Starting phenix.real_space_refine on Tue Feb 13 13:57:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8p_21577/02_2024/6w8p_21577.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8p_21577/02_2024/6w8p_21577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8p_21577/02_2024/6w8p_21577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8p_21577/02_2024/6w8p_21577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8p_21577/02_2024/6w8p_21577.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8p_21577/02_2024/6w8p_21577.pdb" } resolution = 3.6 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= 0.009 sd= 0.067 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 41 5.16 5 C 4309 2.51 5 N 1051 2.21 5 O 1105 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 41": "OD1" <-> "OD2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ASP 371": "OD1" <-> "OD2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 135": "OD1" <-> "OD2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B ASP 283": "OD1" <-> "OD2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6509 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3216 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 398} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3290 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 406} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.27, per 1000 atoms: 0.66 Number of scatterers: 6509 At special positions: 0 Unit cell: (98.175, 97.35, 80.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 41 16.00 O 1105 8.00 N 1051 7.00 C 4309 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 196 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.4 seconds 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 0 sheets defined 81.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 34 through 48 removed outlier: 3.841A pdb=" N SER A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.524A pdb=" N THR A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 101 removed outlier: 4.030A pdb=" N ILE A 87 " --> pdb=" O MET A 83 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A 91 " --> pdb=" O ILE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 136 through 163 removed outlier: 4.269A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 150 " --> pdb=" O CYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.601A pdb=" N SER A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 180 through 202 removed outlier: 4.007A pdb=" N HIS A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLY A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 211 through 224 removed outlier: 3.663A pdb=" N VAL A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 3.854A pdb=" N SER A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 274 Processing helix chain 'A' and resid 276 through 284 removed outlier: 4.561A pdb=" N GLU A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 5.681A pdb=" N ARG A 294 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 295 " --> pdb=" O LYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.839A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 332 Processing helix chain 'A' and resid 338 through 363 removed outlier: 3.657A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Proline residue: A 356 - end of helix removed outlier: 3.537A pdb=" N SER A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 396 removed outlier: 3.848A pdb=" N ARG A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.833A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 443 through 470 removed outlier: 4.396A pdb=" N ILE A 447 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Proline residue: A 456 - end of helix removed outlier: 4.891A pdb=" N LEU A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU A 461 " --> pdb=" O CYS A 457 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.903A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 removed outlier: 3.550A pdb=" N THR B 56 " --> pdb=" O ILE B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 102 Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 122 through 132 removed outlier: 3.651A pdb=" N THR B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 163 removed outlier: 4.366A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE B 150 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 152 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 180 through 206 removed outlier: 3.704A pdb=" N GLY B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLY B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Proline residue: B 193 - end of helix removed outlier: 3.724A pdb=" N LEU B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 228 Proline residue: B 221 - end of helix removed outlier: 5.811A pdb=" N LYS B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL B 226 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 