Starting phenix.real_space_refine on Mon Mar 11 15:07:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lly_23436/03_2024/7lly_23436.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lly_23436/03_2024/7lly_23436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lly_23436/03_2024/7lly_23436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lly_23436/03_2024/7lly_23436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lly_23436/03_2024/7lly_23436.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lly_23436/03_2024/7lly_23436.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 53 5.16 5 C 5427 2.51 5 N 1496 2.21 5 O 1573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N ARG 19": "NH1" <-> "NH2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "P ARG 18": "NH1" <-> "NH2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "R ARG 267": "NH1" <-> "NH2" Residue "R GLU 294": "OE1" <-> "OE2" Residue "R ARG 299": "NH1" <-> "NH2" Residue "R ARG 326": "NH1" <-> "NH2" Residue "R GLU 364": "OE1" <-> "OE2" Residue "R ARG 376": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Residue "R GLU 412": "OE1" <-> "OE2" Residue "R ARG 414": "NH1" <-> "NH2" Residue "R ARG 419": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8549 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1660 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 6, 'TRANS': 189} Chain breaks: 3 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 222 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "R" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2652 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 13, 'TRANS': 341} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 419 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 6, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 206 Time building chain proxies: 5.11, per 1000 atoms: 0.60 Number of scatterers: 8549 At special positions: 0 Unit cell: (86.92, 170.66, 99.64, 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 53 16.00 O 1573 8.00 N 1496 7.00 C 5427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 41.3% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 4.320A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.623A pdb=" N ASN A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.906A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.930A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.858A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.652A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.827A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.735A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.139A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 26 Processing helix chain 'R' and resid 36 through 53 Processing helix chain 'R' and resid 89 through 94 removed outlier: 4.041A pdb=" N SER R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 168 removed outlier: 3.649A pdb=" N VAL R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 173 removed outlier: 3.597A pdb=" N HIS R 173 " --> pdb=" O ARG R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 206 Processing helix chain 'R' and resid 223 through 256 removed outlier: 4.431A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 Processing helix chain 'R' and resid 275 through 292 removed outlier: 3.545A pdb=" N LEU R 279 " --> pdb=" O GLY R 275 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 337 removed outlier: 3.606A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.663A pdb=" N ILE R 323 " --> pdb=" O VAL R 319 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA R 337 " --> pdb=" O SER R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 361 removed outlier: 3.565A pdb=" N THR R 355 " --> pdb=" O LYS R 351 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 368 removed outlier: 3.897A pdb=" N ALA R 368 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 387 removed outlier: 4.004A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR R 386 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 389 through 404 removed outlier: 3.923A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 421 removed outlier: 4.394A pdb=" N GLU R 418 " --> pdb=" O ARG R 414 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG R 419 " --> pdb=" O LYS R 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 9.847A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.305A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 