8826 (tttt) cc_final: 0.8493 (ttmm) REVERT: A 269 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6672 (mt-10) REVERT: A 281 ASP cc_start: 0.7845 (t0) cc_final: 0.7500 (t0) REVERT: A 284 ASP cc_start: 0.7073 (m-30) cc_final: 0.6816 (m-30) REVERT: A 291 SER cc_start: 0.8335 (p) cc_final: 0.8107 (t) REVERT: A 300 GLU cc_start: 0.7248 (pt0) cc_final: 0.6960 (pt0) REVERT: A 307 VAL cc_start: 0.8729 (t) cc_final: 0.8427 (p) REVERT: A 339 LEU cc_start: 0.8643 (mp) cc_final: 0.8442 (mt) REVERT: A 341 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7289 (mm-30) REVERT: A 345 GLU cc_start: 0.7441 (mp0) cc_final: 0.7212 (mp0) REVERT: A 368 GLN cc_start: 0.7194 (tm-30) cc_final: 0.6916 (tm-30) REVERT: A 377 LYS cc_start: 0.7716 (mttp) cc_final: 0.7500 (mttp) REVERT: A 379 ASP cc_start: 0.7138 (t0) cc_final: 0.6904 (t0) REVERT: B 34 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7082 (mm-30) REVERT: B 37 LYS cc_start: 0.7523 (mmtt) cc_final: 0.7290 (mmtt) REVERT: B 39 ASP cc_start: 0.7476 (m-30) cc_final: 0.7190 (m-30) REVERT: B 68 TYR cc_start: 0.8597 (p90) cc_final: 0.8231 (p90) REVERT: B 108 ASP cc_start: 0.7484 (p0) cc_final: 0.7069 (p0) REVERT: B 115 LYS cc_start: 0.7538 (mtpt) cc_final: 0.7322 (mtpp) REVERT: B 164 TYR cc_start: 0.8017 (m-80) cc_final: 0.7633 (m-80) REVERT: B 192 ASP cc_start: 0.7085 (t70) cc_final: 0.6870 (t70) REVERT: B 254 LYS cc_start: 0.7384 (mmmt) cc_final: 0.6664 (mmmt) REVERT: B 265 LYS cc_start: 0.7604 (mmtt) cc_final: 0.7214 (mmmm) REVERT: B 294 TYR cc_start: 0.7648 (m-10) cc_final: 0.7231 (m-80) REVERT: B 324 LYS cc_start: 0.7706 (mtmm) cc_final: 0.7419 (mtmm) REVERT: B 336 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7835 (ttmm) REVERT: C 10 GLN cc_start: 0.7656 (tt0) cc_final: 0.7425 (tt0) REVERT: C 26 PRO cc_start: 0.7888 (Cg_exo) cc_final: 0.7644 (Cg_endo) REVERT: C 104 SER cc_start: 0.7940 (m) cc_final: 0.7695 (t) REVERT: C 107 TYR cc_start: 0.7831 (p90) cc_final: 0.7598 (p90) REVERT: C 120 GLU cc_start: 0.7677 (pt0) cc_final: 0.7262 (pt0) REVERT: C 186 ASN cc_start: 0.8121 (m110) cc_final: 0.7795 (m110) REVERT: C 242 GLN cc_start: 0.7512 (tp40) cc_final: 0.7064 (tp-100) REVERT: C 245 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7490 (mtpt) REVERT: C 246 ASP cc_start: 0.6730 (m-30) cc_final: 0.6221 (m-30) REVERT: C 254 THR cc_start: 0.8431 (p) cc_final: 0.8181 (t) REVERT: C 261 ILE cc_start: 0.8122 (mm) cc_final: 0.7747 (mm) REVERT: C 392 GLN cc_start: 0.7847 (mt0) cc_final: 0.7636 (mt0) REVERT: D 31 ILE cc_start: 0.8056 (tt) cc_final: 0.7746 (tt) REVERT: D 33 ILE cc_start: 0.8354 (mt) cc_final: 0.8150 (mt) REVERT: D 49 THR cc_start: 0.8221 (m) cc_final: 0.7926 (t) REVERT: D 64 ARG cc_start: 0.7214 (mmm-85) cc_final: 0.6856 (mtp85) REVERT: D 74 ILE cc_start: 0.8146 (mt) cc_final: 0.7868 (mt) REVERT: D 75 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8101 (mttm) REVERT: D 77 ILE cc_start: 0.8345 (mt) cc_final: 0.7970 (tt) REVERT: D 82 VAL cc_start: 0.8663 (t) cc_final: 0.8377 (p) REVERT: D 94 ASP cc_start: 0.7005 (t0) cc_final: 0.6719 (t0) REVERT: D 112 MET cc_start: 0.7367 (ttm) cc_final: 0.7156 (ttm) REVERT: D 122 SER cc_start: 0.8492 (t) cc_final: 0.8176 (m) REVERT: D 130 LYS cc_start: 0.7949 (mtmm) cc_final: 0.7387 (mtmm) REVERT: D 134 VAL cc_start: 0.8547 (t) cc_final: 0.8300 (t) REVERT: D 180 SER cc_start: 0.7830 (p) cc_final: 0.7433 (m) REVERT: D 215 LYS cc_start: 0.7921 (ttmt) cc_final: 0.7561 (ttmm) REVERT: D 242 LYS cc_start: 0.8087 (mttm) cc_final: 0.7667 (mttp) REVERT: D 254 LYS cc_start: 0.8528 (mtmp) cc_final: 0.8198 (mtpp) REVERT: D 266 CYS cc_start: 0.4953 (m) cc_final: 0.4664 (m) REVERT: D 277 THR cc_start: 0.8251 (m) cc_final: 0.7837 (p) REVERT: D 309 GLU cc_start: 0.7268 (tt0) cc_final: 0.7026 (tt0) REVERT: D 316 VAL cc_start: 0.8693 (p) cc_final: 0.8464 (t) REVERT: D 338 PHE cc_start: 0.8157 (m-10) cc_final: 0.7833 (m-80) REVERT: E 6 THR cc_start: 0.8180 (m) cc_final: 0.7762 (p) REVERT: E 35 LYS cc_start: 0.7905 (ttmt) cc_final: 0.7657 (mtpp) REVERT: E 47 VAL cc_start: 0.8327 (m) cc_final: 0.8000 (p) REVERT: E 123 LYS cc_start: 0.8415 (mttt) cc_final: 0.8168 (mttt) REVERT: E 202 ASP cc_start: 0.7986 (p0) cc_final: 0.7750 (p0) REVERT: E 222 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7639 (mt0) REVERT: E 246 ASP cc_start: 0.7104 (m-30) cc_final: 0.6728 (m-30) REVERT: E 252 LYS cc_start: 0.8120 (tttt) cc_final: 0.7773 (ptmm) REVERT: E 260 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6182 (mt-10) REVERT: E 262 TYR cc_start: 0.7603 (m-80) cc_final: 0.6021 (m-80) REVERT: E 269 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7152 (mt-10) REVERT: E 300 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6876 (tm-30) REVERT: E 324 LYS cc_start: 0.8205 (mtmp) cc_final: 0.7928 (mtmm) REVERT: E 338 THR cc_start: 0.8341 (m) cc_final: 0.8054 (t) REVERT: E 340 LYS cc_start: 0.7650 (tttt) cc_final: 0.7348 (ttmt) REVERT: F 8 GLU cc_start: 0.7438 (tp30) cc_final: 0.7139 (tp30) REVERT: F 37 LYS cc_start: 0.7557 (mmtt) cc_final: 0.7212 (mmtm) REVERT: F 53 TYR cc_start: 0.8179 (m-80) cc_final: 0.7625 (m-80) REVERT: F 57 SER cc_start: 0.8440 (p) cc_final: 0.8159 (t) REVERT: F 60 ASN cc_start: 0.7939 (m-40) cc_final: 0.7471 (m-40) REVERT: F 69 ASP cc_start: 0.7486 (t70) cc_final: 0.7233 (t70) REVERT: F 75 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7456 (mmtp) REVERT: F 120 ARG cc_start: 0.7293 (ptp-110) cc_final: 0.7085 (ttp80) REVERT: F 167 MET cc_start: 0.7598 (ptt) cc_final: 0.7295 (ptp) REVERT: F 175 ASP cc_start: 0.8282 (t0) cc_final: 0.7926 (t0) REVERT: F 177 SER cc_start: 0.8662 (m) cc_final: 0.8319 (p) REVERT: F 215 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7747 (tttp) REVERT: F 254 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7731 (mtmt) REVERT: F 290 LYS cc_start: 0.7696 (mttt) cc_final: 0.7417 (mttt) REVERT: F 347 ASN cc_start: 0.8283 (t0) cc_final: 0.7973 (t0) REVERT: H 38 ARG cc_start: 0.7047 (ptm-80) cc_final: 0.6627 (ptm-80) REVERT: H 39 GLN cc_start: 0.8180 (tt0) cc_final: 0.7748 (tt0) REVERT: H 76 ASN cc_start: 0.6341 (p0) cc_final: 0.5686 (p0) REVERT: H 85 GLU cc_start: 0.7994 (tp30) cc_final: 0.7125 (tp30) REVERT: H 103 TRP cc_start: 0.7965 (m100) cc_final: 0.7682 (m100) REVERT: L 4 MET cc_start: 0.6449 (mmt) cc_final: 0.6241 (mmt) REVERT: L 20 THR cc_start: 0.8586 (t) cc_final: 0.8313 (p) REVERT: L 42 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7994 (mmmt) REVERT: L 47 LEU cc_start: 0.8222 (mp) cc_final: 0.8008 (mp) REVERT: L 54 LEU cc_start: 0.8511 (tp) cc_final: 0.8296 (tt) REVERT: L 104 VAL cc_start: 0.7994 (t) cc_final: 0.7733 (p) outliers start: 40 outliers final: 29 residues processed: 741 average time/residue: 0.3291 time to fit residues: 356.2111 Evaluate side-chains 720 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 690 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 183 optimal weight: 0.0470 chunk 150 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 221 optimal weight: 8.9990 chunk 238 optimal weight: 0.9980 chunk 196 optimal weight: 0.0270 chunk 219 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 155 ASN A 235 GLN A 270 ASN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN D 71 HIS E 242 GLN E 270 ASN F 81 GLN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 HIS F 318 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19647 Z= 0.163 Angle : 0.572 7.550 26742 Z= 0.296 Chirality : 0.044 0.152 2935 Planarity : 0.005 0.043 3462 Dihedral : 5.268 26.515 2674 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.12 % Favored : 92.84 % Rotamer: Outliers : 2.67 % Allowed : 12.71 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.16), residues: 2445 helix: -2.61 (0.56), residues: 54 sheet: -1.27 (0.17), residues: 904 loop : -2.40 (0.15), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 170 HIS 0.004 0.001 HIS F 168 PHE 0.024 0.001 PHE C 356 TYR 0.017 0.001 TYR A 122 ARG 0.005 0.000 ARG D 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 685 time to evaluate : 2.074 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: A 9 SER cc_start: 0.7666 (t) cc_final: 0.7396 (t) REVERT: A 18 ILE cc_start: 0.8128 (pt) cc_final: 0.7853 (mm) REVERT: A 30 SER cc_start: 0.8146 (m) cc_final: 0.7611 (p) REVERT: A 35 LYS cc_start: 0.8434 (ttmt) cc_final: 0.7414 (ttmm) REVERT: A 37 LYS cc_start: 0.8172 (mttt) cc_final: 0.7960 (mtmm) REVERT: A 42 VAL cc_start: 0.8517 (t) cc_final: 0.8024 (m) REVERT: A 45 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6708 (mm-30) REVERT: A 52 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8066 (ttpp) REVERT: A 75 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: A 76 GLU cc_start: 0.6967 (tm-30) cc_final: 0.6235 (tm-30) REVERT: A 82 THR cc_start: 0.7551 (m) cc_final: 0.7201 (p) REVERT: A 105 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7732 (mtpp) REVERT: A 123 LYS cc_start: 0.7608 (mtmt) cc_final: 0.7307 (mtmt) REVERT: A 126 THR cc_start: 0.7679 (m) cc_final: 0.7464 (m) REVERT: A 130 GLN cc_start: 0.7519 (tt0) cc_final: 0.7212 (tt0) REVERT: A 147 TYR cc_start: 0.7724 (m-10) cc_final: 0.7198 (m-80) REVERT: A 176 LYS cc_start: 0.8250 (mttt) cc_final: 0.7903 (mtpp) REVERT: A 252 LYS cc_start: 0.8814 (tttt) cc_final: 0.8468 (ttmm) REVERT: A 269 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6244 (mt-10) REVERT: A 281 ASP cc_start: 0.7798 (t0) cc_final: 0.7467 (t0) REVERT: A 303 LEU cc_start: 0.8681 (tp) cc_final: 0.8473 (tp) REVERT: A 307 VAL cc_start: 0.8663 (t) cc_final: 0.8371 (p) REVERT: A 332 VAL cc_start: 0.8472 (t) cc_final: 0.8229 (m) REVERT: A 344 VAL cc_start: 0.8224 (m) cc_final: 0.7985 (p) REVERT: A 368 GLN cc_start: 0.7196 (tm-30) cc_final: 0.6880 (tm-30) REVERT: A 379 ASP cc_start: 0.7061 (t0) cc_final: 0.6816 (t0) REVERT: B 34 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7012 (mm-30) REVERT: B 68 TYR cc_start: 0.8582 (p90) cc_final: 0.8201 (p90) REVERT: B 108 ASP cc_start: 0.7475 (p0) cc_final: 0.7077 (p0) REVERT: B 112 MET cc_start: 0.8299 (ttt) cc_final: 0.8085 (ttm) REVERT: B 115 LYS cc_start: 0.7527 (mtpt) cc_final: 0.7308 (mtpp) REVERT: B 164 TYR cc_start: 0.8027 (m-80) cc_final: 0.7404 (m-80) REVERT: B 230 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8096 (ptp-110) REVERT: B 265 LYS cc_start: 0.7717 (mmtt) cc_final: 0.7326 (mmmm) REVERT: B 294 TYR cc_start: 0.7726 (m-10) cc_final: 0.7397 (m-80) REVERT: B 324 LYS cc_start: 0.7637 (mtmm) cc_final: 0.7339 (mtmm) REVERT: B 336 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7853 (ttmm) REVERT: C 10 GLN cc_start: 0.7640 (tt0) cc_final: 0.7355 (tt0) REVERT: C 37 LYS cc_start: 0.7527 (ttmt) cc_final: 0.7112 (mtpt) REVERT: C 107 TYR cc_start: 0.7634 (p90) cc_final: 0.7257 (p90) REVERT: C 120 GLU cc_start: 0.7587 (pt0) cc_final: 0.7180 (pt0) REVERT: C 186 ASN cc_start: 0.8180 (m110) cc_final: 0.7882 (m110) REVERT: C 245 LYS cc_start: 0.7780 (mtpt) cc_final: 0.7478 (mtpt) REVERT: C 246 ASP cc_start: 0.6699 (m-30) cc_final: 0.6356 (m-30) REVERT: C 254 THR cc_start: 0.8461 (p) cc_final: 0.8216 (t) REVERT: C 260 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6712 (mt-10) REVERT: C 261 ILE cc_start: 0.8071 (mm) cc_final: 0.7641 (mm) REVERT: C 281 ASP cc_start: 0.6658 (t0) cc_final: 0.6428 (t0) REVERT: C 334 SER cc_start: 0.8576 (t) cc_final: 0.8140 (p) REVERT: C 338 THR cc_start: 0.7914 (m) cc_final: 0.7465 (t) REVERT: D 31 ILE cc_start: 0.8035 (tt) cc_final: 0.7724 (tt) REVERT: D 33 ILE cc_start: 0.8300 (mt) cc_final: 0.8097 (mt) REVERT: D 64 ARG cc_start: 0.7259 (mmm-85) cc_final: 0.6772 (mtt-85) REVERT: D 74 ILE cc_start: 0.8128 (mt) cc_final: 0.7856 (mt) REVERT: D 75 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8111 (mttm) REVERT: D 77 ILE cc_start: 0.8344 (mt) cc_final: 0.7979 (tt) REVERT: D 94 ASP cc_start: 0.6786 (t0) cc_final: 0.6494 (t0) REVERT: D 130 LYS cc_start: 0.7868 (mtmm) cc_final: 0.7376 (mtmm) REVERT: D 134 VAL cc_start: 0.8548 (t) cc_final: 0.8294 (t) REVERT: D 180 SER cc_start: 0.8000 (p) cc_final: 0.7539 (m) REVERT: D 215 LYS cc_start: 0.7856 (ttmt) cc_final: 0.7490 (ttmm) REVERT: D 241 ASP cc_start: 0.7785 (p0) cc_final: 0.7473 (p0) REVERT: D 242 LYS cc_start: 0.8085 (mttm) cc_final: 0.7764 (mttp) REVERT: D 254 LYS cc_start: 0.8521 (mtmp) cc_final: 0.8124 (mtpp) REVERT: D 277 THR cc_start: 0.8279 (m) cc_final: 0.7913 (p) REVERT: D 286 LYS cc_start: 0.7924 (tptm) cc_final: 0.7579 (tptm) REVERT: D 316 VAL cc_start: 0.8656 (p) cc_final: 0.8446 (t) REVERT: D 338 PHE cc_start: 0.8142 (m-10) cc_final: 0.7860 (m-80) REVERT: E 6 THR cc_start: 0.8199 (m) cc_final: 0.7799 (p) REVERT: E 9 SER cc_start: 0.8471 (t) cc_final: 0.8213 (t) REVERT: E 35 LYS cc_start: 0.7916 (ttmt) cc_final: 0.7624 (mtpp) REVERT: E 47 VAL cc_start: 0.8293 (m) cc_final: 0.8019 (p) REVERT: E 110 LYS cc_start: 0.8506 (ptpp) cc_final: 0.8129 (mtmm) REVERT: E 202 ASP