283 removed outlier: 4.423A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 296 removed outlier: 6.067A pdb=" N ARG B 294 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 295 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.827A pdb=" N ALA B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 363 removed outlier: 3.608A pdb=" N LEU B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Proline residue: B 356 - end of helix removed outlier: 3.558A pdb=" N SER B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 395 removed outlier: 4.075A pdb=" N ARG B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 399 through 403 removed outlier: 4.529A pdb=" N ALA B 402 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 435 removed outlier: 5.144A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 443 through 455 removed outlier: 4.313A pdb=" N ILE B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.626A pdb=" N LEU B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1275 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: 1.74 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1995 1.35 - 1.46: 1633 1.46 - 1.58: 2978 1.58 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 6669 Sorted by residual: bond pdb=" CA PHE A 99 " pdb=" C PHE A 99 " ideal model delta sigma weight residual 1.522 1.495 0.027 1.37e-02 5.33e+03 3.97e+00 bond pdb=" N LEU A 460 " pdb=" CA LEU A 460 " ideal model delta sigma weight residual 1.459 1.480 -0.021 1.25e-02 6.40e+03 2.87e+00 bond pdb=" CA SER A 379 " pdb=" C SER A 379 " ideal model delta sigma weight residual 1.522 1.499 0.023 1.38e-02 5.25e+03 2.78e+00 bond pdb=" N PRO A 208 " pdb=" CA PRO A 208 " ideal model delta sigma weight residual 1.469 1.480 -0.011 7.40e-03 1.83e+04 2.14e+00 bond pdb=" C VAL B 272 " pdb=" O VAL B 272 " ideal model delta sigma weight residual 1.236 1.252 -0.016 1.10e-02 8.26e+03 2.09e+00 ... (remaining 6664 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.79: 202 106.79 - 113.60: 3808 113.60 - 120.41: 2645 120.41 - 127.22: 2377 127.22 - 134.03: 74 Bond angle restraints: 9106 Sorted by residual: angle pdb=" N ILE A 87 " pdb=" CA ILE A 87 " pdb=" C ILE A 87 " ideal model delta sigma weight residual 113.71 108.21 5.50 9.50e-01 1.11e+00 3.36e+01 angle pdb=" N ILE A 60 " pdb=" CA ILE A 60 " pdb=" C ILE A 60 " ideal model delta sigma weight residual 111.77 107.25 4.52 1.04e+00 9.25e-01 1.89e+01 angle pdb=" N SER A 408 " pdb=" CA SER A 408 " pdb=" C SER A 408 " ideal model delta sigma weight residual 114.39 108.96 5.43 1.45e+00 4.76e-01 1.40e+01 angle pdb=" N LEU B 355 " pdb=" CA LEU B 355 " pdb=" C LEU B 355 " ideal model delta sigma weight residual 109.81 117.71 -7.90 2.21e+00 2.05e-01 1.28e+01 angle pdb=" N ILE B 60 " pdb=" CA ILE B 60 " pdb=" C ILE B 60 " ideal model delta sigma weight residual 112.83 109.33 3.50 9.90e-01 1.02e+00 1.25e+01 ... (remaining 9101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 3341 17.55 - 35.11: 391 35.11 - 52.66: 130 52.66 - 70.21: 34 70.21 - 87.76: 9 Dihedral angle restraints: 3905 sinusoidal: 1433 harmonic: 2472 Sorted by residual: dihedral pdb=" CB CYS A 144 " pdb=" SG CYS A 144 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 167.40 -74.40 1 1.00e+01 1.00e-02 7.02e+01 dihedral pdb=" CA VAL A 223 " pdb=" C VAL A 223 " pdb=" N SER A 224 " pdb=" CA SER A 224 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA GLN B 406 " pdb=" C GLN B 406 " pdb=" N PRO B 407 " pdb=" CA PRO B 407 " ideal model delta harmonic sigma weight residual 180.00 -159.86 -20.14 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 3902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 687 0.032 - 0.063: 276 0.063 - 0.095: 99 0.095 - 0.126: 49 0.126 - 0.158: 8 Chirality restraints: 1119 Sorted by residual: chirality pdb=" CG LEU A 398 " pdb=" CB LEU A 398 " pdb=" CD1 LEU A 398 " pdb=" CD2 LEU A 398 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA TYR A 426 " pdb=" N TYR A 426 " pdb=" C TYR A 426 " pdb=" CB TYR A 426 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA ILE B 150 " pdb=" N ILE B 150 " pdb=" C ILE B 150 " pdb=" CB ILE B 150 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 1116 not shown) Planarity restraints: 1117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 459 " 0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C PHE A 459 " -0.066 2.00e-02 2.50e+03 pdb=" O PHE A 459 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU A 460 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 285 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO B 286 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 286 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 286 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 287 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 288 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " 0.019 5.00e-02 4.00e+02 ... (remaining 1114 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 2131 2.82 - 3.40: 8000 3.40 - 3.98: 12103 3.98 - 4.56: 16687 4.56 - 5.14: 23602 Nonbonded interactions: 62523 Sorted by model distance: nonbonded pdb=" O ALA A 200 " pdb=" OG SER A 203 " model vdw 2.236 2.440 nonbonded pdb=" OG1 THR B 319 " pdb=" OH TYR B 359 " model vdw 2.262 2.440 nonbonded pdb=" O SER A 363 " pdb=" OG SER A 363 " model vdw 2.303 2.440 nonbonded pdb=" O ALA B 200 " pdb=" OG SER B 203 " model vdw 2.307 2.440 nonbonded pdb=" O GLN A 401 " pdb=" NE1 TRP A 410 " model vdw 2.308 2.520 ... (remaining 62518 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 471 or resid 601)) selection = (chain 'B' and (resid 33 through 173 or (resid 174 and (name N or name CA or nam \ e C or name O or name CB )) or resid 175 through 228 or resid 250 through 471 or \ resid 601)) } 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=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.690 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.290 Find NCS groups from input model: 0.390 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.004 0.066 6669 Z= 0.262 Angle : 0.759 8.391 9106 Z= 0.432 Chirality : 0.043 0.158 1119 Planarity : 0.004 0.048 1117 Dihedral : 18.044 87.764 2287 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 10.89 % Allowed : 24.93 % Favored : 64.18 % 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: -3.47 (0.25), residues: 836 helix: -1.70 (0.17), residues: 633 sheet: None (None), residues: 0 loop : -3.79 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 92 HIS 0.006 0.001 HIS B 449 PHE 0.012 0.001 PHE B 351 TYR 0.014 0.002 TYR A 313 ARG 0.007 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 161 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 254 GLU cc_start: 0.7417 (pm20) cc_final: 0.7147 (pm20) REVERT: A 341 MET cc_start: 0.7426 (tpp) cc_final: 0.7203 (mmm) REVERT: A 359 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.6994 (t80) REVERT: A 377 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7976 (mtm-85) REVERT: B 196 CYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7125 (t) REVERT: B 415 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8257 (pm20) outliers start: 76 outliers final: 53 residues processed: 217 average time/residue: 0.1653 time to fit residues: 48.0940 Evaluate side-chains 182 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 125 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 470 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0370 chunk 25 optimal weight: 0.0070 chunk 39 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 HIS B 368 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6669 Z= 0.223 Angle : 0.728 8.831 9106 Z= 0.354 Chirality : 0.043 0.209 1119 Planarity : 0.005 0.052 1117 Dihedral : 12.030 71.949 1001 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 11.03 % Allowed : 30.09 % Favored : 58.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.27), residues: 836 helix: -0.49 (0.20), residues: 611 sheet: None (None), residues: 0 loop : -3.33 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 324 HIS 0.006 0.001 HIS A 449 PHE 0.011 0.001 PHE A 317 TYR 0.020 0.002 TYR A 313 ARG 0.002 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 142 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.7647 (m) REVERT: A 112 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8928 (mm) REVERT: A 254 GLU cc_start: 0.7469 (pm20) cc_final: 0.7120 (pm20) REVERT: A 341 MET cc_start: 0.7403 (tpp) cc_final: 0.7194 (mmm) REVERT: A 359 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7023 (t80) REVERT: A 377 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7789 (mtm-85) REVERT: A 415 GLU cc_start: 0.8646 (pm20) cc_final: 0.8095 (pm20) REVERT: B 196 CYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7032 (t) REVERT: B 372 GLU cc_start: 0.6505 (mt-10) cc_final: 0.5285 (mt-10) REVERT: B 374 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7593 (mm-30) outliers start: 77 outliers final: 52 residues processed: 199 average time/residue: 0.1473 time to fit residues: 40.7925 Evaluate side-chains 185 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 127 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 470 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0040 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6669 Z= 0.232 Angle : 0.707 8.660 9106 Z= 0.347 Chirality : 0.043 0.177 1119 Planarity : 0.005 0.049 1117 Dihedral : 10.551 58.001 970 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 11.89 % Allowed : 28.94 % Favored : 59.17 % 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: -1.20 (0.29), residues: 836 helix: 0.05 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -3.04 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 324 HIS 0.006 0.001 HIS B 449 PHE 0.011 0.001 PHE B 351 TYR 