7.051A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.700A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.725A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.371A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.403A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.076A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.580A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU N 20 " --> pdb=" O LEU N 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.160A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 79 through 81 removed outlier: 3.560A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1218 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: 2.48 Time building geometry restraints manager: 3.56 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: 2803 1.34 - 1.46: 1775 1.46 - 1.58: 4073 1.58 - 1.70: 0 1.70 - 1.82: 71 Bond restraints: 8722 Sorted by residual: bond pdb=" C PRO R 54 " pdb=" N PRO R 55 " ideal model delta sigma weight residual 1.329 1.372 -0.043 1.18e-02 7.18e+03 1.34e+01 bond pdb=" N ARG N 118 " pdb=" CA ARG N 118 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.15e-02 7.56e+03 1.16e+01 bond pdb=" N THR N 122 " pdb=" CA THR N 122 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.31e-02 5.83e+03 8.49e+00 bond pdb=" N ASP R 59 " pdb=" CA ASP R 59 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.15e-02 7.56e+03 8.38e+00 bond pdb=" N GLN N 123 " pdb=" CA GLN N 123 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.22e-02 6.72e+03 8.01e+00 ... (remaining 8717 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.34: 224 107.34 - 114.01: 4825 114.01 - 120.67: 3697 120.67 - 127.33: 2983 127.33 - 134.00: 91 Bond angle restraints: 11820 Sorted by residual: angle pdb=" C PRO R 54 " pdb=" N PRO R 55 " pdb=" CA PRO R 55 " ideal model delta sigma weight residual 120.38 126.35 -5.97 1.03e+00 9.43e-01 3.36e+01 angle pdb=" CA GLN N 123 " pdb=" C GLN N 123 " pdb=" O GLN N 123 " ideal model delta sigma weight residual 121.16 117.05 4.11 1.12e+00 7.97e-01 1.35e+01 angle pdb=" CA VAL N 124 " pdb=" C VAL N 124 " pdb=" O VAL N 124 " ideal model delta sigma weight residual 120.48 116.46 4.02 1.10e+00 8.26e-01 1.34e+01 angle pdb=" CA GLN N 120 " pdb=" C GLN N 120 " pdb=" O GLN N 120 " ideal model delta sigma weight residual 122.14 117.66 4.48 1.24e+00 6.50e-01 1.31e+01 angle pdb=" CA GLY N 121 " pdb=" C GLY N 121 " pdb=" O GLY N 121 " ideal model delta sigma weight residual 122.24 117.56 4.68 1.30e+00 5.92e-01 1.29e+01 ... (remaining 11815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4579 17.73 - 35.47: 452 35.47 - 53.20: 107 53.20 - 70.94: 11 70.94 - 88.67: 11 Dihedral angle restraints: 5160 sinusoidal: 1951 harmonic: 3209 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 36.63 56.37 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CB GLU A 322 " pdb=" CG GLU A 322 " pdb=" CD GLU A 322 " pdb=" OE1 GLU A 322 " ideal model delta sinusoidal sigma weight residual 0.00 -84.22 84.22 1 3.00e+01 1.11e-03 9.59e+00 dihedral pdb=" CA ASP B 66 " pdb=" CB ASP B 66 " pdb=" CG ASP B 66 " pdb=" OD1 ASP B 66 " ideal model delta sinusoidal sigma weight residual -30.00 -82.86 52.86 1 2.00e+01 2.50e-03 9.51e+00 ... (remaining 5157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1093 0.043 - 0.086: 167 0.086 - 0.129: 65 0.129 - 0.172: 1 0.172 - 0.215: 3 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA VAL N 124 " pdb=" N VAL N 124 " pdb=" C VAL N 124 " pdb=" CB VAL N 124 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA LEU R 60 " pdb=" N LEU R 60 " pdb=" C LEU R 60 " pdb=" CB LEU R 60 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA GLN N 123 " pdb=" N GLN N 123 " pdb=" C GLN N 123 " pdb=" CB GLN N 123 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 1326 not shown) Planarity restraints: 1509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 124 " -0.009 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C VAL N 124 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL N 124 " -0.013 2.00e-02 2.50e+03 pdb=" N THR N 125 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY N 121 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C GLY N 121 " -0.025 2.00e-02 2.50e+03 pdb=" O GLY N 121 " 0.009 2.00e-02 2.50e+03 pdb=" N THR N 122 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 276 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO R 277 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO R 277 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 