Starting phenix.real_space_refine on Sun Apr 7 13:06:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot0_20190/04_2024/6ot0_20190_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot0_20190/04_2024/6ot0_20190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot0_20190/04_2024/6ot0_20190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot0_20190/04_2024/6ot0_20190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot0_20190/04_2024/6ot0_20190_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ot0_20190/04_2024/6ot0_20190_updated.pdb" } resolution = 3.84 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= 0.003 sd= 0.067 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 71 5.16 5 C 6723 2.51 5 N 1792 2.21 5 O 1986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ASP 229": "OD1" <-> "OD2" Residue "R TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "R PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 382": "OD1" <-> "OD2" Residue "R PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 439": "OE1" <-> "OE2" Residue "R PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 482": "NH1" <-> "NH2" Residue "R ASP 486": "OD1" <-> "OD2" Residue "R ARG 512": "NH1" <-> "NH2" Residue "R PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 547": "NH1" <-> "NH2" Residue "A ASP 20": "OD1" <-> "OD2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 94": "OD1" <-> "OD2" Residue "A ASP 102": "OD1" <-> "OD2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10572 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2887 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 13, 'TRANS': 350} Chain: "A" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2832 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 349} Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 778 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 995 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CO1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.85, per 1000 atoms: 0.55 Number of scatterers: 10572 At special positions: 0 Unit cell: (143.38, 131.61, 120.91, 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 71 16.00 O 1986 8.00 N 1792 7.00 C 6723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 193 " - pdb=" SG CYS R 213 " distance=2.03 Simple disulfide: pdb=" SG CYS R 490 " - pdb=" SG CYS R 507 " distance=2.02 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " 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: 4.17 Conformation dependent library (CDL) restraints added in 1.9 seconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 13 sheets defined 33.4% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'R' and resid 224 through 254 removed outlier: 4.194A pdb=" N THR R 251 " --> pdb=" O PHE R 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE R 252 " --> pdb=" O THR R 248 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA R 254 " --> pdb=" O ALA R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 272 removed outlier: 4.661A pdb=" N ASN R 271 " --> pdb=" O LEU R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 282 removed outlier: 3.705A pdb=" N GLY R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 308 No H-bonds generated for 'chain 'R' and resid 306 through 308' Processing helix chain 'R' and resid 315 through 344 Processing helix chain 'R' and resid 357 through 376 Proline residue: R 368 - end of helix Processing helix chain 'R' and resid 398 through 425 removed outlier: 4.676A pdb=" N GLY R 402 " --> pdb=" O ARG R 398 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE R 403 " --> pdb=" O TYR R 399 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL R 404 " --> pdb=" O ARG R 400 " (cutoff:3.500A) Proline residue: R 407 - end of helix Processing helix chain 'R' and resid 439 through 493 removed outlier: 3.682A pdb=" N LYS R 444 " --> pdb=" O LYS R 440 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL R 463 " --> pdb=" O ALA R 459 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU R 464 " --> pdb=" O PHE R 460 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR R 466 " --> pdb=" O PHE R 462 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE R 475 " --> pdb=" O PHE R 471 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN R 476 " --> pdb=" O TYR R 472 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA R 478 " --> pdb=" O PHE R 474 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU R 479 " --> pdb=" O PHE R 475 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA R 492 " --> pdb=" O VAL R 488 " (cutoff:3.500A) Processing helix chain 'R' and resid 518 through 531 Processing helix chain 'R' and resid 533 through 536 No H-bonds generated for 'chain 'R' and resid 533 through 536' Processing helix chain 'R' and resid 541 through 550 Processing helix chain 'A' and resid 4 through 30 removed outlier: 4.387A pdb=" N GLU A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASP A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLY A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 66 through 90 Processing helix chain 'A' and resid 101 through 111 removed outlier: 3.904A pdb=" N LEU A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 removed outlier: 4.096A pdb=" N ARG A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.873A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 152 through 157' Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 211 through 214 Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.702A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.807A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.443A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 6 through 21 Processing helix chain 'G' and resid 30 through 44 removed outlier: 3.690A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing sheet with id= A, first strand: chain 'R' and resid 197 through 199 Processing sheet with id= B, first strand: chain 'A' and resid 263 through 268 removed outlier: 3.574A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 60 through 63 removed outlier: 4.413A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.352A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.403A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.163A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 240 through 242 removed outlier: 3.837A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 284 through 288 removed outlier: 3.878A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 