cc_start: 0.8036 (p0) cc_final: 0.7770 (p0) REVERT: E 222 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7647 (mt0) REVERT: E 246 ASP cc_start: 0.7122 (m-30) cc_final: 0.6760 (m-30) REVERT: E 252 LYS cc_start: 0.8081 (tttt) cc_final: 0.7757 (ptmm) REVERT: E 262 TYR cc_start: 0.7623 (m-80) cc_final: 0.6333 (m-80) REVERT: E 269 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7096 (mt-10) REVERT: E 280 PHE cc_start: 0.8388 (m-10) cc_final: 0.7927 (m-10) REVERT: E 324 LYS cc_start: 0.8136 (mtmp) cc_final: 0.7891 (mtmm) REVERT: E 338 THR cc_start: 0.8403 (m) cc_final: 0.8112 (t) REVERT: E 340 LYS cc_start: 0.7702 (tttt) cc_final: 0.7394 (ttmt) REVERT: F 8 GLU cc_start: 0.7360 (tp30) cc_final: 0.7074 (tp30) REVERT: F 37 LYS cc_start: 0.7588 (mmtt) cc_final: 0.7224 (mmtm) REVERT: F 53 TYR cc_start: 0.8154 (m-80) cc_final: 0.7699 (m-80) REVERT: F 57 SER cc_start: 0.8439 (p) cc_final: 0.8188 (t) REVERT: F 69 ASP cc_start: 0.7335 (t70) cc_final: 0.7112 (t0) REVERT: F 75 LYS cc_start: 0.7876 (mmtt) cc_final: 0.7633 (mmtp) REVERT: F 167 MET cc_start: 0.7615 (ptt) cc_final: 0.7244 (ptp) REVERT: F 175 ASP cc_start: 0.8358 (t0) cc_final: 0.7954 (t0) REVERT: F 215 LYS cc_start: 0.8056 (tttt) cc_final: 0.7779 (tttt) REVERT: F 261 LEU cc_start: 0.8536 (tp) cc_final: 0.8238 (mt) REVERT: F 286 LYS cc_start: 0.8224 (tppp) cc_final: 0.7935 (ttmm) REVERT: F 290 LYS cc_start: 0.7696 (mttt) cc_final: 0.7421 (mttt) REVERT: F 347 ASN cc_start: 0.8311 (t0) cc_final: 0.8006 (t0) REVERT: H 39 GLN cc_start: 0.8214 (tt0) cc_final: 0.7840 (tt0) REVERT: H 76 ASN cc_start: 0.6323 (p0) cc_final: 0.5624 (p0) REVERT: H 85 GLU cc_start: 0.8076 (tp30) cc_final: 0.7749 (tp30) REVERT: L 20 THR cc_start: 0.8604 (t) cc_final: 0.8328 (p) REVERT: L 42 LYS cc_start: 0.8269 (mmmt) cc_final: 0.8009 (mmmt) REVERT: L 104 VAL cc_start: 0.7971 (t) cc_final: 0.7722 (p) outliers start: 56 outliers final: 38 residues processed: 708 average time/residue: 0.3443 time to fit residues: 357.0556 Evaluate side-chains 708 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 669 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 325 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 148 optimal weight: 0.0030 chunk 221 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 218 ASN B 333 HIS ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN C 362 HIS D 288 HIS E 125 HIS F 305 HIS F 318 ASN L 37 GLN L 79 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.104 19647 Z= 0.537 Angle : 0.750 11.416 26742 Z= 0.392 Chirality : 0.049 0.209 2935 Planarity : 0.006 0.064 3462 Dihedral : 6.129 30.775 2674 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.96 % Favored : 90.88 % Rotamer: Outliers : 3.90 % Allowed : 13.85 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.74 (0.16), residues: 2445 helix: -2.80 (0.54), residues: 48 sheet: -1.10 (0.17), residues: 914 loop : -2.35 (0.15), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP H 103 HIS 0.008 0.002 HIS F 168 PHE 0.023 0.003 PHE F 328 TYR 0.052 0.003 TYR F 9 ARG 0.008 0.001 ARG D 230 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 720 time to evaluate : 2.066 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: A 7 MET cc_start: 0.7248 (ptm) cc_final: 0.6940 (ptt) REVERT: A 9 SER cc_start: 0.7757 (t) cc_final: 0.7481 (t) REVERT: A 30 SER cc_start: 0.8217 (m) cc_final: 0.7580 (p) REVERT: A 35 LYS cc_start: 0.8491 (ttmt) cc_final: 0.7998 (ttmm) REVERT: A 37 LYS cc_start: 0.8292 (mttt) cc_final: 0.7822 (mtmm) REVERT: A 42 VAL cc_start: 0.8737 (t) cc_final: 0.8524 (m) REVERT: A 45 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6943 (mm-30) REVERT: A 52 LYS cc_start: 0.8399 (ttpt) cc_final: 0.8101 (ttpp) REVERT: A 75 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7905 (m-30) REVERT: A 76 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6345 (tm-30) REVERT: A 99 GLU cc_start: 0.7913 (mt-10) cc_final: 0.6928 (tt0) REVERT: A 105 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7778 (mtpp) REVERT: A 108 VAL cc_start: 0.8885 (t) cc_final: 0.8358 (m) REVERT: A 123 LYS cc_start: 0.7970 (mtmt) cc_final: 0.7706 (mtmt) REVERT: A 130 GLN cc_start: 0.7590 (tt0) cc_final: 0.7316 (tt0) REVERT: A 136 THR cc_start: 0.7351 (m) cc_final: 0.6936 (p) REVERT: A 147 TYR cc_start: 