277 " -0.017 5.00e-02 4.00e+02 ... (remaining 1506 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 82 2.57 - 3.15: 7364 3.15 - 3.73: 13225 3.73 - 4.32: 17878 4.32 - 4.90: 29803 Nonbonded interactions: 68352 Sorted by model distance: nonbonded pdb=" O GLU R 387 " pdb=" OG1 THR R 391 " model vdw 1.982 2.440 nonbonded pdb=" O HIS B 183 " pdb=" OG1 THR B 184 " model vdw 2.125 2.440 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.167 2.520 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.254 2.440 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.296 2.520 ... (remaining 68347 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.360 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.310 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 0.003 0.050 8722 Z= 0.175 Angle : 0.473 5.970 11820 Z= 0.301 Chirality : 0.038 0.215 1329 Planarity : 0.002 0.031 1509 Dihedral : 15.152 88.671 3065 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.68 % Allowed : 6.72 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.22), residues: 1075 helix: -0.80 (0.23), residues: 411 sheet: -1.74 (0.32), residues: 215 loop : -2.31 (0.24), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 234 HIS 0.002 0.000 HIS R 363 PHE 0.007 0.001 PHE R 367 TYR 0.006 0.001 TYR N 60 ARG 0.008 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 244 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8712 (m-30) cc_final: 0.8035 (m-30) REVERT: B 9 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8861 (tm-30) REVERT: B 10 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8535 (mt-10) REVERT: B 36 ASN cc_start: 0.9299 (p0) cc_final: 0.9026 (p0) REVERT: B 118 ASP cc_start: 0.7372 (p0) cc_final: 0.7159 (p0) REVERT: B 172 GLU cc_start: 0.7586 (mp0) cc_final: 0.7336 (mp0) REVERT: B 215 GLU cc_start: 0.7350 (mp0) cc_final: 0.6993 (mp0) REVERT: G 19 LEU cc_start: 0.9355 (mp) cc_final: 0.9073 (mp) REVERT: G 36 ASP cc_start: 0.8315 (m-30) cc_final: 0.8099 (m-30) REVERT: N 73 ASP cc_start: 0.7928 (t0) cc_final: 0.7649 (t0) REVERT: N 123 GLN cc_start: 0.7341 (tm-30) cc_final: 0.7126 (tm-30) REVERT: R 204 MET cc_start: 0.8987 (tmm) cc_final: 0.8734 (tmm) REVERT: R 221 GLN cc_start: 0.8338 (mp10) cc_final: 0.8037 (mp10) REVERT: R 277 PRO cc_start: 0.8873 (Cg_exo) cc_final: 0.8605 (Cg_endo) REVERT: R 288 LYS cc_start: 0.9198 (tppp) cc_final: 0.8892 (tppt) REVERT: R 351 LYS cc_start: 0.9094 (tmmt) cc_final: 0.8565 (pttm) REVERT: R 387 GLU cc_start: 0.8927 (mp0) cc_final: 0.8481 (mp0) outliers start: 6 outliers final: 1 residues processed: 248 average time/residue: 0.2299 time to fit residues: 75.1336 Evaluate side-chains 200 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 42 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 155 ASN B 175 GLN B 259 GLN P 1 HIS P 24 GLN ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8722 Z= 0.251 Angle : 0.537 10.753 11820 Z= 0.281 Chirality : 0.040 0.141 1329 Planarity : 0.004 0.042 1509 Dihedral : 3.553 47.479 1199 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.76 % Allowed : 14.81 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1075 helix: 1.44 (0.26), residues: 410 sheet: -1.48 (0.32), residues: 226 loop : -1.65 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 297 HIS 0.008 0.001 HIS A 220 PHE 0.019 0.001 PHE R 184 TYR 0.014 0.001 TYR R 148 ARG 0.007 0.001 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 197 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8825 (tm-30) REVERT: B 10 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8451 (mt-10) REVERT: B 36 ASN cc_start: 0.9291 (p0) cc_final: 0.8961 (p0) REVERT: B 45 MET cc_start: 0.8614 (mmm) cc_final: 0.7834 (mpp) REVERT: B 59 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8725 (m-80) REVERT: B 118 ASP cc_start: 0.7591 (p0) cc_final: 0.7385 (p0) REVERT: B 215 GLU cc_start: 0.7865 (mp0) cc_final: 0.7478 (mp0) REVERT: B 234 PHE cc_start: 0.9327 (OUTLIER) cc_final: 0.8653 (m-80) REVERT: G 19 LEU cc_start: 0.9336 (mp) cc_final: 0.9100 (mp) REVERT: G 20 LYS cc_start: 0.9114 (mtmm) cc_final: 0.8768 (mtmm) REVERT: N 73 ASP cc_start: 0.7678 (t0) cc_final: 0.7361 (t0) REVERT: N 95 TYR cc_start: 0.8817 (m-80) cc_final: 0.8561 (m-80) REVERT: R 202 LYS cc_start: 0.8672 (pptt) cc_final: 0.8102 (ptmt) REVERT: R 204 MET cc_start: 0.8947 (tmm) cc_final: 0.8509 (tmm) REVERT: R 221 GLN cc_start: 0.8311 (mp10) cc_final: 0.7980 (mp10) REVERT: R 257 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6742 (m-10) REVERT: R 269 TYR cc_start: 0.9225 (m-10) cc_final: 0.8999 (m-80) REVERT: R 297 TRP cc_start: 0.8820 (m-10) cc_final: 0.8604 (m-90) REVERT: R 351 LYS cc_start: 0.9055 (tmmt) cc_final: 0.8490 (pttm) REVERT: R 393 PHE cc_start: 0.9025 (m-10) cc_final: 0.8726 (m-10) REVERT: R 397 MET cc_start: 0.9068 (mmp) cc_final: 0.8510 (mtt) outliers start: 33 outliers final: 17 residues processed: 216 average time/residue: 0.2416 time to fit residues: 69.4720 Evaluate side-chains 206 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 293 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 77 optimal weight: 50.