Starting phenix.real_space_refine on Sun Mar 17 11:46:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lpb_0940/03_2024/6lpb_0940.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lpb_0940/03_2024/6lpb_0940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lpb_0940/03_2024/6lpb_0940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lpb_0940/03_2024/6lpb_0940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lpb_0940/03_2024/6lpb_0940.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lpb_0940/03_2024/6lpb_0940.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 120 5.16 5 C 11216 2.51 5 N 3044 2.21 5 O 3254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 120": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "I GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17634 Number of models: 1 Model: "" Number of chains: 12 Chain: "P" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 225 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "R" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2710 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 319} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "A" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1864 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 225 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "D" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2710 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 319} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "F" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1864 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 1 Chain: "H" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "I" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Time building chain proxies: 9.51, per 1000 atoms: 0.54 Number of scatterers: 17634 At special positions: 0 Unit cell: (100.413, 191.697, 119.974, 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 120 16.00 O 3254 8.00 N 3044 7.00 C 11216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS R 34 " - pdb=" SG CYS R 63 " distance=2.03 Simple disulfide: pdb=" SG CYS R 54 " - pdb=" SG CYS R 118 " distance=2.03 Simple disulfide: pdb=" SG CYS R 77 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 63 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 118 " distance=2.03 Simple disulfide: pdb=" SG CYS D 77 " - pdb=" SG CYS D 134 " distance=2.03 Simple disulfide: pdb=" SG CYS D 226 " - pdb=" SG CYS D 296 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.60 Conformation dependent library (CDL) restraints added in 3.2 seconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 24 sheets defined 39.1% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'P' and resid 2 through 26 Processing helix chain 'R' and resid 27 through 46 Processing helix chain 'R' and resid 80 through 85 Processing helix chain 'R' and resid 129 through 134 Processing helix chain 'R' and resid 147 through 175 Processing helix chain 'R' and resid 184 through 211 Processing helix chain 'R' and resid 224 through 257 Processing helix chain 'R' and resid 263 through 274 removed outlier: 3.651A pdb=" N TYR R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR R 270 " --> pdb=" O PHE R 266 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE R 271 " --> pdb=" O TYR R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 290 Processing helix chain 'R' and resid 302 through 307 Processing helix chain 'R' and resid 310 through 337 removed outlier: 4.002A pdb=" N SER R 337 " --> pdb=" O GLN R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 347 through 356 Processing helix chain 'R' and resid 358 through 363 Processing helix chain 'R' and resid 377 through 387 Processing helix chain 'R' and resid 391 through 400 Processing helix chain 'R' and resid 405 through 414 removed outlier: 3.687A pdb=" N ALA R 409 " --> pdb=" O GLY R 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.690A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.602A pdb=" N GLN B 32 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.570A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.664A pdb=" N ILE A 56 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL A 57 " --> pdb=" O SER A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 57' Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.556A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 239' Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 283 through 294 removed outlier: 3.790A pdb=" N LEU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 321 through 340 Processing helix chain 'A' and resid 360 through 379 removed outlier: 3.690A pdb=" N ARG A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.501A pdb=" N ASP N 90 " --> pdb=" O LYS N 87 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 87 through 91' Processing helix chain 'G' and resid 8 through 21 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'C' and resid 2 through 26 Processing helix chain 'D' and resid 27 through 46 Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 147 through 175 Processing helix chain 'D' and resid 184 through 211 Processing helix chain 'D' and resid 224 through 257 Processing helix chain 'D' and resid 263 through 274 removed outlier: 3.651A pdb=" N TYR D 267 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 270 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE D 271 " --> pdb=" O TYR D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 290 Processing helix chain 'D' and resid 302 through 307 Processing helix chain 'D' and resid 310 through 337 removed outlier: 4.002A pdb=" N SER D 337 " --> pdb=" O GLN D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 356 Processing helix chain 'D' and resid 358 through 363 Processing helix chain 'D' and resid 377 through 387 Processing helix chain 'D' and resid 391 through 400 Processing helix chain 'D' and resid 405 through 414 removed outlier: 3.687A pdb=" N ALA D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 25 removed outlier: 3.690A pdb=" N LYS E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 33 removed outlier: 3.602A pdb=" N GLN E 32 " --> pdb=" O THR E 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 40 removed outlier: 3.570A pdb=" N THR F 40 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 removed outlier: 3.664A pdb=" N ILE F 56 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL F 57 " --> pdb=" O SER F 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 53 through 57' Processing helix chain 'F' and resid 235 through 239 removed outlier: 3.556A pdb=" N PHE F 238 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN F 239 " --> pdb=" O GLN F 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 235 through 239' Processing helix chain 'F' and resid 252 through 254 No H-bonds generated for 'chain 'F' and resid 252 through 254' Processing helix chain 'F' and resid 255 through 268 Processing helix chain 'F' and resid 283 through 294 removed outlier: 3.790A pdb=" N LEU F 287 " --> pdb=" O LYS F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 321 through 340 Processing helix chain 'F' and resid 360 through 379 removed outlier: 3.690A pdb=" N ARG F 364 " --> pdb=" O GLU F 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.501A pdb=" N ASP H 90 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR H 91 " --> pdb=" O PRO H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'I' and resid 8 through 21 Processing helix chain 'I' and resid 29 through 44 Processing sheet with id= 1, first strand: chain 'R' and resid 57 through 58 removed outlier: 3.578A pdb=" N MET R 57 " --> pdb=" O TRP R 64 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'R' and resid 72 through 76 Processing sheet with id= 3, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.858A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.042A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.812A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.742A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.097A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.550A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 275 through 276 removed outlier: 3.923A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.722A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= 12, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.182A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 57 through 58 removed outlier: 3.578A pdb=" N MET D 57 " --> pdb=" O TRP D 64 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 72 through 76 Processing sheet with id= 15, first strand: chain 'E' and resid 47 through 49 removed outlier: 6.858A pdb=" N ILE E 338 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 58 through 63 removed outlier: 4.042A pdb=" N ALA E 60 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU E 79 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA E 92 " --> pdb=" O LEU E 79 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE E 81 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 100 through 105 removed outlier: 3.812A pdb=" N THR E 102 " --> pdb=" O GLY E 115 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA E 104 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS E 121 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASN E 125 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL E 135 " --> pdb=" O ASN E 125 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'E' and resid 146 through 151 removed outlier: 3.742A pdb=" N CYS E 148 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ASP E 170 " --> pdb=" O GLN E 176 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN E 176 " --> pdb=" O ASP E 170 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'E' and resid 187 through 192 removed outlier: 7.097A pdb=" N GLY E 202 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU E 190 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL E 200 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU E 192 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N LEU E 198 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASP E 212 " --> pdb=" O CYS E 218 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N CYS E 218 " --> pdb=" O ASP E 212 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'E' and resid 229 through 234 removed outlier: 6.550A pdb=" N ASP E 254 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLU E 260 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'E' and resid 275 through 276 removed outlier: 3.923A pdb=" N SER E 275 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP E 298 " --> pdb=" O ARG E 304 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG E 304 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'F' and resid 209 through 214 removed outlier: 6.722A pdb=" N HIS F 41 " --> pdb=" O HIS F 220 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE F 222 " --> pdb=" O HIS F 41 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU F 43 " --> pdb=" O PHE F 222 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL F 247 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE F 244 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE F 280 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N PHE F 246 " --> pdb=" O PHE F 280 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN F 282 " --> pdb=" O PHE F 246 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N VAL F 248 " --> pdb=" O ASN F 282 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= 24, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.182A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) 836 hydrogen bonds defined for protein. 2412 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: 4.85 Time building geometry restraints manager: 7.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5658 1.34 - 1.46: 4576 1.46 - 1.59: 7616 1.59 - 1.71: 0 1.71 - 1.84: 168 Bond restraints: 18018 Sorted by residual: bond pdb=" CB TRP R 243 " pdb=" CG TRP R 243 " ideal model delta sigma weight residual 1.498 1.385 0.113 3.10e-02 1.04e+03 1.34e+01 bond pdb=" CB TRP D 243 " pdb=" CG TRP D 243 " ideal model delta sigma weight residual 1.498 1.385 0.113 3.10e-02 1.04e+03 1.34e+01 bond pdb=" CB VAL R 322 " pdb=" CG2 VAL R 322 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.01e+01 bond pdb=" CB VAL D 322 " pdb=" CG2 VAL D 322 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.01e+01 bond pdb=" CA PHE A 246 " pdb=" CB PHE A 246 " ideal model delta sigma weight residual 1.532 1.491 0.042 1.74e-02 3.30e+03 5.69e+00 ... (remaining 18013 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.07: 324 106.07 - 113.13: 9538 113.13 - 120.20: 7072 120.20 - 127.27: 7254 127.27 - 134.34: 200 Bond angle restraints: 24388 Sorted by residual: angle pdb=" C PRO D 126 " pdb=" N PHE D 127 " pdb=" CA PHE D 127 " ideal model delta sigma weight residual 121.57 130.84 -9.27 1.62e+00 3.81e-01 3.28e+01 angle pdb=" C PRO R 126 " pdb=" N PHE R 127 " pdb=" CA PHE R 127 " ideal model delta sigma weight residual 121.57 130.84 -9.27 1.62e+00 3.81e-01 3.28e+01 angle pdb=" N ILE E 270 " pdb=" CA ILE E 270 " pdb=" C ILE E 270 " ideal model delta sigma weight residual 113.20 108.73 4.47 9.60e-01 1.09e+00 2.17e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 