0.7847 (m-10) cc_final: 0.7426 (m-10) REVERT: A 176 LYS cc_start: 0.8236 (mttt) cc_final: 0.7870 (mtpp) REVERT: A 216 ASN cc_start: 0.8315 (t0) cc_final: 0.8049 (t0) REVERT: A 241 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6820 (tm-30) REVERT: A 252 LYS cc_start: 0.8790 (tttt) cc_final: 0.8532 (ttmm) REVERT: A 281 ASP cc_start: 0.7897 (t0) cc_final: 0.7588 (t0) REVERT: A 307 VAL cc_start: 0.8703 (t) cc_final: 0.8430 (p) REVERT: A 317 THR cc_start: 0.8132 (m) cc_final: 0.7818 (p) REVERT: A 368 GLN cc_start: 0.7381 (tm-30) cc_final: 0.6986 (tm-30) REVERT: B 34 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7104 (mm-30) REVERT: B 68 TYR cc_start: 0.8589 (p90) cc_final: 0.8055 (p90) REVERT: B 108 ASP cc_start: 0.7562 (p0) cc_final: 0.7203 (p0) REVERT: B 115 LYS cc_start: 0.7660 (mtpt) cc_final: 0.7451 (mtpp) REVERT: B 148 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7108 (mm-30) REVERT: B 230 ARG cc_start: 0.8429 (mtp85) cc_final: 0.7876 (ttm110) REVERT: B 265 LYS cc_start: 0.7647 (mmtt) cc_final: 0.7322 (mmtt) REVERT: B 290 LYS cc_start: 0.7479 (ttmt) cc_final: 0.7168 (ttmt) REVERT: B 294 TYR cc_start: 0.8424 (m-10) cc_final: 0.7999 (m-80) REVERT: B 324 LYS cc_start: 0.7861 (mtmm) cc_final: 0.7554 (mtmm) REVERT: B 336 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7860 (ttmm) REVERT: C 10 GLN cc_start: 0.7668 (tt0) cc_final: 0.7368 (tt0) REVERT: C 107 TYR cc_start: 0.8013 (p90) cc_final: 0.7628 (p90) REVERT: C 109 MET cc_start: 0.7661 (ptp) cc_final: 0.7436 (ptp) REVERT: C 186 ASN cc_start: 0.8331 (m110) cc_final: 0.7960 (m110) REVERT: C 222 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7628 (mt0) REVERT: C 242 GLN cc_start: 0.7887 (tp40) cc_final: 0.7656 (tp40) REVERT: C 245 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7511 (mtpt) REVERT: C 246 ASP cc_start: 0.6789 (m-30) cc_final: 0.6576 (m-30) REVERT: C 260 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6853 (mt-10) REVERT: C 261 ILE cc_start: 0.8376 (mm) cc_final: 0.8063 (mm) REVERT: C 334 SER cc_start: 0.8584 (t) cc_final: 0.8096 (p) REVERT: D 64 ARG cc_start: 0.7375 (mmm-85) cc_final: 0.6953 (mtp85) REVERT: D 74 ILE cc_start: 0.8173 (mt) cc_final: 0.7856 (mt) REVERT: D 75 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8098 (mttm) REVERT: D 77 ILE cc_start: 0.8381 (mt) cc_final: 0.8040 (tt) REVERT: D 112 MET cc_start: 0.7553 (ttm) cc_final: 0.7312 (ttt) REVERT: D 120 ARG cc_start: 0.6795 (tpt-90) cc_final: 0.6478 (tpt-90) REVERT: D 130 LYS cc_start: 0.8012 (mtmm) cc_final: 0.7464 (mtmm) REVERT: D 180 SER cc_start: 0.7999 (p) cc_final: 0.7461 (m) REVERT: D 215 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7714 (ttmm) REVERT: D 241 ASP cc_start: 0.7795 (p0) cc_final: 0.7382 (p0) REVERT: D 242 LYS cc_start: 0.8168 (mttm) cc_final: 0.7843 (mttp) REVERT: D 254 LYS cc_start: 0.8650 (mtmp) cc_final: 0.8250 (mtpp) REVERT: D 261 LEU cc_start: 0.8734 (tp) cc_final: 0.8104 (mt) REVERT: D 286 LYS cc_start: 0.8085 (tptm) cc_final: 0.7750 (tptm) REVERT: D 338 PHE cc_start: 0.8101 (m-10) cc_final: 0.7884 (m-80) REVERT: E 6 THR cc_start: 0.8313 (m) cc_final: 0.7917 (p) REVERT: E 35 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7700 (mtpp) REVERT: E 99 GLU cc_start: 0.7342 (tt0) cc_final: 0.6999 (tt0) REVERT: E 110 LYS cc_start: 0.8638 (ptpp) cc_final: 0.8287 (mtmm) REVERT: E 174 ASP cc_start: 0.7016 (m-30) cc_final: 0.6718 (m-30) REVERT: E 222 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7751 (mt0) REVERT: E 257 PHE cc_start: 0.7963 (m-80) cc_final: 0.7759 (m-10) REVERT: E 262 TYR cc_start: 0.7796 (m-80) cc_final: 0.6547 (m-80) REVERT: E 269 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7186 (mt-10) REVERT: E 280 PHE cc_start: 0.8475 (m-10) cc_final: 0.7985 (m-10) REVERT: E 324 LYS cc_start: 0.8259 (mtmp) cc_final: 0.7920 (mtmm) REVERT: E 336 THR cc_start: 0.7352 (m) cc_final: 0.7103 (m) REVERT: E 338 THR cc_start: 0.8522 (m) cc_final: 0.8262 (t) REVERT: E 340 LYS cc_start: 0.7890 (tttt) cc_final: 0.7495 (ttmt) REVERT: E 344 VAL cc_start: 0.8852 (t) cc_final: 0.8638 (m) REVERT: E 349 GLN cc_start: 0.7271 (tp40) cc_final: 0.6719 (tp40) REVERT: E 351 SER cc_start: 0.8024 (t) cc_final: 0.7774 (p) REVERT: E 386 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.7083 (p-80) REVERT: F 8 GLU cc_start: 0.7411 (tp30) cc_final: 0.7060 (tp30) REVERT: F 37 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7258 (mmtm) REVERT: F 53 TYR cc_start: 0.8127 (m-80) cc_final: 0.7727 (m-80) REVERT: F 69 ASP cc_start: 0.7381 (t70) cc_final: 0.7152 (t0) REVERT: F 75 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7678 (mmtp) REVERT: F 115 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7674 (mttm) REVERT: F 129 VAL cc_start: 0.8217 (t) cc_final: 0.7874 (p) REVERT: F 175 ASP cc_start: 0.8438 (t0) cc_final: 0.8124 (t0) REVERT: F 177 SER cc_start: 0.8711 (m) cc_final: 0.8366 (p) REVERT: F 215 LYS cc_start: 0.8165 (tttt) cc_final: 0.7909 (tttp) REVERT: F 227 ARG cc_start: 0.7517 (tpp80) cc_final: 0.7180 (mmt-90) REVERT: F 261 LEU cc_start: 0.8604 (tp) cc_final: 0.8354 (mt) REVERT: F 286 LYS cc_start: 0.8300 (tppp) cc_final: 0.8090 (tppp) REVERT: F 290 LYS cc_start: 0.7943 (mttt) cc_final: 0.7626 (mttt) REVERT: F 303 GLU cc_start: 0.6873 (tt0) cc_final: 0.6649 (tt0) REVERT: F 347 ASN cc_start: 0.8572 (t0) cc_final: 0.8322 (t0) REVERT: H 38 ARG cc_start: 0.7050 (ptm-80) cc_final: 0.6629 (ptt-90) REVERT: H 52 LYS cc_start: 0.8295 (tptp) cc_final: 0.7947 (tptp) REVERT: H 103 TRP cc_start: 0.8060 (m100) cc_final: 0.7772 (m100) REVERT: L 20 THR cc_start: 0.8651 (t) cc_final: 0.8328 (p) REVERT: L 42 LYS cc_start: 0.8323 (mmmt) cc_final: 0.8018 (mmmt) REVERT: L 47 LEU cc_start: 0.8320 (mp) cc_final: 0.8113 (mm) REVERT: L 90 GLN cc_start: 0.6875 (OUTLIER) cc_final: 0.6327 (tm130) REVERT: L 104 VAL cc_start: 0.8074 (t) cc_final: 0.7826 (p) outliers start: 82 outliers final: 57 residues processed: 760 average time/residue: 0.3174 time to fit residues: 353.4797 Evaluate side-chains 757 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 696 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 75 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 396 GLN Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 369 ILE Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 0.6980 chunk 133 optimal weight: 0.0270 chunk 3 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 200 optimal weight: 0.6980 chunk 162 optimal weight: 0.0050 chunk 0 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 210 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 overall best weight: 0.4052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 218 ASN A 270 ASN C 66 GLN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN ** C 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 GLN E 360 ASN F 81 GLN F 305 HIS F 318 ASN H 39 GLN L 79 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19647 Z= 0.163 Angle : 0.581 10.216 26742 Z= 0.299 Chirality : 0.044 0.160 2935 Planarity : 0.004 0.041 3462 Dihedral : 5.217 25.426 2674 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.09 % Allowed : 15.99 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.16), residues: 2445 helix: -2.13 (0.64), residues: 49 sheet: -0.80 (0.17), residues: 918 loop : -2.05 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.011 0.001 HIS A 362 PHE 0.024 0.001 PHE C 356 TYR 0.036 0.001 TYR F 9 ARG 0.004 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4890 Ramachandran restraints generated. 2445 Oldfield, 0 Emsley, 2445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 699 time to evaluate : 1.925 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: A 9 SER cc_start: 0.7645 (t) cc_final: 0.7387 (t) REVERT: A 35 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8036 (ttmm) REVERT: A 42 VAL cc_start: 0.8573 (t) cc_final: 0.8098 (m) REVERT: A 45 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6642 (mm-30) REVERT: A 52 LYS cc_start: 0.8437 (ttpt) cc_final: 0.8159 (ttpp) REVERT: A 76 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6318 (tm-30) REVERT: A 82 THR cc_start: 0.7536 (m) cc_final: 0.7189 (p) REVERT: A 105 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7806 (mtpp) REVERT: A 111 SER cc_start: 0.8291 (p) cc_final: 0.8033 (t) REVERT: A 123 LYS cc_start: 0.7754 (mtmt) cc_final: 0.7458 (mtmt) REVERT: A 126 THR cc_start: 0.7757 (m) cc_final: 0.7519 (m) REVERT: A 130 GLN cc_start: 0.7542 (tt0) cc_final: 0.6938 (tt0) REVERT: A 147 TYR cc_start: 0.7840 (m-10) cc_final: 0.7166 (m-80) REVERT: A 176 