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 175 GLN G 18 GLN N 5 GLN N 39 GLN N 120 GLN R 173 HIS R 234 GLN ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8722 Z= 0.271 Angle : 0.527 10.563 11820 Z= 0.279 Chirality : 0.040 0.211 1329 Planarity : 0.003 0.044 1509 Dihedral : 3.868 49.415 1199 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.44 % Allowed : 18.11 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1075 helix: 2.00 (0.26), residues: 410 sheet: -1.07 (0.32), residues: 224 loop : -1.41 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 297 HIS 0.010 0.001 HIS A 220 PHE 0.015 0.001 PHE N 108 TYR 0.013 0.001 TYR R 148 ARG 0.005 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 184 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8864 (m-30) cc_final: 0.8138 (m-30) REVERT: B 9 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8745 (tm-30) REVERT: B 10 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8417 (mt-10) REVERT: B 59 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8592 (m-80) REVERT: B 215 GLU cc_start: 0.7942 (mp0) cc_final: 0.7672 (mp0) REVERT: B 234 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.8679 (m-80) REVERT: G 19 LEU cc_start: 0.9342 (mp) cc_final: 0.9086 (mp) REVERT: G 20 LYS cc_start: 0.9126 (mtmm) cc_final: 0.8831 (mtmm) REVERT: N 73 ASP cc_start: 0.7731 (t0) cc_final: 0.7456 (t0) REVERT: N 95 TYR cc_start: 0.8865 (m-80) cc_final: 0.8529 (m-80) REVERT: R 202 LYS cc_start: 0.8812 (pptt) cc_final: 0.8340 (ptmt) REVERT: R 221 GLN cc_start: 0.8341 (mp10) cc_final: 0.7964 (mp10) REVERT: R 233 MET cc_start: 0.8915 (tmm) cc_final: 0.8652 (tmm) REVERT: R 234 GLN cc_start: 0.9389 (mm-40) cc_final: 0.9165 (mm-40) REVERT: R 297 TRP cc_start: 0.8871 (m-10) cc_final: 0.8630 (m-90) REVERT: R 351 LYS cc_start: 0.8986 (tmmt) cc_final: 0.8381 (pttm) REVERT: R 393 PHE cc_start: 0.8989 (m-10) cc_final: 0.8590 (m-10) REVERT: R 397 MET cc_start: 0.9009 (mmp) cc_final: 0.8584 (mtt) outliers start: 39 outliers final: 24 residues processed: 210 average time/residue: 0.2348 time to fit residues: 65.3818 Evaluate side-chains 209 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN N 39 GLN N 120 GLN ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 8722 Z= 0.234 Angle : 0.522 9.009 11820 Z= 0.272 Chirality : 0.040 0.186 1329 Planarity : 0.003 0.043 1509 Dihedral : 3.962 50.548 1199 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.01 % Allowed : 19.13 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1075 helix: 2.10 (0.26), residues: 410 sheet: -0.79 (0.33), residues: 224 loop : -1.30 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 297 HIS 0.009 0.001 HIS A 220 PHE 0.020 0.001 PHE R 230 TYR 0.016 0.001 TYR A 358 ARG 0.005 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 194 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8847 (m-30) cc_final: 0.8104 (m-30) REVERT: B 9 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8777 (tm-30) REVERT: B 10 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8408 (mt-10) REVERT: B 45 MET cc_start: 0.8615 (mmm) cc_final: 0.7942 (mmm) REVERT: B 59 TYR cc_start: 0.8942 (OUTLIER) cc_final: 0.8648 (m-80) REVERT: B 61 MET cc_start: 0.8297 (ptm) cc_final: 0.8018 (ptm) REVERT: B 183 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7653 (t-90) REVERT: B 215 GLU cc_start: 0.8040 (mp0) cc_final: 0.7818 (mp0) REVERT: B 234 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.8677 (m-80) REVERT: G 20 LYS cc_start: 0.9123 (mtmm) cc_final: 0.8850 (mtmm) REVERT: N 73 ASP cc_start: 0.7767 (t0) cc_final: 0.7502 (t0) REVERT: N 95 TYR cc_start: 0.8813 (m-80) cc_final: 0.8424 (m-80) REVERT: R 202 LYS cc_start: 0.8804 (pptt) cc_final: 0.8361 (ptmt) REVERT: R 204 MET cc_start: 0.8912 (tmm) cc_final: 0.8648 (tmm) REVERT: R 221 GLN cc_start: 0.8340 (mp10) cc_final: 0.7962 (mp10) REVERT: R 309 