335 through 339 removed outlier: 4.446A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 7 through 9 Processing sheet with id= K, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.593A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 7 through 10 Processing sheet with id= M, first strand: chain 'H' and resid 125 through 127 removed outlier: 6.062A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1170 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: 2.75 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3036 1.34 - 1.45: 1735 1.45 - 1.57: 5923 1.57 - 1.69: 11 1.69 - 1.81: 101 Bond restraints: 10806 Sorted by residual: bond pdb=" C TYR R 262 " pdb=" O TYR R 262 " ideal model delta sigma weight residual 1.238 1.550 -0.312 1.28e-02 6.10e+03 5.95e+02 bond pdb=" C14 CO1 R 601 " pdb=" C7 CO1 R 601 " ideal model delta sigma weight residual 1.519 1.629 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C11 CO1 R 601 " pdb=" C5 CO1 R 601 " ideal model delta sigma weight residual 1.530 1.605 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" CA VAL R 195 " pdb=" CB VAL R 195 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.35e+01 bond pdb=" C12 CO1 R 601 " pdb=" C5 CO1 R 601 " ideal model delta sigma weight residual 1.532 1.605 -0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 10801 not shown) Histogram of bond angle deviations from ideal: 56.01 - 71.64: 3 71.64 - 87.28: 0 87.28 - 102.91: 48 102.91 - 118.54: 8430 118.54 - 134.17: 6172 Bond angle restraints: 14653 Sorted by residual: angle pdb=" C TYR R 262 " pdb=" N PRO R 263 " pdb=" CA PRO R 263 " ideal model delta sigma weight residual 119.84 128.24 -8.40 1.25e+00 6.40e-01 4.51e+01 angle pdb=" C GLU R 305 " pdb=" N PRO R 306 " pdb=" CA PRO R 306 " ideal model delta sigma weight residual 119.19 125.75 -6.56 1.06e+00 8.90e-01 3.83e+01 angle pdb=" CA VAL R 195 " pdb=" C VAL R 195 " pdb=" N PRO R 196 " ideal model delta sigma weight residual 120.83 117.75 3.08 6.10e-01 2.69e+00 2.54e+01 angle pdb=" N GLY R 347 " pdb=" CA GLY R 347 " pdb=" C GLY R 347 " ideal model delta sigma weight residual 113.18 102.43 10.75 2.37e+00 1.78e-01 2.06e+01 angle pdb=" N ASP B 246 " pdb=" CA ASP B 246 " pdb=" C ASP B 246 " ideal model delta sigma weight residual 112.87 118.27 -5.40 1.20e+00 6.94e-01 2.03e+01 ... (remaining 14648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 5627 15.50 - 31.00: 598 31.00 - 46.49: 164 46.49 - 61.99: 29 61.99 - 77.49: 14 Dihedral angle restraints: 6432 sinusoidal: 2532 harmonic: 3900 Sorted by residual: dihedral pdb=" CA TYR R 262 " pdb=" C TYR R 262 " pdb=" N PRO R 263 " pdb=" CA PRO R 263 " ideal model delta harmonic sigma weight residual 180.00 -110.37 -69.63 0 5.00e+00 4.00e-02 1.94e+02 dihedral pdb=" CA GLY R 347 " pdb=" C GLY R 347 " pdb=" N THR R 348 " pdb=" CA THR R 348 " ideal model delta harmonic sigma weight residual -180.00 -145.34 -34.66 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA LEU R 346 " pdb=" C LEU R 346 " pdb=" N GLY R 347 " pdb=" CA GLY R 347 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 6429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1322 0.085 - 0.171: 275 0.171 - 0.256: 30 0.256 - 0.341: 5 0.341 - 0.427: 3 Chirality restraints: 1635 Sorted by residual: chirality pdb=" C5 CO1 R 601 " pdb=" C10 CO1 R 601 " pdb=" C11 CO1 R 601 " pdb=" C2 CO1 R 601 " both_signs ideal model delta sigma weight residual False -2.93 -3.36 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" C7 CO1 R 601 " pdb=" C14 CO1 R 601 " pdb=" C15 CO1 R 601 " pdb=" C3 CO1 R 601 " both_signs ideal model delta sigma weight residual False 2.86 3.27 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C2 CO1 R 601 " pdb=" C1 CO1 R 601 " pdb=" C5 CO1 R 601 " pdb=" C6 CO1 R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 1632 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 262 " -0.055 2.00e-02 2.50e+03 1.01e-01 1.02e+02 pdb=" C TYR R 262 " 0.175 2.00e-02 2.50e+03 pdb=" O TYR R 262 " -0.056 2.00e-02 2.50e+03 pdb=" N PRO R 263 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 262 " 0.088 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO R 263 " -0.228 5.00e-02 4.00e+02 pdb=" CA PRO R 263 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO R 263 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS R 433 " -0.045 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO R 434 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 434 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 434 " -0.038 5.00e-02 4.00e+02 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3116 2.84 - 3.35: 9952 3.35 - 3.87: 17382 3.87 - 4.38: 18418 4.38 - 4.90: 31346 Nonbonded interactions: 80214 Sorted by model distance: nonbonded pdb=" OD2 ASP A 231 " pdb=" NZ LYS A 277 " model vdw 2.324 2.520 nonbonded pdb=" ND2 ASN A 311 " pdb=" O LYS A 314 " model vdw 2.365 2.520 nonbonded pdb=" O VAL R 333 " pdb=" OG1 THR R 336 " model vdw 2.389 2.440 nonbonded pdb=" O CYS R 490 " pdb=" N VAL R 494 " model vdw 2.393 2.520 nonbonded pdb=" O THR R 245 " pdb=" OG1 THR R 248 " model vdw 2.405 2.440 ... (remaining 80209 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.110 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 30.410 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 0.312 10806 Z= 0.595 Angle : 1.130 14.010 14653 Z= 0.726 Chirality : 0.070 0.427 1635 Planarity : 0.006 0.132 1857 Dihedral : 14.443 77.489 3917 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.79 % Allowed : 7.67 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % 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: -3.15 (0.20), residues: 1333 helix: -1.55 (0.20), residues: 439 sheet: -1.21 (0.32), residues: 254 loop : -2.89 (0.21), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 206 HIS 0.007 0.002 HIS R 433 PHE 0.016 0.002 PHE B 151 TYR 0.015 0.002 TYR A 302 ARG 0.009 0.001 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 432 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 218 GLN cc_start: 0.8475 (mt0) cc_final: 0.8171 (mp10) REVERT: R 255 ASP cc_start: 0.8055 (t0) cc_final: 0.7718 (t0) REVERT: R 257 ARG cc_start: 0.8215 (mtp180) cc_final: 0.7758 (mtt-85) REVERT: R 269 TYR cc_start: 0.9103 (m-80) cc_final: 0.8860 (m-10) REVERT: R 271 ASN cc_start: 0.8814 (p0) cc_final: 0.8606 (p0) REVERT: R 281 TRP cc_start: 0.8442 (m-10) cc_final: 0.7854 (m-10) REVERT: R 325 LEU cc_start: 0.8967 (pp) cc_final: 0.8679 (pp) REVERT: R 