108.73 4.47 9.60e-01 1.09e+00 2.17e+01 angle pdb=" CA TYR D 157 " pdb=" CB TYR D 157 " pdb=" CG TYR D 157 " ideal model delta sigma weight residual 113.90 121.61 -7.71 1.80e+00 3.09e-01 1.83e+01 ... (remaining 24383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 9230 17.62 - 35.23: 1188 35.23 - 52.85: 196 52.85 - 70.47: 32 70.47 - 88.08: 16 Dihedral angle restraints: 10662 sinusoidal: 4240 harmonic: 6422 Sorted by residual: dihedral pdb=" CB CYS R 54 " pdb=" SG CYS R 54 " pdb=" SG CYS R 118 " pdb=" CB CYS R 118 " ideal model delta sinusoidal sigma weight residual -86.00 -157.05 71.05 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CB CYS D 54 " pdb=" SG CYS D 54 " pdb=" SG CYS D 118 " pdb=" CB CYS D 118 " ideal model delta sinusoidal sigma weight residual -86.00 -157.05 71.05 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CB CYS D 77 " pdb=" SG CYS D 77 " pdb=" SG CYS D 134 " pdb=" CB CYS D 134 " ideal model delta sinusoidal sigma weight residual 93.00 155.56 -62.56 1 1.00e+01 1.00e-02 5.18e+01 ... (remaining 10659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1960 0.058 - 0.116: 592 0.116 - 0.175: 118 0.175 - 0.233: 14 0.233 - 0.291: 8 Chirality restraints: 2692 Sorted by residual: chirality pdb=" CB ILE R 272 " pdb=" CA ILE R 272 " pdb=" CG1 ILE R 272 " pdb=" CG2 ILE R 272 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB ILE D 272 " pdb=" CA ILE D 272 " pdb=" CG1 ILE D 272 " pdb=" CG2 ILE D 272 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB ILE E 157 " pdb=" CA ILE E 157 " pdb=" CG1 ILE E 157 " pdb=" CG2 ILE E 157 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 2689 not shown) Planarity restraints: 3106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 311 " -0.055 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO D 312 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO D 312 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 312 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 311 " 0.055 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO R 312 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO R 312 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO R 312 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 127 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO D 128 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 128 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 128 " 0.038 5.00e-02 4.00e+02 ... (remaining 3103 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3726 2.77 - 3.30: 15358 3.30 - 3.83: 28749 3.83 - 4.37: 31837 4.37 - 4.90: 56606 Nonbonded interactions: 136276 Sorted by model distance: nonbonded pdb=" O ALA A 48 " pdb=" OG SER A 51 " model vdw 2.232 2.440 nonbonded pdb=" O ALA F 48 " pdb=" OG SER F 51 " model vdw 2.232 2.440 nonbonded pdb=" OG SER C 2 " pdb=" OE1 GLU D 385 " model vdw 2.257 2.440 nonbonded pdb=" OG SER P 2 " pdb=" OE1 GLU R 385 " model vdw 2.257 2.440 nonbonded pdb=" OG SER E 161 " pdb=" OG1 THR E 165 " model vdw 2.276 2.440 ... (remaining 136271 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.410 Check model and map are aligned: 0.320 Set scattering table: 0.150 Process input model: 45.870 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.110 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 : 0.009 0.113 18018 Z= 0.579 Angle : 1.055 12.387 24388 Z= 0.600 Chirality : 0.058 0.291 2692 Planarity : 0.007 0.083 3106 Dihedral : 15.620 88.082 6484 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.26 % Allowed : 13.72 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.86 (0.15), residues: 2160 helix: -2.93 (0.12), residues: 804 sheet: -1.36 (0.23), residues: 492 loop : -2.73 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP B 297 HIS 0.008 0.002 HIS E 266 PHE 0.031 0.003 PHE B 234 TYR 0.031 0.003 TYR R 157 ARG 0.006 0.001 ARG R 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 345 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 17 MET cc_start: 0.7200 (ttm) cc_final: 0.6806 (ttp) REVERT: R 82 ARG cc_start: 0.6088 (mtt90) cc_final: 0.5196 (ptm160) REVERT: R 300 ASN cc_start: 0.8770 (m-40) cc_final: 0.8565 (m110) REVERT: R 356 LEU cc_start: 0.8490 (tt) cc_final: 0.8038 (tp) REVERT: B 217 MET cc_start: 0.7874 (mtt) cc_final: 0.7629 (mtm) REVERT: B 218 CYS cc_start: 0.8394 (t) cc_final: 0.7338 (p) REVERT: B 219 ARG cc_start: 0.7241 (mmt-90) cc_final: 0.6219 (mtp180) REVERT: B 258 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6599 (t70) REVERT: B 289 TYR cc_start: 0.8928 (m-80) cc_final: 0.8714 (m-80) REVERT: A 231 ARG cc_start: 0.8456 (ptt90) cc_final: 0.6041 (mpt-90) REVERT: A 255 ARG cc_start: 0.7770 (mtp180) cc_final: 0.7525 (mtp85) REVERT: A 320 GLU cc_start: 0.6381 (mp0) cc_final: 0.5865 (mp0) REVERT: A 376 MET cc_start: 0.8120 (tmm) cc_final: 0.7348 (ttt) REVERT: N 70 ILE cc_start: 0.7182 (pt) cc_final: 0.6551 (pt) REVERT: N 82 GLN cc_start: 0.6638 (mt0) cc_final: 0.6421 (mt0) REVERT: C 17 MET cc_start: 0.7202 (ttm) cc_final: 0.6811 (ttp) REVERT: D 82 ARG cc_start: 0.6089 (mtt90) cc_final: 0.5199 (ptm160) REVERT: D 300 ASN cc_start: 0.8771 (m-40) cc_final: 0.8565 (m110) REVERT: D 356 LEU cc_start: 0.8491 (tt) cc_final: 0.8038 (tp) REVERT: E 217 MET cc_start: 0.7874 (mtt) cc_final: 0.7630 (mtm) REVERT: E 218 CYS cc_start: 0.8402 (t) cc_final: 0.7336 (p) REVERT: E 219 ARG cc_start: 0.7239 (mmt-90) cc_final: 0.6218 (mtp180) REVERT: E 258 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6605 (t70) REVERT: E 289 TYR cc_start: 0.8928 (m-80) cc_final: 0.8713 (m-80) REVERT: F 231 ARG cc_start: 0.8454 (ptt90) cc_final: 0.6038 (mpt-90) REVERT: F 255 ARG cc_start: 0.7769 (mtp180) cc_final: 0.7528 (mtp85) REVERT: F 320 GLU cc_start: 0.6384 (mp0) cc_final: 0.5868 (mp0) REVERT: F 376 MET cc_start: 0.8122 (tmm) cc_final: 0.7348 (ttt) REVERT: H 70 ILE cc_start: 0.7184 (pt) cc_final: 0.6556 (pt) REVERT: H 82 GLN cc_start: 0.6638 (mt0) cc_final: 0.6417 (mt0) outliers start: 24 outliers final: 14 residues processed: 365 average time/residue: 0.3314 time to fit residues: 175.4141 Evaluate side-chains 271 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 255 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain H residue 2 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 196 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS R 117 ASN R 129 HIS R 234 HIS R 333 GLN R 365 HIS B 32 GLN B 88 ASN B 220 GLN B 340 ASN A 23 ASN A 257 GLN A 347 HIS N 39 GLN N 123 GLN D 68 HIS D 117 ASN D 129 HIS D 234 HIS D 333 GLN D 365 HIS E 32 GLN E 88 ASN E 220 GLN E 340 ASN F 23 ASN F 257 GLN F 347 HIS H 39 GLN H 123 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18018 