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9129 (tp) REVERT: R 351 LYS cc_start: 0.8974 (tmmt) cc_final: 0.8373 (pttm) REVERT: R 387 GLU cc_start: 0.9170 (mp0) cc_final: 0.8903 (mp0) REVERT: R 393 PHE cc_start: 0.9002 (m-10) cc_final: 0.8560 (m-10) REVERT: R 397 MET cc_start: 0.9000 (mmp) cc_final: 0.8596 (mtt) outliers start: 44 outliers final: 28 residues processed: 223 average time/residue: 0.2520 time to fit residues: 75.2871 Evaluate side-chains 215 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 50.0000 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN N 31 ASN N 120 GLN R 234 GLN ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8722 Z= 0.252 Angle : 0.521 8.460 11820 Z= 0.274 Chirality : 0.040 0.182 1329 Planarity : 0.003 0.042 1509 Dihedral : 4.064 51.644 1199 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.24 % Allowed : 19.59 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1075 helix: 2.22 (0.26), residues: 407 sheet: -0.69 (0.33), residues: 225 loop : -1.26 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 297 HIS 0.008 0.001 HIS A 220 PHE 0.017 0.001 PHE R 230 TYR 0.014 0.001 TYR A 358 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 188 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 HIS cc_start: 0.8156 (m170) cc_final: 0.7908 (m-70) REVERT: A 378 ASP cc_start: 0.8860 (m-30) cc_final: 0.8115 (m-30) REVERT: B 9 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8798 (tm-30) REVERT: B 10 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8418 (mt-10) REVERT: B 59 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.8651 (m-80) REVERT: B 61 MET cc_start: 0.8294 (ptm) cc_final: 0.8007 (ptm) REVERT: B 183 HIS cc_start: 0.8096 (OUTLIER) cc_final: 0.7696 (t-90) REVERT: B 228 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7995 (p0) REVERT: B 234 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.8731 (m-80) REVERT: G 20 LYS cc_start: 0.9106 (mtmm) cc_final: 0.8869 (mtmm) REVERT: G 21 MET cc_start: 0.8807 (tpp) cc_final: 0.8376 (tpp) REVERT: G 42 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8236 (tm-30) REVERT: N 95 TYR cc_start: 0.8782 (m-80) cc_final: 0.8367 (m-80) REVERT: N 123 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7601 (tm-30) REVERT: R 202 LYS cc_start: 0.8769 (pptt) cc_final: 0.8304 (ptmt) REVERT: R 204 MET cc_start: 0.8886 (tmm) cc_final: 0.8677 (tmm) REVERT: R 221 GLN cc_start: 0.8459 (mp10) cc_final: 0.8170 (mp10) REVERT: R 309 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9157 (tp) REVERT: R 351 LYS cc_start: 0.8960 (tmmt) cc_final: 0.8340 (pttm) REVERT: R 387 GLU cc_start: 0.9161 (mp0) cc_final: 0.8879 (mp0) REVERT: R 393 PHE cc_start: 0.8997 (m-10) cc_final: 0.8545 (m-10) REVERT: R 397 MET cc_start: 0.8997 (mmp) cc_final: 0.8607 (mtt) outliers start: 46 outliers final: 31 residues processed: 220 average time/residue: 0.2362 time to fit residues: 69.0674 Evaluate side-chains 220 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN G 18 GLN N 120 GLN R 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8722 Z= 0.286 Angle : 0.559 8.024 11820 Z= 0.292 Chirality : 0.040 0.175 1329 Planarity : 0.003 0.041 1509 Dihedral : 4.196 52.858 1199 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.69 % Allowed : 20.73 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1075 helix: 2.22 (0.26), residues: 407 sheet: -0.65 (0.33), residues: 224 loop : -1.19 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP R 297 HIS 0.006 0.001 HIS A 220 PHE 0.017 0.001 PHE R 230 TYR 0.015 0.001 TYR A 318 ARG 0.005 0.000 ARG R 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 186 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 HIS cc_start: 0.8225 (m170) cc_final: 0.8024 (m170) REVERT: A 346 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9145 (mp) REVERT: A 378 ASP cc_start: 0.8853 (m-30) cc_final: 0.8088 (m-30) REVERT: B 10 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8539 (mt-10) REVERT: B 42 ARG cc_start: 0.8401 (tmm-80) cc_final: 0.8192 (tmm-80) REVERT: B 45 MET cc_start: 0.8745 (mmm) cc_final: 0.8144 (mmm) REVERT: B 59 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: B 183 HIS cc_start: 0.8143 (OUTLIER) cc_final: 0.7746 (t-90) REVERT: B 215 GLU cc_start: 0.8001 (mp0) cc_final: 0.7648 (mp0) REVERT: B 228 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8082 (p0) REVERT: B 234 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8758 (m-80) REVERT: G 20 LYS cc_start: 0.9201 (mtmm) cc_final: 0.8978 (mtmm) REVERT: G 21 MET cc_start: 0.8803 (tpp) cc_final: 0.8347 (tpp) REVERT: G 29 LYS cc_start: 0.8850 (mmmt) cc_final: 0.8285 (tptp) REVERT: G 42 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8348 (tm-30) REVERT: N 95 TYR cc_start: 0.8811 (m-80) cc_final: 0.8474 (m-80) REVERT: R 202 LYS cc_start: 0.8846 (pptt) cc_final: 0.8458 (tttt) REVERT: R 204 MET cc_start: 0.8871 (tmm) cc_final: 0.8663 (tmm) REVERT: R 221 GLN cc_start: 0.8582 (mp10) cc_final: 0.8291 (mp10) REVERT: R 309 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9157 (tp) REVERT: R 351 LYS cc_start: 0.8957 (tmmt) cc_final: 0.8331 (pttm) REVERT: R 371 MET cc_start: 0.9151 (mmp) cc_final: 0.8937 (mmp) REVERT: R 387 GLU cc_start: 0.9143 (mp0) cc_final: 0.8624 (mp0) REVERT: R 393 PHE cc_start: 0.9009 (m-10) cc_final: 0.8551 (m-10) REVERT: R 394 GLN cc_start: 0.9253 (tt0) cc_final: 0.8836 (tt0) REVERT: R 397 MET cc_start: 0.8984 (mmp) cc_final: 0.8602 (mtt) outliers start: 50 outliers final: 33 residues processed: 221 average time/residue: 0.2331 time to fit residues: 68.5735 Evaluate side-chains 221 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 182 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 74 optimal weight: 50.0000 chunk 86 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 40 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8722 Z= 0.179 Angle : 0.537 7.932 11820 Z= 0.277 Chirality : 0.040 0.185 1329 Planarity : 0.003 0.041 1509 Dihedral : 4.156 53.949 1199 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.24 % Allowed : 21.87 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1075 helix: 2.28 (0.26), residues: 407 sheet: -0.48 (0.33), residues: 225 loop : -1.24 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP R 297 HIS 0.003 0.001 HIS A 362 PHE 0.013 0.001 PHE R 230 TYR 0.015 0.001 TYR A 318 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 200 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9100 (mp) REVERT: A 378 ASP cc_start: 0.8822 (m-30) cc_final: 0.8045 (m-30) REVERT: B 10 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8546 (mt-10) REVERT: B 45 MET cc_start: 0.8761 (mmm) cc_final: 0.8146 (mmm) REVERT: B 59 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8695 (m-80) REVERT: B 183 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.7620 (t-90) REVERT: B 215 GLU cc_start: 0.8040 (mp0) cc_final: 0.7758 (mp0) REVERT: B 228 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7730 (p0) REVERT: B 234 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8682 (m-80) REVERT: G 20 LYS cc_start: 0.9188 (mtmm) cc_final: 0.8968 (mtmm) REVERT: G 21 MET cc_start: 0.8798 (tpp) cc_final: 0.8337 (tpp) REVERT: G 42 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8384 (tm-30) REVERT: G 47 GLU cc_start: 0.8512 (mp0) cc_final: 0.8262 (mp0) REVERT: N 73 ASP cc_start: 0.7843 (t70) cc_final: 0.7445 (t0) REVERT: N 91 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8811 (t) REVERT: N 95 TYR cc_start: 0.8788 (m-80) cc_final: 0.8446 (m-80) REVERT: R 139 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8072 (tp30) REVERT: R 202 LYS cc_start: 0.8833 (pptt) cc_final: 0.8448 (tttt) REVERT: R 204 MET cc_start: 0.8880 (tmm) cc_final: 0.8568 (tmm) REVERT: R 221 GLN cc_start: 0.8591 (mp10) cc_final: 0.8235 (mp10) REVERT: R 309 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9130 (tp) REVERT: R 351 LYS cc_start: 0.8941 (tmmt) cc_final: 0.8312 (pttm) REVERT: R 371 MET cc_start: 0.9110 (mmp) cc_final: 0.8907 (mmp) REVERT: R 387 GLU cc_start: 0.9098 (mp0) cc_final: 0.8549 (mp0) REVERT: R 393 PHE cc_start: 0.8967 (m-10) cc_final: 0.8500 (m-10) REVERT: R 394 GLN cc_start: 0.9198 (tt0) cc_final: 0.8774 (tt0) REVERT: R 397 MET cc_start: 0.8951 (mmp) cc_final: 0.8526 (mtt) outliers start: 46 outliers final: 33 residues processed: 235 average time/residue: 0.2233 time to fit residues: 70.0058 Evaluate side-chains 227 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 187 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8722 Z= 0.169 Angle : 0.550 7.308 11820 Z= 0.283 Chirality : 0.040 0.201 1329 Planarity : 0.003 0.033 1509 Dihedral : 4.151 55.474 1199 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.35 % Allowed : 22.21 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1075 helix: 2.30 (0.26), residues: 407 sheet: -0.47 (0.33), residues: 224 loop : -1.19 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 297 HIS 0.006 0.001 HIS A 220 PHE 0.012 0.001 PHE R 