326 MET cc_start: 0.9046 (tpp) cc_final: 0.8763 (mmt) REVERT: R 343 PHE cc_start: 0.9212 (m-10) cc_final: 0.8375 (m-80) REVERT: R 344 LYS cc_start: 0.8491 (ttmt) cc_final: 0.7721 (mttp) REVERT: R 351 GLN cc_start: 0.8650 (tt0) cc_final: 0.8051 (tp-100) REVERT: R 400 ARG cc_start: 0.9277 (ttp80) cc_final: 0.9028 (ttp80) REVERT: R 485 ARG cc_start: 0.6033 (ttt180) cc_final: 0.4728 (tpp80) REVERT: R 491 GLN cc_start: 0.8927 (tt0) cc_final: 0.8632 (mm-40) REVERT: R 510 LYS cc_start: 0.8040 (tptm) cc_final: 0.6984 (ttpp) REVERT: A 18 MET cc_start: 0.7521 (mmm) cc_final: 0.6865 (tpp) REVERT: A 22 ASN cc_start: 0.8816 (m-40) cc_final: 0.8432 (m110) REVERT: A 36 LEU cc_start: 0.9106 (mp) cc_final: 0.8892 (mp) REVERT: A 47 ASN cc_start: 0.9253 (m-40) cc_final: 0.8965 (p0) REVERT: A 74 TYR cc_start: 0.8196 (m-10) cc_final: 0.7929 (m-80) REVERT: A 79 GLN cc_start: 0.9203 (tp-100) cc_final: 0.8683 (mt0) REVERT: A 147 GLN cc_start: 0.9143 (tp-100) cc_final: 0.8892 (tm-30) REVERT: A 188 HIS cc_start: 0.8250 (p-80) cc_final: 0.7890 (p-80) REVERT: A 195 HIS cc_start: 0.8805 (m-70) cc_final: 0.8399 (m90) REVERT: A 211 TRP cc_start: 0.8902 (p-90) cc_final: 0.8550 (p-90) REVERT: A 243 MET cc_start: 0.8824 (ptt) cc_final: 0.8362 (ptt) REVERT: A 244 HIS cc_start: 0.9241 (m170) cc_final: 0.8931 (m170) REVERT: A 269 ASN cc_start: 0.7581 (p0) cc_final: 0.7262 (p0) REVERT: A 320 TYR cc_start: 0.8823 (m-10) cc_final: 0.8619 (m-10) REVERT: B 3 GLU cc_start: 0.8883 (pt0) cc_final: 0.8593 (tp30) REVERT: B 23 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7545 (ptpp) REVERT: B 80 ILE cc_start: 0.8523 (tt) cc_final: 0.8186 (tt) REVERT: B 82 TRP cc_start: 0.8946 (m100) cc_final: 0.8469 (m100) REVERT: B 127 LYS cc_start: 0.9258 (mmmm) cc_final: 0.8638 (mttt) REVERT: B 171 ILE cc_start: 0.9401 (pt) cc_final: 0.9142 (pt) REVERT: B 183 HIS cc_start: 0.7937 (m-70) cc_final: 0.7430 (m170) REVERT: B 211 TRP cc_start: 0.8798 (m100) cc_final: 0.8299 (m100) REVERT: B 212 ASP cc_start: 0.7020 (p0) cc_final: 0.5568 (p0) REVERT: B 215 GLU cc_start: 0.9183 (tp30) cc_final: 0.8809 (tp30) REVERT: B 289 TYR cc_start: 0.8824 (m-80) cc_final: 0.7956 (m-80) REVERT: B 295 ASN cc_start: 0.8392 (p0) cc_final: 0.8148 (p0) REVERT: B 301 LYS cc_start: 0.7830 (mtmt) cc_final: 0.7080 (mmtt) REVERT: G 14 LYS cc_start: 0.9045 (mttm) cc_final: 0.8792 (mttm) REVERT: G 17 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8858 (mt-10) REVERT: L 37 TYR cc_start: 0.8607 (m-80) cc_final: 0.7363 (m-80) REVERT: L 59 VAL cc_start: 0.9373 (t) cc_final: 0.9119 (p) REVERT: L 97 ILE cc_start: 0.9480 (mm) cc_final: 0.8907 (mp) REVERT: L 104 LYS cc_start: 0.8983 (pttp) cc_final: 0.8758 (ptpt) REVERT: H 39 TRP cc_start: 0.9106 (m100) cc_final: 0.8891 (m100) REVERT: H 54 ILE cc_start: 0.8461 (tp) cc_final: 0.8017 (tt) REVERT: H 68 LYS cc_start: 0.9262 (pttt) cc_final: 0.9026 (ptpt) REVERT: H 103 PRO cc_start: 0.9106 (Cg_endo) cc_final: 0.8855 (Cg_exo) REVERT: H 128 THR cc_start: 0.9010 (p) cc_final: 0.8789 (t) outliers start: 9 outliers final: 3 residues processed: 436 average time/residue: 0.2452 time to fit residues: 144.5456 Evaluate side-chains 309 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 306 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain A residue 221 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 258 ASN R 309 ASN R 446 ASN A 22 ASN A 68 GLN A 256 ASN A 294 ASN A 333 GLN B 16 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 155 ASN B 293 ASN B 340 ASN G 44 HIS L 80 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10806 Z= 0.186 Angle : 0.644 11.370 14653 Z= 0.331 Chirality : 0.041 0.172 1635 Planarity : 0.005 0.106 1857 Dihedral : 5.766 44.642 1537 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.20 % Favored : 95.72 % Rotamer: Outliers : 3.00 % Allowed : 17.97 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.21), residues: 1333 helix: -0.50 (0.22), residues: 446 sheet: -0.97 (0.30), residues: 277 loop : -2.72 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 339 HIS 0.007 0.001 HIS R 433 PHE 0.024 0.002 PHE B 235 TYR 0.016 0.001 TYR H 120 ARG 0.007 0.001 ARG R 261 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 308 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 218 GLN cc_start: 0.8487 (mt0) cc_final: 0.8129 (mp10) REVERT: R 228 GLN cc_start: 0.9270 (mt0) cc_final: 0.8964 (tp40) REVERT: R 257 ARG cc_start: 0.8345 (mtp180) cc_final: 0.7809 (mmt90) REVERT: R 265 VAL cc_start: 0.9588 (m) cc_final: 0.9291 (t) REVERT: R 269 TYR cc_start: 0.9106 (m-80) cc_final: 0.8779 (m-10) REVERT: R 301 MET cc_start: 0.7099 (pmm) cc_final: 0.6324 (pmm) REVERT: R 339 TRP cc_start: 0.9237 (OUTLIER) cc_final: 0.9029 (m-90) REVERT: R 351 GLN cc_start: 0.8422 (tt0) cc_final: 0.7756 (tp-100) REVERT: R 391 PHE cc_start: 0.5427 (OUTLIER) cc_final: 0.5222 (t80) REVERT: R 400 ARG cc_start: 0.9271 (ttp80) cc_final: 0.9041 (ttp80) REVERT: R 447 GLU cc_start: 0.7558 (tp30) cc_final: 0.6984 (tm-30) REVERT: R 485 ARG cc_start: 0.6184 (ttt180) cc_final: 0.4877 (tpp80) REVERT: R 491 GLN cc_start: 0.8874 (tt0) cc_final: 0.8548 (mm-40) REVERT: A 18 MET cc_start: 0.7524 (mmm) cc_final: 0.7112 (mmm) REVERT: A 22 ASN cc_start: 0.8751 (m110) cc_final: 0.8494 (m110) REVERT: A 72 VAL cc_start: 0.9159 (t) cc_final: 0.8935 (t) REVERT: A 76 ASN cc_start: 0.9469 (m-40) cc_final: 0.9163 (m-40) REVERT: A 79 GLN cc_start: 0.9229 (tp-100) cc_final: 0.8857 (mt0) REVERT: A 106 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8830 (tp40) REVERT: A 147 GLN cc_start: 0.9131 (tp-100) cc_final: 0.8871 (tm-30) REVERT: A 175 LEU cc_start: 0.8652 (mm) cc_final: 0.8386 (pp) REVERT: A 188 HIS cc_start: 0.8326 (p-80) cc_final: 0.8100 (p-80) REVERT: A 243 MET cc_start: 0.8752 (ptt) cc_final: 0.8327 (ptt) REVERT: A 244 HIS cc_start: 0.9385 (m170) cc_final: 0.9127 (m170) REVERT: A 247 MET cc_start: 0.9287 (mtp) cc_final: 0.9086 (ptp) REVERT: B 57 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8387 (mtpt) REVERT: B 61 MET cc_start: 0.8140 (ppp) cc_final: 0.7689 (ppp) REVERT: B 82 TRP cc_start: 0.8830 (m100) cc_final: 0.8449 (m100) REVERT: B 127 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8617 (mttt) REVERT: B 289 TYR cc_start: 0.8916 (m-80) cc_final: 0.8119 (m-80) REVERT: B 295 ASN cc_start: 0.8381 (p0) cc_final: 0.8121 (p0) REVERT: B 325 MET cc_start: 0.7174 (mtm) cc_final: 0.6604 (ttp) REVERT: B 333 ASP cc_start: 0.8376 (p0) cc_final: 0.8161 (p0) REVERT: G 17 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8958 (mt-10) REVERT: G 21 MET cc_start: 0.8126 (mmt) cc_final: 0.7835 (mmt) REVERT: G 29 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8737 (mmmt) REVERT: G 36 ASP cc_start: 0.9099 (t0) cc_final: 0.8572 (m-30) REVERT: L 37 TYR cc_start: 0.8251 (m-80) cc_final: 0.7819 (m-80) REVERT: L 47 LEU cc_start: 0.9315 (pt) cc_final: 0.9011 (pp) REVERT: L 59 VAL cc_start: 0.9388 (t) cc_final: 0.9106 (p) REVERT: L 97 ILE cc_start: 0.9344 (mm) cc_final: 0.8882 (mp) REVERT: H 39 TRP cc_start: 0.9116 (m100) cc_final: 0.8844 (m100) REVERT: H 68 LYS cc_start: 0.9245 (pttt) cc_final: 0.8918 (ptpp) REVERT: H 118 MET cc_start: 0.8528 (mpp) cc_final: 0.8078 (mpp) REVERT: H 120 TYR cc_start: 0.7992 (m-10) cc_final: 0.7709 (m-80) REVERT: H 128 THR cc_start: 0.9002 (p) cc_final: 0.8750 (t) outliers start: 34 outliers final: 19 residues processed: 323 average time/residue: 0.2161 time to fit residues: 100.4507 Evaluate side-chains 298 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 277 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 298 ASP Chi-restraints excluded: chain R residue 339 TRP Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 466 THR Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 32 optimal weight: 0.0870 chunk 119 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 340 HIS ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 47 ASN A 79 GLN A 164 GLN B 110 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10806 Z= 0.347 Angle : 0.712 12.580 14653 Z= 0.373 Chirality : 0.044 0.166 1635 Planarity : 0.005 0.116 1857 Dihedral : 6.198 54.473 1536 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 6.08 % Allowed : 18.94 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.22), residues: 1333 helix: -0.19 (0.23), residues: 448 sheet: -0.99 (0.31), residues: 266 loop : -2.78 (0.22), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 339 HIS 0.006 0.002 HIS R 340 PHE 0.021 0.002 PHE H 32 TYR 0.021 0.002 TYR R 337 ARG 0.011 0.001 ARG R 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 265 time to evaluate : 1.150 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: R 198 VAL cc_start: 0.8611 (m) cc_final: 0.8287 (p) REVERT: R 218 GLN cc_start: 0.8539 (mt0) cc_final: 0.8093 (mp10) REVERT: R 257 ARG cc_start: 0.8469 (mtp180) cc_final: 0.7864 (mmt90) REVERT: R 301 MET cc_start: 0.7629 (pmm) cc_final: 0.6956 (pmm) REVERT: R 351 GLN cc_start: 0.8258 (tt0) cc_final: 0.7622 (tp-100) REVERT: R 391 PHE cc_start: 0.5357 (OUTLIER) cc_final: 0.5080 (t80) REVERT: R 485 ARG cc_start: 0.6404 (ttt180) cc_final: 0.5186 (tpp80) REVERT: R 491 GLN cc_start: 0.9085 (tt0) cc_final: 0.8457 (mm-40) REVERT: A 18 MET cc_start: 0.7232 (mmm) cc_final: 0.6847 (mmm) REVERT: A 22 ASN cc_start: 0.8654 (m110) cc_final: 0.8445 (m110) REVERT: A 72 VAL cc_start: 0.9211 (t) cc_final: 0.8989 (t) REVERT: A 76 ASN cc_start: 0.9533 (m-40) cc_final: 0.9252 (m-40) REVERT: A 79 GLN cc_start: 0.9201 (tp40) cc_final: 0.8918 (mt0) REVERT: A 147 GLN cc_start: 0.9068 (tp-100) cc_final: 0.8774 (tm-30) REVERT: A 175 LEU cc_start: 0.8673 (mm) cc_final: 0.8412 (pp) REVERT: A 198 MET cc_start: 0.8422 (tpt) cc_final: 0.7904 (tpt) REVERT: A 243 MET cc_start: 0.8815 (ptt) cc_final: 0.8425 (ptt) REVERT: A 244 HIS cc_start: 0.9318 (m170) cc_final: 0.9118 (m170) REVERT: A 283 LEU cc_start: 0.8621 (tt) cc_final: 0.8385 (tp) REVERT: B 45 MET cc_start: 0.8298 (tpp) cc_final: 0.7899 (mmm) REVERT: B 46 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6773 (mtt-85) REVERT: B 61 MET cc_start: 0.8242 (ppp) cc_final: 0.7746 (ppp) REVERT: B 127 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8436 (mttt) REVERT: B 289 TYR cc_start: 0.8912 (m-80) cc_final: 0.8271 (m-80) REVERT: B 292 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: B 295 ASN cc_start: 0.8653 (p0) cc_final: 0.8224 (p0) REVERT: B 325 MET cc_start: 0.7700 (mtm) cc_final: 0.7102 (ttp) REVERT: B 333 ASP cc_start: 0.8618 (p0) cc_final: 0.8411 (p0) REVERT: G 17 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8990 (mt-10) REVERT: G 21 MET cc_start: 0.8264 (mmt) cc_final: 0.7933 (mmm) REVERT: L 37 TYR cc_start: 0.8656 (m-80) cc_final: 0.7595 (m-80) REVERT: L 59 VAL cc_start: 0.9447 (t) cc_final: 0.9079 (p) REVERT: L 97 ILE cc_start: 0.9339 (mm) cc_final: 0.8941 (mm) REVERT: H 6 GLN cc_start: 0.9325 (mm110) cc_final: 0.9093 (mm110) REVERT: H 7 LEU cc_start: 0.8016 (mt) cc_final: 0.7307 (tt) REVERT: H 68 LYS cc_start: 0.9230 (pttt) cc_final: 0.9005 (ptmm) REVERT: H 118 MET cc_start: 0.8550 (mpp) cc_final: 0.7953 (mpp) REVERT: H 120 TYR cc_start: 0.8142 (m-10) cc_final: 0.7746 (m-10) REVERT: H 128 THR cc_start: 0.8966 (p) cc_final: 0.8722 (t) outliers start: 69 outliers final: 52 residues processed: 303 average time/residue: 0.2071 time to fit residues: 90.7020 Evaluate side-chains 292 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 237 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 298 ASP Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 316 ILE Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 466 THR Chi-restraints excluded: chain R residue 467 PHE Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 56 optimal weight: 0.0040 chunk 80 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 113 optimal weight: 0.0770 chunk 34 optimal weight: 4.9990 overall best weight: 1.9554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 340 HIS R 351 GLN ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 155 ASN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10806 Z= 0.200 Angle : 0.631 9.844 14653 Z= 0.321 Chirality : 0.041 0.176 1635 Planarity : 0.005 0.110 1857 Dihedral : 5.870 60.919 1536 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.90 % Allowed : 20.35 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % 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: -1.92 (0.22), residues: 1333 helix: 0.07 (0.24), residues: 450 sheet: -0.81 (0.31), residues: 265 loop : -2.57 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 339 HIS 0.005 0.001 HIS R 433 PHE 0.015 0.001 PHE R 427 TYR 0.014 0.001 TYR A 69 ARG 0.003 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 268 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8615 (m) cc_final: 0.8291 (p) REVERT: R 218 GLN cc_start: 0.8588 (mt0) cc_final: 0.8154 (mp10) REVERT: R 257 ARG cc_start: 0.8445 (mtp180) cc_final: 0.7852 (mmt90) REVERT: R 301 MET cc_start: 0.7778 (pmm) cc_final: 0.7021 (pmm) REVERT: R 339 TRP cc_start: 