Z= 0.165 Angle : 0.544 6.997 24388 Z= 0.295 Chirality : 0.040 0.143 2692 Planarity : 0.005 0.055 3106 Dihedral : 6.338 79.979 2438 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.04 % Allowed : 18.74 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.16), residues: 2160 helix: -0.26 (0.17), residues: 820 sheet: -1.23 (0.23), residues: 456 loop : -2.19 (0.18), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 243 HIS 0.003 0.001 HIS I 44 PHE 0.025 0.001 PHE N 29 TYR 0.020 0.001 TYR H 80 ARG 0.002 0.000 ARG D 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 274 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 17 MET cc_start: 0.7234 (ttm) cc_final: 0.7001 (ttp) REVERT: R 82 ARG cc_start: 0.6289 (mtt90) cc_final: 0.5143 (ptm160) REVERT: R 300 ASN cc_start: 0.8441 (m-40) cc_final: 0.8194 (m-40) REVERT: R 354 SER cc_start: 0.9262 (t) cc_final: 0.9024 (p) REVERT: R 356 LEU cc_start: 0.8261 (tt) cc_final: 0.7843 (tp) REVERT: B 118 ASP cc_start: 0.7245 (m-30) cc_final: 0.6909 (m-30) REVERT: B 218 CYS cc_start: 0.8430 (t) cc_final: 0.7576 (p) REVERT: B 219 ARG cc_start: 0.6775 (mmt-90) cc_final: 0.5985 (ttm170) REVERT: A 49 ASP cc_start: 0.7233 (t0) cc_final: 0.6914 (t0) REVERT: A 231 ARG cc_start: 0.8074 (ptt90) cc_final: 0.5754 (mmt90) REVERT: A 271 TRP cc_start: 0.8903 (m-90) cc_final: 0.8511 (m-90) REVERT: A 376 MET cc_start: 0.8065 (tmm) cc_final: 0.7228 (ttt) REVERT: N 68 PHE cc_start: 0.7072 (m-80) cc_final: 0.6872 (m-80) REVERT: N 70 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6490 (pt) REVERT: C 17 MET cc_start: 0.7236 (ttm) cc_final: 0.7006 (ttp) REVERT: D 82 ARG cc_start: 0.6288 (mtt90) cc_final: 0.5143 (ptm160) REVERT: D 300 ASN cc_start: 0.8446 (m-40) cc_final: 0.8201 (m-40) REVERT: D 354 SER cc_start: 0.9261 (t) cc_final: 0.9025 (p) REVERT: D 356 LEU cc_start: 0.8260 (tt) cc_final: 0.7841 (tp) REVERT: E 118 ASP cc_start: 0.7246 (m-30) cc_final: 0.6909 (m-30) REVERT: E 218 CYS cc_start: 0.8442 (t) cc_final: 0.7581 (p) REVERT: E 219 ARG cc_start: 0.6777 (mmt-90) cc_final: 0.5985 (ttm170) REVERT: F 49 ASP cc_start: 0.7229 (t0) cc_final: 0.6911 (t0) REVERT: F 231 ARG cc_start: 0.8075 (ptt90) cc_final: 0.5756 (mmt90) REVERT: F 271 TRP cc_start: 0.8903 (m-90) cc_final: 0.8512 (m-90) REVERT: F 376 MET cc_start: 0.8064 (tmm) cc_final: 0.7226 (ttt) REVERT: H 68 PHE cc_start: 0.7075 (m-80) cc_final: 0.6873 (m-80) REVERT: H 70 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.6492 (pt) outliers start: 58 outliers final: 40 residues processed: 322 average time/residue: 0.3075 time to fit residues: 147.8271 Evaluate side-chains 288 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 246 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 36 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 0.0040 chunk 175 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 GLN B 142 HIS B 225 HIS N 82 GLN G 11 GLN D 31 GLN E 142 HIS E 225 HIS H 82 GLN I 11 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18018 Z= 0.316 Angle : 0.622 7.451 24388 Z= 0.334 Chirality : 0.043 0.164 2692 Planarity : 0.004 0.055 3106 Dihedral : 6.340 83.234 2432 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.65 % Allowed : 20.42 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2160 helix: 0.48 (0.18), residues: 818 sheet: -1.07 (0.24), residues: 448 loop : -1.92 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 243 HIS 0.002 0.001 HIS B 266 PHE 0.019 0.002 PHE N 29 TYR 0.035 0.002 TYR R 157 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 274 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 17 MET cc_start: 0.7289 (ttm) cc_final: 0.7053 (ttp) REVERT: R 82 ARG cc_start: 0.6127 (mtt90) cc_final: 0.5110 (ptm160) REVERT: R 300 ASN cc_start: 0.8793 (m-40) cc_final: 0.8446 (m110) REVERT: R 356 LEU cc_start: 0.8544 (tt) cc_final: 0.8084 (tp) REVERT: B 66 ASP cc_start: 0.7671 (p0) cc_final: 0.7149 (p0) REVERT: B 195 ASP cc_start: 0.6086 (OUTLIER) cc_final: 0.5880 (p0) REVERT: B 218 CYS cc_start: 0.8521 (t) cc_final: 0.7760 (p) REVERT: B 219 ARG cc_start: 0.6877 (mmt-90) cc_final: 0.5951 (ttm170) REVERT: B 301 LYS cc_start: 0.7144 (tttt) cc_final: 0.6760 (tptt) REVERT: A 231 ARG cc_start: 0.8369 (ptt90) cc_final: 0.6036 (mmt90) REVERT: A 271 TRP cc_start: 0.8972 (m-90) cc_final: 0.8413 (m-90) REVERT: A 376 MET cc_start: 0.8006 (tmm) cc_final: 0.7285 (ttt) REVERT: N 70 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6427 (pt) REVERT: G 38 MET cc_start: 0.7348 (tpt) cc_final: 0.7002 (tpp) REVERT: C 17 MET cc_start: 0.7292 (ttm) cc_final: 0.7058 (ttp) REVERT: D 82 ARG cc_start: 0.6131 (mtt90) cc_final: 0.5113 (ptm160) REVERT: D 300 ASN cc_start: 0.8798 (m-40) cc_final: 0.8449 (m110) REVERT: D 356 LEU cc_start: 0.8545 (tt) cc_final: 0.8084 (tp) REVERT: E 66 ASP cc_start: 0.7689 (p0) cc_final: 0.7188 (p0) REVERT: E 195 ASP cc_start: 0.6101 (OUTLIER) cc_final: 0.5892 (p0) REVERT: E 218 CYS cc_start: 0.8523 (t) cc_final: 0.7759 (p) REVERT: E 219 ARG cc_start: 0.6881 (mmt-90) cc_final: 0.5953 (ttm170) REVERT: E 301 LYS cc_start: 0.7142 (tttt) cc_final: 0.6759 (tptt) REVERT: F 231 ARG cc_start: 0.8369 (ptt90) cc_final: 0.6034 (mmt90) REVERT: F 271 TRP cc_start: 0.8973 (m-90) cc_final: 0.8411 (m-90) REVERT: F 376 MET cc_start: 0.8005 (tmm) cc_final: 0.7281 (ttt) REVERT: H 70 ILE cc_start: 0.7039 (OUTLIER) cc_final: 0.6428 (pt) REVERT: I 38 MET cc_start: 0.7343 (tpt) cc_final: 0.6998 (tpp) outliers start: 108 outliers final: 86 residues processed: 348 average time/residue: 0.2985 time to fit residues: 160.2512 Evaluate side-chains 346 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 256 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 195 ASP Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain I residue 36 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 208 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 234 HIS B 225 HIS ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18018 Z= 0.252 Angle : 0.573 7.177 24388 Z= 0.306 Chirality : 0.042 0.152 2692 Planarity : 0.004 0.053 3106 Dihedral : 6.105 86.367 2432 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 6.60 % Allowed : 21.62 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.18), residues: 2160 helix: 0.87 (0.18), residues: 820 sheet: -1.10 (0.25), residues: 420 loop : -1.82 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 243 HIS 0.002 0.000 HIS B 225 PHE 0.029 0.002 PHE N 29 TYR 0.027 0.002 TYR R 157 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 265 time to evaluate : 2.103 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: P 17 MET cc_start: 0.7263 (ttm) cc_final: 0.6890 (ttp) REVERT: R 61 ILE cc_start: 0.6424 (OUTLIER) cc_final: 0.5600 (mt) REVERT: R 82 ARG cc_start: 0.6149 (mtt90) cc_final: 0.5139 (ptm160) REVERT: R 157 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.8132 (p90) REVERT: R 300 ASN cc_start: 0.8688 (m-40) cc_final: 0.8412 (m-40) REVERT: R 328 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8203 (tp) REVERT: R 356 LEU cc_start: 0.8507 (tt) cc_final: 0.8040 (tp) REVERT: B 66 ASP cc_start: 0.7603 (p0) cc_final: 0.7060 (p0) REVERT: B 218 CYS cc_start: 0.8406 (t) cc_final: 0.7718 (p) REVERT: B 219 ARG cc_start: 0.6807 (mmt-90) cc_final: 0.5868 (ttm170) REVERT: A 231 ARG cc_start: 0.8372 (ptt90) cc_final: 0.5995 (mmt90) REVERT: A 271 TRP cc_start: 0.8942 (m-90) cc_final: 0.8475 (m-90) REVERT: A 376 MET cc_start: 0.8020 (tmm) cc_final: 0.7178 (ttt) REVERT: A 379 ARG cc_start: 0.6872 (ttp80) cc_final: 0.6474 (ttp-170) REVERT: N 70 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6436 (pt) REVERT: G 38 MET cc_start: 0.7345 (tpt) cc_final: 0.7082 (tpp) REVERT: G 42 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7614 (mm-30) REVERT: C 17 MET cc_start: 0.7267 (ttm) cc_final: 0.6894 (ttp) REVERT: D 61 ILE cc_start: 0.6426 (OUTLIER) cc_final: 0.5600 (mt) REVERT: D 82 ARG cc_start: 0.6144 (mtt90) cc_final: 0.5138 (ptm160) REVERT: D 157 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.8134 (p90) REVERT: D 300 ASN cc_start: 0.8691 (m-40) cc_final: 0.8415 (m-40) REVERT: D 328 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8205 (tp) REVERT: D 356 LEU cc_start: 0.8506 (tt) cc_final: 0.8038 (tp) REVERT: E 66 ASP cc_start: 0.7598 (p0) cc_final: 0.7054 (p0) REVERT: E 218 CYS cc_start: 0.8409 (t) cc_final: 0.7720 (p) REVERT: E 219 ARG cc_start: 0.6810 (mmt-90) cc_final: 0.5866 (ttm170) REVERT: F 231 ARG cc_start: 0.8374 (ptt90) cc_final: 0.5994 (mmt90) REVERT: F 271 TRP cc_start: 0.8940 (m-90) cc_final: 0.8473 (m-90) REVERT: F 376 MET cc_start: 0.8018 (tmm) cc_final: 0.7174 (ttt) REVERT: F 379 ARG cc_start: 0.6871 (ttp80) cc_final: 0.6473 (ttp-170) REVERT: H 70 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6436 (pt) REVERT: I 38 MET cc_start: 0.7346 (tpt) cc_final: 0.7085 (tpp) REVERT: I 42 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7612 (mm-30) outliers start: 126 outliers final: 98 residues processed: 353 average time/residue: 0.2743 time to fit residues: 149.1538 Evaluate side-chains 358 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 252 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 157 TYR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 SER Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain I residue 36 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS N 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18018 Z= 0.205 Angle : 0.541 7.827 24388 Z= 0.286 Chirality : 0.041 0.142 2692 Planarity : 0.004 0.050 3106 Dihedral : 5.872 87.981 2430 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 6.86 % Allowed : 22.04 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 2160 helix: 1.22 (0.18), residues: 822 sheet: -1.01 (0.25), residues: 422 loop : -1.68 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 243 HIS 0.004 0.000 HIS B 225 PHE 0.018 0.001 PHE H 29 TYR 0.022 0.001 TYR D 157 ARG 0.003 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 264 time to evaluate : 2.008 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: P 17 MET cc_start: 0.7243 (ttm) cc_final: 0.6851 (ttp) REVERT: R 61 ILE cc_start: 0.6428 (OUTLIER) cc_final: 0.5620 (mt) REVERT: R 82 ARG cc_start: 0.6137 (mtt90) cc_final: 0.4984 (ptm160) REVERT: R 157 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.8072 (p90) REVERT: R 300 ASN cc_start: 0.8618 (m-40) cc_final: 0.8336 (m-40) REVERT: R 328 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8203 (tp) REVERT: R 356 LEU cc_start: 0.8422 (tt) cc_final: 0.7951 (tp) REVERT: B 66 ASP cc_start: 0.7583 (p0) cc_final: 0.7058 (p0) REVERT: B 218 CYS cc_start: 0.8350 (t) cc_final: 0.7677 (p) REVERT: B 219 ARG cc_start: 0.6687 (mmt-90) cc_final: 0.5756 (ttm170) REVERT: A 43 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8045 (mp) REVERT: A 231 ARG cc_start: 0.8330 (ptt90) cc_final: 0.5940 (mmt90) REVERT: A 271 TRP cc_start: 0.8932 (m-90) cc_final: 0.8488 (m-90) REVERT: A 308 TYR cc_start: 0.6181 (t80) cc_final: 0.5898 (t80) REVERT: A 376 MET cc_start: 0.8051 (tmm) cc_final: 0.7128 (ttt) REVERT: A 379 ARG cc_start: 0.6864 (ttp80) cc_final: 0.6389 (ttp-170) REVERT: N 46 GLU cc_start: 0.6453 (pm20) cc_final: 0.6215 (pm20) REVERT: N 70 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6452 (pt) REVERT: G 38 MET cc_start: 0.7167 (tpt) cc_final: 0.6823 (tpp) REVERT: G 42 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7439 (mm-30) REVERT: C 17 MET cc_start: 0.7246 (ttm) cc_final: 0.6856 (ttp) REVERT: D 61 ILE cc_start: 0.6427 (OUTLIER) cc_final: 0.5622 (mt) REVERT: D 82 ARG cc_start: 0.6137 (mtt90) cc_final: 0.4984 (ptm160) REVERT: D 157 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.8081 (p90) REVERT: D 300 ASN cc_start: 0.8621 (m-40) cc_final: 0.8342 (m-40) REVERT: D 328 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8203 (tp) REVERT: D 356 LEU cc_start: 0.8422 (tt) cc_final: 0.7949 (tp) REVERT: E 66 ASP cc_start: 0.7592 (p0) cc_final: 0.7110 (p0) REVERT: E 218 CYS cc_start: 0.8353 (t) cc_final: 0.7680 (p) REVERT: E 219 ARG cc_start: 0.6685 (mmt-90) cc_final: 0.5753 (ttm170) REVERT: F 43 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8049 (mp) REVERT: F 231 ARG cc_start: 0.8325 (ptt90) cc_final: 0.5939 (mmt90) REVERT: F 271 TRP cc_start: 0.8934 (m-90) cc_final: 0.8490 (m-90) REVERT: F 308 TYR cc_start: 0.6180 (t80) cc_final: 0.5896 (t80) REVERT: F 376 MET cc_start: 0.8052 (tmm) cc_final: 0.7130 (ttt) REVERT: F 379 ARG cc_start: 0.6867 (ttp80) cc_final: 0.6391 (ttp-170) REVERT: H 46 GLU cc_start: 0.6453 (pm20) cc_final: 0.6214 (pm20) REVERT: H 70 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6455 (pt) REVERT: I 38 MET cc_start: 0.7169 (tpt) cc_final: 0.6823 (tpp) REVERT: I 42 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7435 (mm-30) outliers start: 131 outliers final: 95 residues processed: 362 average time/residue: 0.2693 time to fit residues: 149.9623 Evaluate side-chains 365 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 260 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 157 TYR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 239 SER Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 364 ILE Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain I residue 36 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 5.9990 chunk 188 