230 TYR 0.013 0.001 TYR A 360 ARG 0.005 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 196 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9095 (mp) REVERT: A 378 ASP cc_start: 0.8809 (m-30) cc_final: 0.8018 (m-30) REVERT: B 10 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8441 (mt-10) REVERT: B 45 MET cc_start: 0.8758 (mmm) cc_final: 0.8095 (mmm) REVERT: B 59 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.8689 (m-80) REVERT: B 183 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7699 (t-90) REVERT: B 215 GLU cc_start: 0.8080 (mp0) cc_final: 0.7752 (mp0) REVERT: B 234 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8675 (m-80) REVERT: B 292 PHE cc_start: 0.8663 (m-80) cc_final: 0.8458 (m-80) REVERT: G 20 LYS cc_start: 0.9173 (mtmm) cc_final: 0.8948 (mtmm) REVERT: G 21 MET cc_start: 0.8814 (tpp) cc_final: 0.8329 (tpp) REVERT: G 42 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8352 (tm-30) REVERT: G 47 GLU cc_start: 0.8488 (mp0) cc_final: 0.8241 (mp0) REVERT: N 91 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8571 (t) REVERT: N 95 TYR cc_start: 0.8764 (m-80) cc_final: 0.8393 (m-80) REVERT: R 139 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8069 (tp30) REVERT: R 202 LYS cc_start: 0.8862 (pptt) cc_final: 0.8496 (tttt) REVERT: R 204 MET cc_start: 0.8865 (tmm) cc_final: 0.8561 (tmm) REVERT: R 221 GLN cc_start: 0.8615 (mp10) cc_final: 0.8273 (mp10) REVERT: R 297 TRP cc_start: 0.8979 (m-10) cc_final: 0.8718 (m-90) REVERT: R 309 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9104 (tp) REVERT: R 351 LYS cc_start: 0.8942 (tmmt) cc_final: 0.8307 (pttm) REVERT: R 387 GLU cc_start: 0.9041 (mp0) cc_final: 0.8578 (mp0) REVERT: R 393 PHE cc_start: 0.8973 (m-10) cc_final: 0.8498 (m-10) REVERT: R 394 GLN cc_start: 0.9196 (tt0) cc_final: 0.8783 (tt0) REVERT: R 397 MET cc_start: 0.8938 (mmp) cc_final: 0.8510 (mtt) outliers start: 47 outliers final: 34 residues processed: 231 average time/residue: 0.2232 time to fit residues: 68.7844 Evaluate side-chains 230 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 190 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 74 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 100 optimal weight: 0.0970 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8722 Z= 0.221 Angle : 0.585 8.345 11820 Z= 0.300 Chirality : 0.041 0.209 1329 Planarity : 0.003 0.034 1509 Dihedral : 4.207 56.709 1199 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.90 % Allowed : 22.89 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1075 helix: 2.29 (0.26), residues: 407 sheet: -0.40 (0.33), residues: 224 loop : -1.17 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 297 HIS 0.009 0.001 HIS A 220 PHE 0.014 0.001 PHE R 230 TYR 0.014 0.001 TYR A 360 ARG 0.008 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 187 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8826 (m-30) cc_final: 0.8039 (m-30) REVERT: B 10 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8449 (mt-10) REVERT: B 45 MET cc_start: 0.8748 (mmm) cc_final: 0.8101 (mmm) REVERT: B 59 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8730 (m-80) REVERT: B 61 MET cc_start: 0.8345 (ptm) cc_final: 0.8099 (ptm) REVERT: B 183 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7739 (t-90) REVERT: B 215 GLU cc_start: 0.8087 (mp0) cc_final: 0.7754 (mp0) REVERT: B 226 GLU cc_start: 0.7782 (tp30) cc_final: 0.7284 (mm-30) REVERT: B 228 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7910 (p0) REVERT: B 234 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.8774 (m-80) REVERT: G 20 LYS cc_start: 0.9188 (mtmm) cc_final: 0.8962 (mtmm) REVERT: G 21 MET cc_start: 0.8778 (tpp) cc_final: 0.8341 (tpp) REVERT: G 42 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8266 (tm-30) REVERT: G 47 GLU cc_start: 0.8450 (mp0) cc_final: 0.8204 (mp0) REVERT: N 91 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8844 (t) REVERT: N 95 TYR cc_start: 0.8789 (m-80) cc_final: 0.8514 (m-80) REVERT: R 139 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8071 (tp30) REVERT: R 202 LYS cc_start: 0.8870 (pptt) cc_final: 0.8498 (tttt) REVERT: R 204 MET cc_start: 0.8861 (tmm) cc_final: 0.8633 (tmm) REVERT: R 221 GLN cc_start: 0.8620 (mp10) cc_final: 0.8311 (mp10) REVERT: R 297 TRP cc_start: 0.8988 (m-10) cc_final: 0.8692 (m-90) REVERT: R 309 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9131 (tp) REVERT: R 351 LYS cc_start: 0.8941 (tmmt) cc_final: 0.8295 (pttm) REVERT: R 387 GLU