0.9199 (OUTLIER) cc_final: 0.8968 (m-90) REVERT: R 351 GLN cc_start: 0.8008 (tt0) cc_final: 0.7524 (tp-100) REVERT: R 391 PHE cc_start: 0.5706 (OUTLIER) cc_final: 0.5341 (t80) REVERT: R 433 HIS cc_start: 0.6193 (OUTLIER) cc_final: 0.5863 (p-80) REVERT: R 447 GLU cc_start: 0.8074 (tp30) cc_final: 0.7497 (tm-30) REVERT: R 485 ARG cc_start: 0.6373 (ttt180) cc_final: 0.5163 (tpp80) REVERT: A 18 MET cc_start: 0.7227 (mmm) cc_final: 0.6827 (mmm) REVERT: A 22 ASN cc_start: 0.8724 (m110) cc_final: 0.8513 (m110) REVERT: A 72 VAL cc_start: 0.9179 (t) cc_final: 0.8922 (t) REVERT: A 76 ASN cc_start: 0.9524 (m-40) cc_final: 0.9173 (m-40) REVERT: A 79 GLN cc_start: 0.9257 (tp40) cc_final: 0.8837 (mt0) REVERT: A 198 MET cc_start: 0.8334 (tpt) cc_final: 0.8021 (tpt) REVERT: A 243 MET cc_start: 0.8839 (ptt) cc_final: 0.8494 (ptt) REVERT: A 298 GLU cc_start: 0.8244 (mp0) cc_final: 0.8035 (mp0) REVERT: B 46 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6874 (mtp85) REVERT: B 61 MET cc_start: 0.8226 (ppp) cc_final: 0.7685 (ppp) REVERT: B 79 LEU cc_start: 0.9079 (tp) cc_final: 0.8858 (tp) REVERT: B 127 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8699 (mtmt) REVERT: B 289 TYR cc_start: 0.8930 (m-80) cc_final: 0.8404 (m-80) REVERT: B 292 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: B 295 ASN cc_start: 0.8389 (p0) cc_final: 0.7955 (p0) REVERT: B 301 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7043 (mmtt) REVERT: B 325 MET cc_start: 0.7371 (mtm) cc_final: 0.7060 (ttp) REVERT: B 333 ASP cc_start: 0.8586 (p0) cc_final: 0.8272 (p0) REVERT: G 14 LYS cc_start: 0.9178 (mtpp) cc_final: 0.8963 (mtmm) REVERT: G 17 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8944 (mt-10) REVERT: G 21 MET cc_start: 0.8200 (mmt) cc_final: 0.7853 (mmm) REVERT: L 37 TYR cc_start: 0.8623 (m-80) cc_final: 0.7573 (m-80) REVERT: L 47 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8913 (pp) REVERT: L 59 VAL cc_start: 0.9357 (t) cc_final: 0.9022 (p) REVERT: L 97 ILE cc_start: 0.9256 (mm) cc_final: 0.9020 (mp) REVERT: H 6 GLN cc_start: 0.9299 (mm110) cc_final: 0.8983 (mp10) REVERT: H 7 LEU cc_start: 0.7888 (mt) cc_final: 0.7179 (tt) REVERT: H 50 TRP cc_start: 0.7732 (t60) cc_final: 0.7456 (t60) REVERT: H 118 MET cc_start: 0.8574 (mpp) cc_final: 0.7904 (mpp) REVERT: H 120 TYR cc_start: 0.8280 (m-10) cc_final: 0.7815 (m-10) outliers start: 67 outliers final: 42 residues processed: 310 average time/residue: 0.2075 time to fit residues: 93.1612 Evaluate side-chains 290 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 242 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 298 ASP Chi-restraints excluded: chain R residue 339 TRP Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 467 PHE Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain R residue 545 TRP Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 5.9990 chunk 71 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 113 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 340 HIS R 361 HIS ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 521 ASN A 164 GLN B 155 ASN B 311 HIS B 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10806 Z= 0.211 Angle : 0.639 14.278 14653 Z= 0.326 Chirality : 0.042 0.171 1635 Planarity : 0.005 0.107 1857 Dihedral : 5.814 70.324 1536 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 6.34 % Allowed : 21.85 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % 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: -1.75 (0.22), residues: 1333 helix: 0.19 (0.24), residues: 450 sheet: -0.72 (0.32), residues: 265 loop : -2.44 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 339 HIS 0.006 0.001 HIS R 433 PHE 0.025 0.001 PHE H 71 TYR 0.014 0.001 TYR A 69 ARG 0.003 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 260 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8746 (m) cc_final: 0.8459 (p) REVERT: R 218 GLN cc_start: 0.8600 (mt0) cc_final: 0.8123 (mp10) REVERT: R 257 ARG cc_start: 0.8456 (mtp180) cc_final: 0.7834 (mmt90) REVERT: R 301 MET cc_start: 0.7784 (pmm) cc_final: 0.6981 (pmm) REVERT: R 351 GLN cc_start: 0.7881 (tt0) cc_final: 0.7359 (tp-100) REVERT: R 391 PHE cc_start: 0.5702 (OUTLIER) cc_final: 0.5324 (t80) REVERT: R 433 HIS cc_start: 0.6230 (OUTLIER) cc_final: 0.5841 (p-80) REVERT: R 447 GLU cc_start: 0.8101 (tp30) cc_final: 0.7511 (tm-30) REVERT: R 485 ARG cc_start: 0.6408 (ttt180) cc_final: 0.5250 (tpp80) REVERT: A 18 MET cc_start: 0.7146 (mmm) cc_final: 0.6723 (mmm) REVERT: A 72 VAL cc_start: 0.9157 (t) cc_final: 0.8887 (t) REVERT: A 76 ASN cc_start: 0.9506 (m-40) cc_final: 0.9152 (m-40) REVERT: A 79 GLN cc_start: 0.9221 (tp40) cc_final: 0.8835 (mt0) REVERT: A 198 MET cc_start: 0.8283 (tpt) cc_final: 0.8002 (tpt) REVERT: A 243 MET cc_start: 0.8752 (ptt) cc_final: 0.8515 (ptt) REVERT: A 283 LEU cc_start: 0.8644 (tt) cc_final: 0.8371 (tp) REVERT: A 298 GLU cc_start: 0.8265 (mp0) cc_final: 0.8030 (mp0) REVERT: B 61 MET cc_start: 0.8245 (ppp) cc_final: 0.7902 (ppp) REVERT: B 79 LEU cc_start: 0.9050 (tp) cc_final: 0.8843 (tp) REVERT: B 82 TRP cc_start: 0.8879 (OUTLIER) cc_final: 0.8561 (m100) REVERT: B 127 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8680 (mtmt) REVERT: B 175 GLN cc_start: 0.8999 (tp-100) cc_final: 0.8452 (tm-30) REVERT: B 235 PHE cc_start: 0.6581 (OUTLIER) cc_final: 0.6352 (t80) REVERT: B 289 TYR cc_start: 0.9008 (m-80) cc_final: 0.8385 (m-80) REVERT: B 292 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: B 295 ASN cc_start: 0.8340 (p0) cc_final: 0.7933 (p0) REVERT: B 301 LYS cc_start: 0.7946 (mtmt) cc_final: 0.7098 (mmtt) REVERT: B 325 MET cc_start: 0.7317 (mtm) cc_final: 0.6838 (ttp) REVERT: B 333 ASP cc_start: 0.8564 (p0) cc_final: 0.8300 (p0) REVERT: G 14 LYS cc_start: 0.9197 (mtpp) cc_final: 0.8969 (mtmm) REVERT: G 17 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8956 (mt-10) REVERT: G 21 MET cc_start: 0.8245 (mmt) cc_final: 0.7903 (mmm) REVERT: L 37 TYR cc_start: 0.8654 (m-80) cc_final: 0.7812 (m-80) REVERT: L 47 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8893 (pp) REVERT: L 59 VAL cc_start: 0.9303 (t) cc_final: 0.8961 (p) REVERT: L 97 ILE cc_start: 0.9365 (mm) cc_final: 0.8983 (mm) REVERT: H 6 GLN cc_start: 0.9293 (mm110) cc_final: 0.9091 (mp10) REVERT: H 118 MET cc_start: 0.8669 (mpp) cc_final: 0.8119 (mpp) REVERT: H 120 TYR cc_start: 0.8328 (m-10) cc_final: 0.7884 (m-10) outliers start: 72 outliers final: 52 residues processed: 305 average time/residue: 0.1951 time to fit residues: 