LYS cc_start: 0.8249 (mttt) cc_final: 0.7874 (mtpp) REVERT: A 216 ASN cc_start: 0.8227 (t0) cc_final: 0.8015 (t0) REVERT: A 241 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6532 (tm-30) REVERT: A 245 LYS cc_start: 0.7701 (mtpt) cc_final: 0.7176 (mtpp) REVERT: A 252 LYS cc_start: 0.8769 (tttt) cc_final: 0.8421 (ttmm) REVERT: A 281 ASP cc_start: 0.7744 (t0) cc_final: 0.7384 (t0) REVERT: A 307 VAL cc_start: 0.8607 (t) cc_final: 0.8356 (p) REVERT: A 317 THR cc_start: 0.8100 (m) cc_final: 0.7832 (p) REVERT: A 368 GLN cc_start: 0.7329 (tm-30) cc_final: 0.6911 (tm-30) REVERT: B 18 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7618 (ptm-80) REVERT: B 34 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6997 (mm-30) REVERT: B 68 TYR cc_start: 0.8542 (p90) cc_final: 0.7968 (p90) REVERT: B 108 ASP cc_start: 0.7510 (p0) cc_final: 0.7161 (p0) REVERT: B 175 ASP cc_start: 0.6974 (t0) cc_final: 0.6760 (m-30) REVERT: B 230 ARG cc_start: 0.8392 (mtp85) cc_final: 0.7981 (ptp-110) REVERT: B 265 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7437 (mmtt) REVERT: B 275 MET cc_start: 0.8097 (mpp) cc_final: 0.7823 (mpp) REVERT: B 324 LYS cc_start: 0.7636 (mtmm) cc_final: 0.7315 (mtmm) REVERT: B 336 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7798 (ttmm) REVERT: C 10 GLN cc_start: 0.7609 (tt0) cc_final: 0.7275 (tt0) REVERT: C 43 ASN cc_start: 0.7824 (t0) cc_final: 0.7608 (t0) REVERT: C 105 LYS cc_start: 0.7566 (ttmt) cc_final: 0.6995 (ttmm) REVERT: C 107 TYR cc_start: 0.7882 (p90) cc_final: 0.7657 (p90) REVERT: C 120 GLU cc_start: 0.7535 (pt0) cc_final: 0.6800 (pt0) REVERT: C 161 ILE cc_start: 0.7877 (mp) cc_final: 0.7618 (mm) REVERT: C 186 ASN cc_start: 0.8214 (m110) cc_final: 0.8001 (m-40) REVERT: C 214 TYR cc_start: 0.8317 (t80) cc_final: 0.7591 (t80) REVERT: C 242 GLN cc_start: 0.7736 (tp40) cc_final: 0.7149 (tp-100) REVERT: C 245 LYS cc_start: 0.7814 (mtpt) cc_final: 0.7512 (mtpt) REVERT: C 246 ASP cc_start: 0.6779 (m-30) cc_final: 0.6450 (m-30) REVERT: C 261 ILE cc_start: 0.8266 (mm) cc_final: 0.7927 (mm) REVERT: C 334 SER cc_start: 0.8591 (t) cc_final: 0.8116 (p) REVERT: C 338 THR cc_start: 0.7973 (m) cc_final: 0.7529 (t) REVERT: C 394 HIS cc_start: 0.7438 (p90) cc_final: 0.7121 (p90) REVERT: D 64 ARG cc_start: 0.7211 (mmm-85) cc_final: 0.6790 (mtp85) REVERT: D 74 ILE cc_start: 0.8207 (mt) cc_final: 0.7825 (mt) REVERT: D 75 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8008 (mttm) REVERT: D 77 ILE cc_start: 0.8306 (mt) cc_final: 0.8046 (tt) REVERT: D 120 ARG cc_start: 0.6780 (tpt-90) cc_final: 0.6508 (tpt-90) REVERT: D 130 LYS cc_start: 0.7922 (mtmm) cc_final: 0.7434 (mtmm) REVERT: D 180 SER cc_start: 0.8266 (p) cc_final: 0.7694 (m) REVERT: D 215 LYS cc_start: 0.7999 (ttmt) cc_final: 0.7472 (ttmm) REVERT: D 227 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.7028 (ttm110) REVERT: D 261 LEU cc_start: 0.8515 (tp) cc_final: 0.8243 (mt) REVERT: D 277 THR cc_start: 0.8313 (m) cc_final: 0.7862 (p) REVERT: D 286 LYS cc_start: 0.8013 (tptm) cc_final: 0.7632 (tptm) REVERT: D 338 PHE cc_start: 0.8068 (m-10) cc_final: 0.7828 (m-80) REVERT: D 354 GLU cc_start: 0.5063 (OUTLIER) cc_final: 0.2881 (tp30) REVERT: E 6 THR cc_start: 0.8254 (m) cc_final: 0.7849 (p) REVERT: E 35 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7675 (mtpp) REVERT: E 102 GLN cc_start: 0.8032 (tt0) cc_final: 0.7787 (tt0) REVERT: E 110 LYS cc_start: 0.8533 (ptpp) cc_final: 0.8228 (mtmm) REVERT: E 161 ILE cc_start: 0.7638 (mt) cc_final: 0.7399 (mt) REVERT: E 174 ASP cc_start: 0.6977 (m-30) cc_final: 0.6743 (m-30) REVERT: E 202 ASP cc_start: 0.8209 (p0) cc_final: 0.7921 (p0) REVERT: E 203 ILE cc_start: 0.8003 (mm) cc_final: 0.7695 (pt) REVERT: E 222 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7790 (mm110) REVERT: E 257 PHE cc_start: 0.7957 (m-80) cc_final: 0.7747 (m-10) REVERT: E 262 TYR cc_start: 0.7725 (m-80) cc_final: 0.6178 (m-80) REVERT: E 269 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7097 (mt-10) REVERT: E 280 PHE cc_start: 0.8355 (m-10) cc_final: 0.7887 (m-10) REVERT: E 300 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: E 307 VAL cc_start: 0.8299 (t) cc_final: 0.8093 (p) REVERT: E 324 LYS cc_start: 0.8244 (mtmp) cc_final: 0.7940 (mtmm) REVERT: E 338 THR cc_start: 0.8542 (m) cc_final: 0.8228 (t) REVERT: E 340 LYS cc_start: 0.7761 (tttt) cc_final: 0.7392 (ttmt) REVERT: E 386 HIS cc_start: 0.7021 (OUTLIER) cc_final: 0.6609 (p-80) REVERT: F 8 GLU cc_start: 0.7365 (tp30) cc_final: 0.6999 (tp30) REVERT: F 37 LYS cc_start: 0.7576 (mmtt) cc_final: 0.7194 (mmtm) REVERT: F 53 TYR cc_start: 0.8143 (m-80) cc_final: 0.7620 (m-80) REVERT: F 57 SER cc_start: 0.8492 (p) cc_final: 0.8127 (t) REVERT: F 75 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7529 (mmtp) REVERT: F 76 GLU cc_start: 0.6525 (tp30) cc_final: 0.6294 (tp30) REVERT: F 115 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7475 (mttm) REVERT: F 175 ASP cc_start: 0.8495 (t0) cc_final: 0.8046 (t0) REVERT: F 177 SER cc_start: 0.8641 (m) cc_final: 0.8359 (p) REVERT: F 261 LEU cc_start: 0.8495 (tp) cc_final: 0.8248 (mt) REVERT: F 277 THR cc_start: 0.8249 (m) cc_final: 0.7980 (p) REVERT: F 286 LYS cc_start: 0.8274 (tppp) cc_final: 0.7872 (tppp) REVERT: F 290 LYS cc_start: 0.7794 (mttt) cc_final: 0.7504 (mttt) REVERT: H 38 ARG cc_start: 0.7034 (ptm-80) cc_final: 0.6558 (ptt-90) REVERT: H 76 ASN cc_start: 0.6454 (p0) cc_final: 0.5457 (p0) REVERT: H 103 TRP cc_start: 0.7958 (m100) cc_final: 0.7628 (m100) REVERT: L 42 LYS cc_start: 0.8288 (mmmt) cc_final: 0.8003 (mmmt) REVERT: L 104 VAL cc_start: 0.8077 (t) cc_final: 0.7814 (p) outliers start: 65 outliers final: 39 residues processed: 727 average time/residue: 0.3599 time to fit residues: 387.1138 Evaluate side-chains 716 residues out of total 2101 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 673 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 191 GLU Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain E residue 386 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain H residue 21 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.0799 > 50: distance: 63 - 237: 22.724 distance: 66 - 234: 10.334 distance: 79 - 221: 31.887 distance: 82 - 218: 9.402 distance: 95 - 198: 31.036 distance: 144 - 255: 24.724 distance: 171 - 177: 22.889 distance: 177 - 178: 37.199 distance: 178 - 179: 39.947 distance: 179 - 180: 17.166 distance: 179 - 181: 32.906 distance: 181 - 182: 11.746 distance: 182 - 183: 14.164 distance: 182 - 185: 10.686 distance: 183 - 184: 25.020 distance: 183 - 191: 18.335 distance: 185 - 186: 16.354 distance: 186 - 187: 40.830 distance: 186 - 188: 33.255 distance: 187 - 189: 42.564 distance: 188 - 190: 42.889 distance: 189 - 190: 38.028 distance: 191 - 192: 6.951 distance: 192 - 193: 19.130 distance: 193 - 194: 6.612 distance: 193 - 195: 31.923 distance: 195 - 196: 25.976 distance: 196 - 197: 9.131 distance: 196 - 199: 26.010 distance: 197 - 198: 30.765 distance: 197 - 207: 25.862 distance: 199 - 200: 15.405 distance: 200 - 201: 18.033 distance: 200 - 202: 10.234 distance: 202 - 204: 11.283 distance: 203 - 205: 5.034 distance: 204 - 205: 7.961 distance: 205 - 206: 6.804 distance: 207 - 208: 37.583 distance: 208 - 209: 32.636 distance: 208 - 211: 18.778 distance: 209 - 210: 19.894 distance: 209 - 218: 22.056 distance: 211 - 212: 12.628 distance: 212 - 213: 16.978 distance: 212 - 214: 15.415 distance: 213 - 215: 9.711 distance: 214 - 216: 9.422 distance: 215 - 217: 7.274 distance: 216 - 217: 9.757 distance: 218 - 219: 33.497 distance: 219 - 220: 8.561 distance: 219 - 222: 17.406 distance: 220 - 221: 22.319 distance: 220 - 226: 34.055 distance: 222 - 223: 9.106 distance: 223 - 224: 10.132 distance: 223 - 225: 14.285 distance: 226 - 227: 6.661 distance: 227 - 228: 12.995 distance: 227 - 230: 10.582 distance: 228 - 229: 22.592 distance: 228 - 234: 13.838 distance: 230 - 231: 16.953 distance: 231 - 232: 20.544 distance: 231 - 233: 12.105 distance: 234 - 235: 30.500 distance: 235 - 236: 11.573 distance: 235 - 238: 21.210 distance: 236 - 237: 30.778 distance: 236 - 239: 32.691 distance: 239 - 240: 23.187 distance: 240 - 241: 29.452 distance: 240 - 243: 27.538 distance: 241 - 242: 25.697 distance: 241 - 250: 20.013 distance: 243 - 244: 7.994 distance: 244 - 245: 9.428 distance: 245 - 246: 10.403 distance: 246 - 247: 6.068 distance: 247 - 248: 7.220 distance: 247 - 249: 9.765 distance: 250 - 251: 14.058 distance: 251 - 252: 29.296 distance: 251 - 254: 26.561 distance: 252 - 253: 20.082 distance: 252 - 256: 18.485 distance: 254 - 255: 37.030