cc_start: 0.9031 (mp0) cc_final: 0.8349 (pm20) REVERT: R 393 PHE cc_start: 0.8981 (m-10) cc_final: 0.8506 (m-10) REVERT: R 394 GLN cc_start: 0.9215 (tt0) cc_final: 0.8799 (tt0) REVERT: R 397 MET cc_start: 0.8945 (mmp) cc_final: 0.8523 (mtt) outliers start: 43 outliers final: 35 residues processed: 218 average time/residue: 0.2312 time to fit residues: 67.0823 Evaluate side-chains 224 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 293 ASP Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN R 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8722 Z= 0.172 Angle : 0.580 7.807 11820 Z= 0.294 Chirality : 0.040 0.204 1329 Planarity : 0.003 0.033 1509 Dihedral : 4.145 57.509 1199 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.21 % Allowed : 24.03 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1075 helix: 2.30 (0.26), residues: 407 sheet: -0.37 (0.34), residues: 224 loop : -1.13 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 297 HIS 0.008 0.001 HIS A 220 PHE 0.012 0.001 PHE R 230 TYR 0.014 0.001 TYR A 360 ARG 0.009 0.000 ARG G 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 194 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8800 (m-30) cc_final: 0.8006 (m-30) REVERT: A 392 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8252 (mp0) REVERT: B 10 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8468 (mt-10) REVERT: B 36 ASN cc_start: 0.9240 (p0) cc_final: 0.9030 (p0) REVERT: B 45 MET cc_start: 0.8750 (mmm) cc_final: 0.8106 (mmm) REVERT: B 59 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8607 (m-80) REVERT: B 61 MET cc_start: 0.8283 (ptm) cc_final: 0.8081 (ptm) REVERT: B 183 HIS cc_start: 0.8050 (OUTLIER) cc_final: 0.7629 (t-90) REVERT: B 215 GLU cc_start: 0.8108 (mp0) cc_final: 0.7775 (mp0) REVERT: B 226 GLU cc_start: 0.7664 (tp30) cc_final: 0.7183 (mm-30) REVERT: B 234 PHE cc_start: 0.9394 (OUTLIER) cc_final: 0.8743 (m-80) REVERT: B 292 PHE cc_start: 0.8729 (m-80) cc_final: 0.8493 (m-80) REVERT: G 20 LYS cc_start: 0.9184 (mtmm) cc_final: 0.8925 (mtmm) REVERT: G 21 MET cc_start: 0.8776 (tpp) cc_final: 0.8377 (tpp) REVERT: G 42 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8264 (tm-30) REVERT: N 91 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8810 (t) REVERT: R 139 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8070 (tp30) REVERT: R 202 LYS cc_start: 0.8856 (pptt) cc_final: 0.8500 (tttt) REVERT: R 204 MET cc_start: 0.8867 (tmm) cc_final: 0.8614 (tmm) REVERT: R 221 GLN cc_start: 0.8629 (mp10) cc_final: 0.8298 (mp10) REVERT: R 234 GLN cc_start: 0.9276 (mm110) cc_final: 0.8992 (mm-40) REVERT: R 288 LYS cc_start: 0.9357 (tppt) cc_final: 0.8661 (tppt) REVERT: R 297 TRP cc_start: 0.8936 (m-10) cc_final: 0.8718 (m-90) REVERT: R 309 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9098 (tp) REVERT: R 351 LYS cc_start: 0.8937 (tmmt) cc_final: 0.8287 (pttm) REVERT: R 387 GLU cc_start: 0.8994 (mp0) cc_final: 0.8360 (pm20) REVERT: R 393 PHE cc_start: 0.8953 (m-10) cc_final: 0.8508 (m-10) REVERT: R 394 GLN cc_start: 0.9115 (tt0) cc_final: 0.8667 (tt0) REVERT: R 397 MET cc_start: 0.8931 (mmp) cc_final: 0.8475 (mtt) outliers start: 37 outliers final: 31 residues processed: 220 average time/residue: 0.2305 time to fit residues: 67.3017 Evaluate side-chains 226 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 40.0000 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 0.0060 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 73 optimal weight: 0.0970 chunk 4 optimal weight: 3.9990 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN R 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.097082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.068984 restraints weight = 19838.755| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.51 r_work: 0.2857 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8722 Z= 0.141 Angle : 0.576 8.728 11820 Z= 0.290 Chirality : 0.040 0.213 1329 Planarity : 0.003 0.033 1509 Dihedral : 3.980 59.355 1199 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.30 % Allowed : 24.26 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1075 helix: 2.36 (0.26), residues: 407 sheet: -0.08 (0.36), residues: 204 loop : -1.18 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 297 HIS 0.007 0.001 HIS A 220 PHE 0.010 0.001 PHE A 212 TYR 0.014 0.001 TYR A 360 ARG 0.010 0.000 ARG G 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2202.72 seconds wall clock time: 40 minutes 33.08 seconds (2433.08 seconds total)