86.6890 Evaluate side-chains 298 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 240 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 298 ASP Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain R residue 545 TRP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 128 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 340 HIS ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 340 ASN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10806 Z= 0.251 Angle : 0.651 11.892 14653 Z= 0.337 Chirality : 0.042 0.179 1635 Planarity : 0.005 0.107 1857 Dihedral : 5.986 80.325 1536 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 6.70 % Allowed : 22.56 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % 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: -1.71 (0.22), residues: 1333 helix: 0.21 (0.23), residues: 451 sheet: -0.69 (0.32), residues: 259 loop : -2.40 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP R 339 HIS 0.006 0.001 HIS R 433 PHE 0.019 0.001 PHE H 32 TYR 0.014 0.001 TYR R 337 ARG 0.004 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 250 time to evaluate : 1.112 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: R 198 VAL cc_start: 0.8690 (m) cc_final: 0.8392 (p) REVERT: R 218 GLN cc_start: 0.8610 (mt0) cc_final: 0.8115 (mp10) REVERT: R 257 ARG cc_start: 0.8568 (mtp180) cc_final: 0.7919 (mmt180) REVERT: R 301 MET cc_start: 0.7662 (pmm) cc_final: 0.6846 (pmm) REVERT: R 339 TRP cc_start: 0.9243 (m-90) cc_final: 0.8921 (m-90) REVERT: R 391 PHE cc_start: 0.5728 (OUTLIER) cc_final: 0.5317 (t80) REVERT: R 433 HIS cc_start: 0.6262 (OUTLIER) cc_final: 0.5882 (p-80) REVERT: R 447 GLU cc_start: 0.8129 (tp30) cc_final: 0.7536 (tm-30) REVERT: R 485 ARG cc_start: 0.6512 (ttt180) cc_final: 0.5410 (tpp80) REVERT: A 72 VAL cc_start: 0.9152 (t) cc_final: 0.8895 (t) REVERT: A 76 ASN cc_start: 0.9520 (m-40) cc_final: 0.9179 (m-40) REVERT: A 79 GLN cc_start: 0.9224 (tp40) cc_final: 0.8927 (mt0) REVERT: A 198 MET cc_start: 0.8236 (tpt) cc_final: 0.7978 (tpt) REVERT: A 283 LEU cc_start: 0.8685 (tt) cc_final: 0.8435 (tp) REVERT: A 298 GLU cc_start: 0.8363 (mp0) cc_final: 0.8101 (mp0) REVERT: B 61 MET cc_start: 0.8237 (ppp) cc_final: 0.8000 (ppp) REVERT: B 79 LEU cc_start: 0.9040 (tp) cc_final: 0.8818 (tp) REVERT: B 127 LYS cc_start: 0.9131 (mmmm) cc_final: 0.8700 (mtmt) REVERT: B 175 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8261 (tm-30) REVERT: B 235 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.6369 (t80) REVERT: B 289 TYR cc_start: 0.8957 (m-80) cc_final: 0.8337 (m-80) REVERT: B 292 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: B 295 ASN cc_start: 0.8414 (p0) cc_final: 0.7980 (p0) REVERT: B 325 MET cc_start: 0.7420 (mtm) cc_final: 0.6959 (ttp) REVERT: B 333 ASP cc_start: 0.8666 (p0) cc_final: 0.8410 (p0) REVERT: G 17 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8886 (mt-10) REVERT: G 21 MET cc_start: 0.8276 (mmt) cc_final: 0.8011 (mmt) REVERT: G 32 LYS cc_start: 0.9618 (mmtp) cc_final: 0.9121 (mmtp) REVERT: G 36 ASP cc_start: 0.9243 (t0) cc_final: 0.8801 (m-30) REVERT: L 37 TYR cc_start: 0.8690 (m-80) cc_final: 0.7853 (m-80) REVERT: L 47 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8905 (pp) REVERT: L 59 VAL cc_start: 0.9325 (t) cc_final: 0.9016 (p) REVERT: H 112 TYR cc_start: 0.8625 (m-10) cc_final: 0.8410 (m-10) REVERT: H 118 MET cc_start: 0.8674 (mpp) cc_final: 0.8130 (mpp) REVERT: H 120 TYR cc_start: 0.8377 (m-10) cc_final: 0.7934 (m-10) outliers start: 76 outliers final: 61 residues processed: 295 average time/residue: 0.1946 time to fit residues: 83.7596 Evaluate side-chains 303 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 237 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 298 ASP Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 466 THR Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain R residue 545 TRP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 128 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 340 HIS ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10806 Z= 0.206 Angle : 0.636 11.025 14653 Z= 0.325 Chirality : 0.041 0.169 1635 Planarity : 0.004 0.106 1857 Dihedral : 5.900 87.023 1536 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 6.34 % Allowed : 23.79 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.08 % 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: -1.68 (0.22), residues: 1333 helix: 0.24 (0.23), residues: 455 sheet: -0.72 (0.32), residues: 261 loop : -2.38 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP R 339 HIS 0.006 0.001 HIS R 433 PHE 0.018 0.001 PHE H 32 TYR 0.014 0.001 TYR A 69 ARG 0.004 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 256 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8683 (m) cc_final: 0.8394 (p) REVERT: R 218 GLN cc_start: 0.8605 (mt0) cc_final: 0.8106 (mp10) REVERT: R 252 PHE cc_start: 0.8882 (m-80) cc_final: 0.8235 (t80) REVERT: R 257 ARG cc_start: 0.8531 (mtp180) cc_final: 0.7883 (mmt180) REVERT: R 301 MET cc_start: 0.7621 (pmm) cc_final: 0.6790 (pmm) REVERT: R 339 TRP cc_start: 0.9171 (OUTLIER) cc_final: 0.8966 (m-90) REVERT: R 391 PHE cc_start: 0.5745 (OUTLIER) cc_final: 0.5490 (t80) REVERT: R 433 HIS cc_start: 0.6253 (OUTLIER) cc_final: 0.5819 (p-80) REVERT: R 447 GLU cc_start: 0.8117 (tp30) cc_final: 0.7536 (tm-30) REVERT: R 485 ARG cc_start: 0.6505 (ttt180) cc_final: 0.5406 (tpp80) REVERT: A 18 MET cc_start: 0.6886 (mmm) cc_final: 0.6434 (tpp) REVERT: A 72 VAL cc_start: 0.9152 (t) cc_final: 0.8894 (t) REVERT: A 76 ASN cc_start: 0.9508 (m-40) cc_final: 0.9154 (m-40) REVERT: A 79 GLN cc_start: 0.9227 (tp40) cc_final: 0.8850 (mt0) REVERT: A 198 MET cc_start: 0.8302 (tpt) cc_final: 0.8009 (tpt) REVERT: A 243 MET cc_start: 0.8861 (ptt) cc_final: 0.8403 (ptt) REVERT: A 283 LEU cc_start: 0.8680 (tt) cc_final: 0.8446 (tp) REVERT: A 298 GLU cc_start: 0.8319 (mp0) cc_final: 0.8072 (mp0) REVERT: B 10 GLU cc_start: 0.7899 (tt0) cc_final: 0.7342 (mm-30) REVERT: B 79 LEU cc_start: 0.9035 (tp) cc_final: 0.8821 (tp) REVERT: B 127 LYS cc_start: 0.9081 (mmmm) cc_final: 0.8628 (mtmt) REVERT: B 175 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8578 (tm-30) REVERT: B 235 PHE cc_start: 0.6584 (OUTLIER) cc_final: 0.6306 (t80) REVERT: B 289 TYR cc_start: 0.8916 (m-80) cc_final: 0.8231 (m-80) REVERT: B 292 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7953 (m-80) REVERT: B 325 MET cc_start: 0.7307 (mtm) cc_final: 0.6983 (ttp) REVERT: B 333 ASP cc_start: 