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS D 31 GLN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18018 Z= 0.193 Angle : 0.537 7.087 24388 Z= 0.284 Chirality : 0.041 0.139 2692 Planarity : 0.003 0.049 3106 Dihedral : 5.793 89.685 2430 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 6.75 % Allowed : 23.51 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2160 helix: 1.43 (0.18), residues: 820 sheet: -0.97 (0.25), residues: 418 loop : -1.60 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 243 HIS 0.003 0.000 HIS B 225 PHE 0.013 0.001 PHE H 68 TYR 0.021 0.001 TYR R 157 ARG 0.003 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 262 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 17 MET cc_start: 0.7226 (ttm) cc_final: 0.6824 (ttp) REVERT: R 61 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.5793 (mt) REVERT: R 82 ARG cc_start: 0.6145 (mtt90) cc_final: 0.4988 (ptm160) REVERT: R 190 MET cc_start: 0.7467 (mmt) cc_final: 0.6755 (mmt) REVERT: R 300 ASN cc_start: 0.8437 (m-40) cc_final: 0.8172 (m-40) REVERT: R 328 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8202 (tp) REVERT: R 356 LEU cc_start: 0.8383 (tt) cc_final: 0.7934 (tp) REVERT: B 66 ASP cc_start: 0.7593 (p0) cc_final: 0.7111 (p0) REVERT: B 218 CYS cc_start: 0.8297 (t) cc_final: 0.7738 (p) REVERT: B 301 LYS cc_start: 0.7640 (tttt) cc_final: 0.7046 (tptt) REVERT: B 325 MET cc_start: 0.7652 (tpp) cc_final: 0.7269 (tpp) REVERT: A 231 ARG cc_start: 0.8349 (ptt90) cc_final: 0.5996 (mmt90) REVERT: A 308 TYR cc_start: 0.6192 (t80) cc_final: 0.5916 (t80) REVERT: A 376 MET cc_start: 0.8071 (tmm) cc_final: 0.7177 (ttt) REVERT: A 379 ARG cc_start: 0.6856 (ttp80) cc_final: 0.6397 (ttp-170) REVERT: N 19 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.5598 (tmm-80) REVERT: N 70 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6255 (pt) REVERT: G 38 MET cc_start: 0.7072 (tpt) cc_final: 0.6790 (tpp) REVERT: G 42 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7384 (mm-30) REVERT: C 17 MET cc_start: 0.7229 (ttm) cc_final: 0.6829 (ttp) REVERT: D 61 ILE cc_start: 0.6590 (OUTLIER) cc_final: 0.5794 (mt) REVERT: D 82 ARG cc_start: 0.6147 (mtt90) cc_final: 0.4989 (ptm160) REVERT: D 190 MET cc_start: 0.7466 (mmt) cc_final: 0.6757 (mmt) REVERT: D 300 ASN cc_start: 0.8440 (m-40) cc_final: 0.8175 (m-40) REVERT: D 328 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8203 (tp) REVERT: D 356 LEU cc_start: 0.8384 (tt) cc_final: 0.7934 (tp) REVERT: E 66 ASP cc_start: 0.7589 (p0) cc_final: 0.7102 (p0) REVERT: E 218 CYS cc_start: 0.8304 (t) cc_final: 0.7739 (p) REVERT: E 301 LYS cc_start: 0.7643 (tttt) cc_final: 0.7046 (tptt) REVERT: E 325 MET cc_start: 0.7651 (tpp) cc_final: 0.7268 (tpp) REVERT: F 231 ARG cc_start: 0.8346 (ptt90) cc_final: 0.5999 (mmt90) REVERT: F 308 TYR cc_start: 0.6194 (t80) cc_final: 0.5921 (t80) REVERT: F 376 MET cc_start: 0.8072 (tmm) cc_final: 0.7174 (ttt) REVERT: F 379 ARG cc_start: 0.6855 (ttp80) cc_final: 0.6402 (ttp-170) REVERT: H 19 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.5596 (tmm-80) REVERT: H 70 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6207 (pt) REVERT: I 38 MET cc_start: 0.7072 (tpt) cc_final: 0.6791 (tpp) REVERT: I 42 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7379 (mm-30) outliers start: 129 outliers final: 108 residues processed: 366 average time/residue: 0.2688 time to fit residues: 151.3750 Evaluate side-chains 369 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 253 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 239 SER Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 258 THR Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 364 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain I residue 36 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 7.9990 chunk 23 optimal weight: 0.0060 chunk 119 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 208 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS D 31 GLN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18018 Z= 0.152 Angle : 0.509 7.336 24388 Z= 0.267 Chirality : 0.039 0.136 2692 Planarity : 0.003 0.048 3106 Dihedral : 5.544 87.045 2430 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.08 % Allowed : 25.60 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2160 helix: 1.72 (0.18), residues: 818 sheet: -0.69 (0.25), residues: 440 loop : -1.56 (0.19), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 64 HIS 0.002 0.000 HIS B 225 PHE 0.010 0.001 PHE H 29 TYR 0.018 0.001 TYR R 157 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 267 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 61 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.5811 (mt) REVERT: R 82 ARG cc_start: 0.6161 (mtt90) cc_final: 0.4901 (ptm160) REVERT: R 190 MET cc_start: 0.7356 (mmt) cc_final: 0.6669 (mmt) REVERT: R 300 ASN cc_start: 0.8268 (m-40) cc_final: 0.8039 (m-40) REVERT: R 328 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8190 (tp) REVERT: R 356 LEU cc_start: 0.8309 (tt) cc_final: 0.7925 (tp) REVERT: B 42 ARG cc_start: 0.6713 (tpp80) cc_final: 0.6331 (tpp80) REVERT: B 66 ASP cc_start: 0.7454 (p0) cc_final: 0.6989 (p0) REVERT: B 218 CYS cc_start: 0.8413 (t) cc_final: 0.7760 (p) REVERT: B 219 ARG cc_start: 0.6161 (mmt180) cc_final: 0.5627 (ttm170) REVERT: B 301 LYS cc_start: 0.7564 (tttt) cc_final: 0.7006 (tptt) REVERT: B 325 MET cc_start: 0.7606 (tpp) cc_final: 0.7209 (tpp) REVERT: A 231 ARG cc_start: 0.8191 (ptt90) cc_final: 0.6066 (mpt-90) REVERT: A 308 TYR cc_start: 0.6190 (t80) cc_final: 0.5862 (t80) REVERT: A 376 MET cc_start: 0.8057 (tmm) cc_final: 0.7687 (tmm) REVERT: A 379 ARG cc_start: 0.6801 (ttp80) cc_final: 0.6250 (ttp-170) REVERT: N 70 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6457 (pt) REVERT: D 61 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.5815 (mt) REVERT: D 82 ARG cc_start: 0.6161 (mtt90) cc_final: 0.4900 (ptm160) REVERT: D 190 MET cc_start: 0.7359 (mmt) cc_final: 0.6670 (mmt) REVERT: D 300 ASN cc_start: 0.8270 (m-40) cc_final: 0.8041 (m-40) REVERT: D 328 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8187 (tp) REVERT: D 356 LEU cc_start: 0.8309 (tt) cc_final: 0.7924 (tp) REVERT: E 42 ARG cc_start: 0.6714 (tpp80) cc_final: 0.6334 (tpp80) REVERT: E 66 ASP cc_start: 0.7448 (p0) cc_final: 0.6982 (p0) REVERT: E 218 CYS cc_start: 0.8422 (t) cc_final: 0.7759 (p) REVERT: E 219 ARG cc_start: 0.6109 (mmt180) cc_final: 0.5547 (ttm170) REVERT: E 251 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7539 (mtt180) REVERT: E 301 LYS cc_start: 0.7569 (tttt) cc_final: 0.7004 (tptt) REVERT: E 325 MET cc_start: 0.7606 (tpp) cc_final: 0.7210 (tpp) REVERT: F 231 ARG cc_start: 0.8188 (ptt90) cc_final: 0.6067 (mpt-90) REVERT: F 308 TYR cc_start: 0.6189 (t80) cc_final: 0.5860 (t80) REVERT: F 376 MET cc_start: 0.8053 (tmm) cc_final: 0.7684 (tmm) REVERT: F 379 ARG cc_start: 0.6796 (ttp80) cc_final: 0.6247 (ttp-170) REVERT: H 70 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6463 (pt) outliers start: 97 outliers final: 80 residues processed: 341 average time/residue: 0.2882 time to fit residues: 150.0291 Evaluate side-chains 339 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 253 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 SER Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 258 THR Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 328 ILE Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain I residue 36 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 141 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS N 82 GLN D 31 GLN ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18018 Z= 0.284 Angle : 0.600 8.216 24388 Z= 0.316 Chirality : 0.043 0.154 2692 Planarity : 0.004 0.056 3106 Dihedral : 5.840 82.669 2430 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.54 % Allowed : 24.87 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.18), residues: 2160 helix: 1.47 (0.18), residues: 818 sheet: -0.95 (0.25), residues: 426 loop : -1.49 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 243 HIS 0.003 0.001 HIS B 225 PHE 0.013 0.002 PHE H 68 TYR 0.032 0.002 TYR R 157 ARG 0.003 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 257 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 82 ARG cc_start: 0.6104 (mtt90) cc_final: 0.4988 (ptm160) REVERT: R 300 ASN cc_start: 0.8601 (m-40) cc_final: 0.8288 (m110) REVERT: R 356 LEU cc_start: 0.8421 (tt) cc_final: 0.7934 (tp) REVERT: B 66 ASP cc_start: 0.7587 (p0) cc_final: 0.7036 (p0) REVERT: B 217 MET cc_start: 0.8093 (mtt) cc_final: 0.7432 (mtm) REVERT: B 218 CYS cc_start: 0.8432 (t) cc_final: 0.7752 (p) REVERT: B 219 ARG cc_start: 0.6480 (mmt180) cc_final: 0.5764 (mtp180) REVERT: B 301 LYS cc_start: 0.7743 (tttt) cc_final: 0.7145 (tptt) REVERT: B 325 MET cc_start: 0.7684 (tpp) cc_final: 0.7336 (tpp) REVERT: A 231 ARG cc_start: 0.8296 (ptt90) cc_final: 0.5985 (mmt90) REVERT: A 308 TYR cc_start: 0.6216 (t80) cc_final: 0.5876 (t80) REVERT: A 376 MET cc_start: 0.8102 (tmm) cc_final: 0.7262 (ttt) REVERT: A 379 ARG cc_start: 0.6959 (ttp80) cc_final: 0.6436 (ttp-170) REVERT: N 70 ILE cc_start: 0.7052 (OUTLIER) cc_final: 0.6394 (pt) REVERT: D 82 ARG cc_start: 0.6105 (mtt90) cc_final: 0.4988 (ptm160) REVERT: D 300 ASN cc_start: 0.8600 (m-40) cc_final: 0.8289 (m110) REVERT: D 356 LEU cc_start: 0.8423 (tt) cc_final: 0.7935 (tp) REVERT: E 66 ASP cc_start: 0.7581 (p0) cc_final: 0.7033 (p0) REVERT: E 218 CYS cc_start: 0.8448 (t) cc_final: 0.7727 (p) REVERT: E 219 ARG cc_start: 0.6473 (mmt180) cc_final: 0.5701 (ttm170) REVERT: E 301 LYS cc_start: 0.7741 (tttt) cc_final: 0.7146 (tptt) REVERT: E 325 MET cc_start: 0.7682 (tpp) cc_final: 0.7332 (tpp) REVERT: F 231 ARG cc_start: 0.8296 (ptt90) cc_final: 0.5989 (mmt90) REVERT: F 308 TYR cc_start: 0.6216 (t80) cc_final: 0.5879 (t80) REVERT: F 376 MET cc_start: 0.8097 (tmm) cc_final: 0.7257 (ttt) REVERT: F 379 ARG cc_start: 0.6956 (ttp80) cc_final: 0.6436 (ttp-170) REVERT: H 70 ILE cc_start: 0.7051 (OUTLIER) cc_final: 0.6402 (pt) outliers start: 125 outliers final: 110 residues processed: 353 average time/residue: 0.2706 time to fit residues: 148.1480 Evaluate side-chains 369 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 257 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 239 SER Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 258 THR Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 376 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 152 optimal weight: 0.0000 chunk 59 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 GLN R 68 HIS ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS N 82 GLN D 31 GLN D 68 HIS ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18018 Z= 0.220 Angle : 0.568 8.484 24388 Z= 0.298 Chirality : 0.041 0.141 2692 Planarity : 0.004 0.050 3106 Dihedral : 5.728 82.104 2430 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.39 % Allowed : 25.03 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.18), residues: 2160 helix: 1.58 (0.18), residues: 820 sheet: -0.80 (0.26), residues: 422 loop : -1.43 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 243 HIS 0.005 0.001 HIS D 68 PHE 0.014 0.001 PHE N 68 TYR 0.022 0.001 TYR R 157 ARG 0.003 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 256 time to evaluate : 2.260 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: P 17 MET cc_start: 0.7032 (ttm) cc_final: 0.6700 (ttp) REVERT: R 82 ARG cc_start: 0.6059 (mtt90) cc_final: 0.4899 (ptm160) REVERT: R 157 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.8097 (p90) REVERT: R 190 MET cc_start: 0.7478 (mmt) cc_final: 0.6782 (mmt) REVERT: R 261 PRO cc_start: 0.7662 (Cg_exo) cc_final: 0.7281 (Cg_endo) REVERT: R 300 ASN cc_start: 0.8541 (m-40) cc_final: 0.8202 (m110) REVERT: R 356 LEU cc_start: 0.8394 (tt) cc_final: 0.7936 (tp) REVERT: B 66 ASP cc_start: 0.7553 (p0) cc_final: 0.7013 (p0) REVERT: B 190 LEU cc_start: 0.8944 (mt) cc_final: 0.8676 (mt) REVERT: B 218 CYS cc_start: 0.8423 (t) cc_final: 0.7715 (p) REVERT: B 219 ARG cc_start: 0.6275 (mmt180) cc_final: 0.5778 (ttm170) REVERT: B 301 LYS cc_start: 0.7721 (tttt) cc_final: 0.7142 (tptt) REVERT: B 325 MET cc_start: 0.7645 (tpp) cc_final: 0.7246 (tpp) REVERT: A 231 ARG cc_start: 0.8294 (ptt90) cc_final: 0.6052 (mmt90) REVERT: A 308 TYR cc_start: 0.6198 (t80) cc_final: 0.5850 (t80) REVERT: A 376 MET cc_start: 0.8088 (tmm) cc_final: 0.7230 (ttt) REVERT: A 379 ARG cc_start: 0.6933 (ttp80) cc_final: 0.6431 (ttp-170) REVERT: N 70 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6289 (pt) REVERT: N 83 MET cc_start: 0.7261 (mtm) cc_final: 0.6707 (ptp) REVERT: C 17 MET cc_start: 0.7033 (ttm) cc_final: 0.6702 (ttp) REVERT: D 82 ARG cc_start: 0.6067 (mtt90) cc_final: 0.4902 (ptm160) REVERT: D 157 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.8100 (p90) REVERT: D 190 MET cc_start: 0.7481 (mmt) cc_final: 0.6785 (mmt) REVERT: D 261 PRO cc_start: 0.7665 (Cg_exo) cc_final: 0.7283 (Cg_endo) REVERT: D 300 ASN cc_start: 0.8544 (m-40) cc_final: 0.8206 (m110) REVERT: D 356 LEU cc_start: 0.8396 (tt) cc_final: 0.7935 (tp) REVERT: E 66 ASP cc_start: 0.7551 (p0) cc_final: 0.7010 (p0) REVERT: E 190 LEU cc_start: 0.8942 (mt) cc_final: 0.8675 (mt) REVERT: E 218 CYS cc_start: 0.8406 (t) cc_final: 0.7712 (p) REVERT: E 219 ARG cc_start: 0.6345 (mmt180) cc_final: 0.5864 (ttm170) REVERT: E 301 LYS cc_start: 0.7718 (tttt) cc_final: 0.7140 (tptt) REVERT: E 325 MET cc_start: 0.7640 (tpp) cc_final: 0.7240 (tpp) REVERT: F 231 ARG cc_start: 0.8288 (ptt90) cc_final: 0.6051 (mmt90) REVERT: F 308 TYR cc_start: 0.6196 (t80) cc_final: 0.5849 (t80) REVERT: F 376 MET cc_start: 0.8084 (tmm) cc_final: 0.7228 (ttt) REVERT: F 379 ARG cc_start: 0.6931 (ttp80) cc_final: 0.6430 (ttp-170) REVERT: H 70 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6292 (pt) REVERT: H 83 MET cc_start: 0.7213 (mtm) cc_final: 0.6649 (ptp) outliers start: 122 outliers final: 112 residues processed: 350 average time/residue: 0.2641 time to fit residues: 143.0097 Evaluate side-chains 372 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 256 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 157 TYR Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 239 SER Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 258 THR Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain R residue 376 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 157 TYR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain E residue 322 ASP Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.3980 chunk 125 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS D 31 GLN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18018 Z= 0.170 Angle : 0.542 8.640 24388 Z= 0.283 Chirality : 0.040 0.137 2692 Planarity : 0.003 0.048 3106 Dihedral : 5.545 79.711 2430 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.71 % Allowed : 25.65 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.18), residues: 2160 helix: 1.73 (0.18), residues: 824 sheet: -0.70 (0.26), residues: 434 loop : -1.37 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 243 HIS 0.006 0.001 HIS B 225 PHE 0.012 0.001 PHE H 68 TYR 0.018 0.001 TYR P 22 ARG 0.003 0.000 ARG E 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 260 time to evaluate : 2.062 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: P 17 MET cc_start: 0.7002 (ttm) cc_final: 0.6662 (ttp) REVERT: R 82 ARG cc_start: 0.6120 (mtt90) cc_final: 0.4985 (ptm160) REVERT: R 190 MET cc_start: 0.7423 (mmt) cc_final: 0.6743 (mmt) REVERT: R 261 PRO cc_start: 0.7555 (Cg_exo) cc_final: 0.7186 (Cg_endo) REVERT: R 300 ASN cc_start: 0.8432 (m-40) cc_final: 0.8179 (m-40) REVERT: R 356 LEU cc_start: 0.8347 (tt) cc_final: 0.7916 (tp) REVERT: B 66 ASP cc_start: 0.7602 (p0) cc_final: 0.7073 (p0) REVERT: B 190 LEU cc_start: 0.9122 (mt) cc_final: 0.8902 (mt) REVERT: B 218 CYS cc_start: 0.8420 (t) cc_final: 0.7741 (p) REVERT: B 219 ARG cc_start: 0.6238 (mmt180) cc_final: 0.5794 (ttm170) REVERT: B 301 LYS cc_start: 0.7687 (tttt) cc_final: 0.7432 (tttp) REVERT: B 325 MET cc_start: 0.7540 (tpp) cc_final: 0.7152 (tpp) REVERT: A 231 ARG cc_start: 0.8125 (ptt90) cc_final: 0.5877 (mmt90) REVERT: A 308 TYR cc_start: 0.6169 (t80) cc_final: 0.5815 (t80) REVERT: A 376 MET cc_start: 0.8076 (tmm) cc_final: 0.7177 (ttt) REVERT: A 379 ARG cc_start: 0.6875 (ttp80) cc_final: 0.6389 (ttp-170) REVERT: N 70 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6548 (pt) REVERT: N 83 MET cc_start: 0.7138 (mtm) cc_final: 0.6571 (ptp) REVERT: C 17 MET cc_start: 0.7005 (ttm) cc_final: 0.6662 (ttp) REVERT: D 82 ARG cc_start: 0.6118 (mtt90) cc_final: 0.4979 (ptm160) REVERT: D 190 MET cc_start: 0.7425 (mmt) cc_final: 0.6744 (mmt) REVERT: D 261 PRO cc_start: 0.7557 (Cg_exo) cc_final: 0.7189 (Cg_endo) REVERT: D 300 ASN cc_start: 0.8437 (m-40) cc_final: 0.8181 (m-40) REVERT: D 356 LEU cc_start: 0.8348 (tt) cc_final: 0.7914 (tp) REVERT: E 66 ASP cc_start: 0.7605 (p0) cc_final: 0.7078 (p0) REVERT: E 190 LEU cc_start: 0.9120 (mt) cc_final: 0.8899 (mt) REVERT: E 218 CYS cc_start: 0.8390 (t) cc_final: 0.7747 (p) REVERT: E 219 ARG cc_start: 0.6280 (mmt180) cc_final: 0.5845 (ttm170) REVERT: E 301 LYS cc_start: 0.7682 (tttt) cc_final: 0.7428 (tttp) REVERT: E 325 MET cc_start: 0.7536 (tpp) cc_final: 0.7148 (tpp) REVERT: F 231 ARG cc_start: 0.8122 (ptt90) cc_final: 0.5883 (mmt90) REVERT: F 308 TYR cc_start: 0.6170 (t80) cc_final: 0.5816 (t80) REVERT: F 376 MET cc_start: 0.8074 (tmm) cc_final: 0.7175 (ttt) REVERT: F 379 ARG cc_start: 0.6874 (ttp80) cc_final: 0.6390 (ttp-170) REVERT: H 70 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6519 (pt) outliers start: 109 outliers final: 103 residues processed: 345 average time/residue: 0.2686 time to fit residues: 142.9990 Evaluate side-chains 365 residues out of total 1912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 260 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 34 CYS Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 223 THR Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 239 SER Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 258 THR Chi-restraints excluded: chain R residue 282 THR Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 316 SER Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 354 SER Chi-restraints excluded: chain R residue 376 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 74 ASN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 8 ASP Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain D residue 34 CYS Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 246 ILE Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 354 SER Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 75 GLN Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 233 CYS Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 303 ASP Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain I residue 36 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS D 31 GLN ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.186634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.154489 restraints weight = 20979.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.148262 restraints weight = 25869.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.148621 restraints weight = 26143.000| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18018 Z= 0.238 Angle : 0.578 8.628 24388 Z= 0.303 Chirality : 0.042 0.146 2692 Planarity : 0.004 0.050 3106 Dihedral : 5.635 76.356 2430 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 6.13 % Allowed : 25.60 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2160 helix: 1.65 (0.18), residues: 820 sheet: -0.74 (0.26), residues: 434 loop : -1.40 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 243 HIS 0.007 0.001 HIS B 225 PHE 0.012 0.001 PHE H 68 TYR 0.024 0.002 TYR R 157 ARG 0.003 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3460.64 seconds wall clock time: 63 minutes 52.83 seconds (3832.83 seconds total)