0.8675 (p0) cc_final: 0.8372 (p0) REVERT: G 17 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8867 (mt-10) REVERT: G 21 MET cc_start: 0.8292 (mmt) cc_final: 0.8023 (mmt) REVERT: G 32 LYS cc_start: 0.9602 (mmtp) cc_final: 0.9101 (mmtp) REVERT: G 36 ASP cc_start: 0.9226 (t0) cc_final: 0.8781 (m-30) REVERT: L 37 TYR cc_start: 0.8671 (m-80) cc_final: 0.7799 (m-80) REVERT: L 47 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8906 (pp) REVERT: L 59 VAL cc_start: 0.9298 (t) cc_final: 0.8906 (p) REVERT: H 39 TRP cc_start: 0.8834 (m-10) cc_final: 0.8603 (m-10) REVERT: H 118 MET cc_start: 0.8680 (mpp) cc_final: 0.8219 (mpp) REVERT: H 120 TYR cc_start: 0.8371 (m-10) cc_final: 0.7936 (m-10) outliers start: 72 outliers final: 62 residues processed: 300 average time/residue: 0.1955 time to fit residues: 85.7819 Evaluate side-chains 307 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 239 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 298 ASP Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 339 TRP Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain R residue 545 TRP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 128 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.0010 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 114 optimal weight: 0.0980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 340 HIS ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN B 155 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10806 Z= 0.161 Angle : 0.652 11.949 14653 Z= 0.325 Chirality : 0.041 0.173 1635 Planarity : 0.004 0.102 1857 Dihedral : 5.698 89.355 1536 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.37 % Allowed : 25.02 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.49 (0.23), residues: 1333 helix: 0.35 (0.24), residues: 444 sheet: -0.50 (0.33), residues: 253 loop : -2.22 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 50 HIS 0.006 0.001 HIS R 433 PHE 0.017 0.001 PHE H 32 TYR 0.013 0.001 TYR A 69 ARG 0.004 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 266 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8668 (m) cc_final: 0.8415 (p) REVERT: R 218 GLN cc_start: 0.8602 (mt0) cc_final: 0.8099 (mp10) REVERT: R 228 GLN cc_start: 0.9331 (mt0) cc_final: 0.9010 (tp40) REVERT: R 252 PHE cc_start: 0.8886 (m-80) cc_final: 0.8327 (t80) REVERT: R 257 ARG cc_start: 0.8518 (mtp180) cc_final: 0.7869 (mmt180) REVERT: R 301 MET cc_start: 0.7689 (pmm) cc_final: 0.6860 (pmm) REVERT: R 391 PHE cc_start: 0.5863 (OUTLIER) cc_final: 0.5304 (t80) REVERT: R 433 HIS cc_start: 0.6246 (OUTLIER) cc_final: 0.5881 (p-80) REVERT: R 447 GLU cc_start: 0.8255 (tp30) cc_final: 0.7704 (tm-30) REVERT: R 485 ARG cc_start: 0.6688 (ttt180) cc_final: 0.5736 (tpp80) REVERT: R 491 GLN cc_start: 0.8310 (tp-100) cc_final: 0.8102 (tp-100) REVERT: A 9 ASP cc_start: 0.8612 (m-30) cc_final: 0.8406 (m-30) REVERT: A 72 VAL cc_start: 0.9144 (t) cc_final: 0.8871 (t) REVERT: A 76 ASN cc_start: 0.9490 (m-40) cc_final: 0.9165 (m-40) REVERT: A 79 GLN cc_start: 0.9259 (tp40) cc_final: 0.8837 (mt0) REVERT: A 283 LEU cc_start: 0.8669 (tt) cc_final: 0.8444 (tp) REVERT: B 166 CYS cc_start: 0.9184 (m) cc_final: 0.8850 (m) REVERT: B 175 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8623 (tm-30) REVERT: B 235 PHE cc_start: 0.6351 (OUTLIER) cc_final: 0.6132 (t80) REVERT: B 289 TYR cc_start: 0.8870 (m-80) cc_final: 0.8319 (m-80) REVERT: B 292 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: B 325 MET cc_start: 0.6997 (mtm) cc_final: 0.6383 (ttm) REVERT: B 333 ASP cc_start: 0.8631 (p0) cc_final: 0.8314 (p0) REVERT: G 14 LYS cc_start: 0.9179 (mtpp) cc_final: 0.8946 (mtmm) REVERT: G 17 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8908 (mt-10) REVERT: G 21 MET cc_start: 0.8236 (mmt) cc_final: 0.7972 (mmt) REVERT: G 32 LYS cc_start: 0.9582 (mmtp) cc_final: 0.9041 (mmtp) REVERT: G 36 ASP cc_start: 0.9214 (t0) cc_final: 0.8760 (m-30) REVERT: L 37 TYR cc_start: 0.8455 (m-80) cc_final: 0.7536 (m-80) REVERT: L 47 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8898 (pp) REVERT: L 59 VAL cc_start: 0.9255 (t) cc_final: 0.8932 (p) REVERT: H 39 TRP cc_start: 0.8780 (m-10) cc_final: 0.8568 (m-10) REVERT: H 112 TYR cc_start: 0.8681 (m-10) cc_final: 0.8399 (m-10) REVERT: H 118 MET cc_start: 0.8619 (mpp) cc_final: 0.8136 (mpp) REVERT: H 120 TYR cc_start: 0.8400 (m-10) cc_final: 0.7993 (m-10) outliers start: 61 outliers final: 45 residues processed: 302 average time/residue: 0.1918 time to fit residues: 84.1927 Evaluate side-chains 290 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 240 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 99 PHE Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 128 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.4980 chunk 110 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 340 HIS ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10806 Z= 0.196 Angle : 0.671 11.717 14653 Z= 0.336 Chirality : 0.042 0.201 1635 Planarity : 0.004 0.102 1857 Dihedral : 5.699 87.859 1536 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.02 % Allowed : 25.55 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.57 (0.23), residues: 1333 helix: 0.22 (0.24), residues: 451 sheet: -0.50 (0.33), residues: 258 loop : -2.29 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP R 339 HIS 0.006 0.001 HIS R 433 PHE 0.031 0.001 PHE H 32 TYR 0.014 0.001 TYR A 69 ARG 0.005 0.000 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 251 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 198 VAL cc_start: 0.8716 (m) cc_final: 0.8475 (p) REVERT: R 218 GLN cc_start: 0.8604 (mt0) cc_final: 0.8073 (mp10) REVERT: R 252 PHE cc_start: 0.8913 (m-80) cc_final: 0.8372 (t80) REVERT: R 257 ARG cc_start: 0.8555 (mtp180) cc_final: 0.7891 (mmt180) REVERT: R 301 MET cc_start: 0.7713 (pmm) cc_final: 0.6894 (pmm) REVERT: R 391 PHE cc_start: 0.5772 (OUTLIER) cc_final: 0.5267 (t80) REVERT: R 433 HIS cc_start: 0.6240 (OUTLIER) cc_final: 0.5868 (p-80) REVERT: R 447 GLU cc_start: 0.8277 (tp30) cc_final: 0.7729 (tm-30) REVERT: R 485 ARG cc_start: 0.6665 (ttt180) cc_final: 0.5732 (tpp80) REVERT: R 491 GLN cc_start: 0.8346 (tp-100) cc_final: 0.8025 (tp-100) REVERT: A 9 ASP cc_start: 0.8643 (m-30) cc_final: 0.8435 (m-30) REVERT: A 18 MET cc_start: 0.7174 (tpp) cc_final: 0.6710 (tpp) REVERT: A 33 GLU cc_start: 0.8131 (tp30) cc_final: 0.7765 (tp30) REVERT: A 72 VAL cc_start: 0.9141 (t) cc_final: 0.8874 (t) REVERT: A 76 ASN cc_start: 0.9501 (m-40) cc_final: 0.9182 (m-40) REVERT: A 79 GLN cc_start: 0.9249 (tp40) cc_final: 0.8830 (mt0) REVERT: A 198 MET cc_start: 0.8134 (tpt) cc_final: 0.7629 (tpt) REVERT: B 10 GLU cc_start: 0.7974 (tt0) cc_final: 0.7434 (mm-30) REVERT: B 51 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8536 (tp) REVERT: B 166 CYS cc_start: 0.9195 (m) cc_final: 0.8843 (m) REVERT: B 175 GLN cc_start: 0.8877 (tp-100) cc_final: 0.8457 (tm-30) REVERT: B 289 TYR cc_start: 0.8987 (m-80) cc_final: 0.8290 (m-80) REVERT: B 292 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: B 325 MET cc_start: 0.7097 (mtm) cc_final: 0.6763 (ttp) REVERT: B 333 ASP cc_start: 0.8641 (p0) cc_final: 0.8324 (p0) REVERT: G 14 LYS cc_start: 0.9186 (mtpp) cc_final: 0.8939 (mtmm) REVERT: G 17 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8874 (mt-10) REVERT: G 21 MET cc_start: 0.8281 (mmt) cc_final: 0.8022 (mmt) REVERT: G 32 LYS cc_start: 0.9568 (mmtp) cc_final: 0.9056 (mmtp) REVERT: G 36 ASP cc_start: 0.9132 (t0) cc_final: 0.8734 (m-30) REVERT: L 37 TYR cc_start: 0.8519 (m-80) cc_final: 0.7499 (m-80) REVERT: L 47 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8896 (pp) REVERT: L 59 VAL cc_start: 0.9251 (t) cc_final: 0.8924 (p) REVERT: H 39 TRP cc_start: 0.8777 (m-10) cc_final: 0.8551 (m-10) REVERT: H 118 MET cc_start: 0.8712 (mpp) cc_final: 0.8103 (mpp) REVERT: H 120 TYR cc_start: 0.8451 (m-10) cc_final: 0.8025 (m-10) outliers start: 57 outliers final: 51 residues processed: 286 average time/residue: 0.1998 time to fit residues: 83.5701 Evaluate side-chains 296 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 240 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 0.1980 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 340 HIS ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10806 Z= 0.230 Angle : 0.687 13.700 14653 Z= 0.346 Chirality : 0.043 0.192 1635 Planarity : 0.004 0.104 1857 Dihedral : 5.823 86.236 1536 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 5.55 % Allowed : 25.90 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.54 (0.23), residues: 1333 helix: 0.26 (0.24), residues: 448 sheet: -0.51 (0.33), residues: 258 loop : -2.25 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP R 339 HIS 0.006 0.001 HIS R 433 PHE 0.028 0.001 PHE H 32 TYR 0.013 0.001 TYR A 69 ARG 0.004 0.000 ARG L 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 246 time to evaluate : 1.246 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: R 198 VAL cc_start: 0.8744 (m) cc_final: 0.8508 (p) REVERT: R 218 GLN cc_start: 0.8605 (mt0) cc_final: 0.8061 (mp10) REVERT: R 257 ARG cc_start: 0.8523 (mtp180) cc_final: 0.7876 (mmt180) REVERT: R 301 MET cc_start: 0.7637 (pmm) cc_final: 0.6845 (pmm) REVERT: R 391 PHE cc_start: 0.5731 (OUTLIER) cc_final: 0.5278 (t80) REVERT: R 433 HIS cc_start: 0.6253 (OUTLIER) cc_final: 0.5843 (p-80) REVERT: R 447 GLU cc_start: 0.8335 (tp30) cc_final: 0.7787 (tm-30) REVERT: R 485 ARG cc_start: 0.6556 (ttt180) cc_final: 0.5643 (tpp80) REVERT: R 491 GLN cc_start: 0.8405 (tp-100) cc_final: 0.8178 (tp-100) REVERT: A 33 GLU cc_start: 0.8119 (tp30) cc_final: 0.7665 (tp30) REVERT: A 72 VAL cc_start: 0.9156 (t) cc_final: 0.8898 (t) REVERT: A 76 ASN cc_start: 0.9510 (m-40) cc_final: 0.9151 (m-40) REVERT: A 79 GLN cc_start: 0.9234 (tp40) cc_final: 0.8820 (mt0) REVERT: A 164 GLN cc_start: 0.8540 (pt0) cc_final: 0.8247 (pm20) REVERT: A 198 MET cc_start: 0.8114 (tpt) cc_final: 0.7629 (tpt) REVERT: B 10 GLU cc_start: 0.7988 (tt0) cc_final: 0.7459 (mm-30) REVERT: B 175 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8348 (tm-30) REVERT: B 176 GLN cc_start: 0.9376 (pt0) cc_final: 0.8740 (pt0) REVERT: B 289 TYR cc_start: 0.8978 (m-80) cc_final: 0.8271 (m-80) REVERT: B 292 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: B 325 MET cc_start: 0.7276 (mtm) cc_final: 0.6659 (ttm) REVERT: B 333 ASP cc_start: 0.8673 (p0) cc_final: 0.8364 (p0) REVERT: G 17 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8890 (mt-10) REVERT: G 21 MET cc_start: 0.8303 (mmt) cc_final: 0.8032 (mmt) REVERT: L 37 TYR cc_start: 0.8680 (m-80) cc_final: 0.7768 (m-80) REVERT: L 47 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8914 (pp) REVERT: L 59 VAL cc_start: 0.9257 (t) cc_final: 0.8918 (p) REVERT: L 90 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8063 (tm-30) REVERT: H 39 TRP cc_start: 0.8797 (m-10) cc_final: 0.8549 (m-10) REVERT: H 118 MET cc_start: 0.8768 (mpp) cc_final: 0.8196 (mpp) REVERT: H 120 TYR cc_start: 0.8462 (m-10) cc_final: 0.8039 (m-10) outliers start: 63 outliers final: 51 residues processed: 286 average time/residue: 0.2002 time to fit residues: 83.3895 Evaluate side-chains 296 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 241 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 350 TYR Chi-restraints excluded: chain R residue 371 LEU Chi-restraints excluded: chain R residue 391 PHE Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 433 HIS Chi-restraints excluded: chain R residue 437 LEU Chi-restraints excluded: chain R residue 473 ASP Chi-restraints excluded: chain R residue 534 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 104 TRP Chi-restraints excluded: chain H residue 126 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 15 optimal weight: 0.0270 chunk 28 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 106 optimal weight: 0.0980 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 340 HIS ** R 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.104067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085770 restraints weight = 35630.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.088246 restraints weight = 20053.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.089905 restraints weight = 13450.316| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10806 Z= 0.218 Angle : 0.689 13.699 14653 Z= 0.345 Chirality : 0.043 0.196 1635 Planarity : 0.004 0.104 1857 Dihedral : 5.825 84.888 1536 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.29 % Allowed : 26.26 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.58 (0.23), residues: 1333 helix: 0.21 (0.24), residues: 451 sheet: -0.48 (0.33), residues: 257 loop : -2.30 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP R 339 HIS 0.006 0.001 HIS R 433 PHE 0.028 0.001 PHE H 32 TYR 0.014 0.001 TYR A 69 ARG 0.004 0.000 ARG L 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2556.11 seconds wall clock time: 47 minutes 38.06 seconds (2858.06 seconds total)