0.015 0.002 TYR A 313 ARG 0.007 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 139 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 88 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.7613 (m) REVERT: A 196 CYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6979 (t) REVERT: A 206 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.6865 (m-10) REVERT: A 254 GLU cc_start: 0.7493 (pm20) cc_final: 0.7084 (pm20) REVERT: A 341 MET cc_start: 0.7283 (tpp) cc_final: 0.7076 (mmm) REVERT: A 359 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7034 (t80) REVERT: A 377 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8195 (tpp80) REVERT: A 415 GLU cc_start: 0.8671 (pm20) cc_final: 0.8087 (pm20) REVERT: B 163 HIS cc_start: 0.8104 (t-90) cc_final: 0.7756 (t-90) REVERT: B 196 CYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7018 (t) REVERT: B 282 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7316 (tm-30) REVERT: B 372 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6551 (mt-10) REVERT: B 374 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7608 (mm-30) outliers start: 83 outliers final: 58 residues processed: 200 average time/residue: 0.1725 time to fit residues: 47.5938 Evaluate side-chains 193 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 128 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 144 CYS Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 470 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 80 optimal weight: 0.0670 chunk 71 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6669 Z= 0.221 Angle : 0.699 8.693 9106 Z= 0.341 Chirality : 0.043 0.204 1119 Planarity : 0.004 0.049 1117 Dihedral : 10.239 59.676 965 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.45 % Favored : 90.43 % Rotamer: Outliers : 11.89 % Allowed : 29.80 % Favored : 58.31 % 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: -0.75 (0.29), residues: 836 helix: 0.34 (0.21), residues: 619 sheet: None (None), residues: 0 loop : -2.85 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 324 HIS 0.006 0.001 HIS A 449 PHE 0.011 0.001 PHE B 351 TYR 0.016 0.002 TYR A 313 ARG 0.007 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 136 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8237 (pm20) cc_final: 0.7976 (pm20) REVERT: A 88 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.7559 (m) REVERT: A 112 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8886 (mm) REVERT: A 196 CYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6802 (t) REVERT: A 206 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.6923 (m-10) REVERT: A 254 GLU cc_start: 0.7510 (pm20) cc_final: 0.7130 (pm20) REVERT: A 257 SER cc_start: 0.8772 (t) cc_final: 0.8430 (m) REVERT: A 359 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7105 (t80) REVERT: A 377 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8110 (tpp80) REVERT: A 415 GLU cc_start: 0.8651 (pm20) cc_final: 0.8178 (pm20) REVERT: B 117 MET cc_start: 0.8168 (tpp) cc_final: 0.7958 (tpp) REVERT: B 163 HIS cc_start: 0.8105 (t-90) cc_final: 0.7795 (t-90) REVERT: B 196 CYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7087 (t) REVERT: B 374 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7549 (mm-30) outliers start: 83 outliers final: 60 residues processed: 197 average time/residue: 0.1408 time to fit residues: 39.1737 Evaluate side-chains 199 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 131 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 470 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6669 Z= 0.232 Angle : 0.699 8.708 9106 Z= 0.341 Chirality : 0.043 0.220 1119 Planarity : 0.005 0.053 1117 Dihedral : 9.964 58.517 962 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.45 % Favored : 90.43 % Rotamer: Outliers : 12.46 % Allowed : 31.23 % Favored : 56.30 % 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: -0.51 (0.30), residues: 836 helix: 0.47 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -2.74 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 324 HIS 0.005 0.001 HIS B 449 PHE 0.011 0.001 PHE B 351 TYR 0.031 0.002 TYR B 125 ARG 0.005 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 136 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8237 (pm20) cc_final: 0.7900 (pm20) REVERT: A 112 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8828 (mm) REVERT: A 196 CYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6664 (t) REVERT: A 206 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: A 254 GLU cc_start: 0.7518 (pm20) cc_final: 0.7156 (pm20) REVERT: A 257 SER cc_start: 0.8709 (t) cc_final: 0.8404 (m) REVERT: A 359 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7282 (t80) REVERT: A 377 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8077 (tpp80) REVERT: A 415 GLU cc_start: 0.8613 (pm20) cc_final: 0.8060 (pm20) REVERT: B 163 HIS cc_start: 0.8126 (t-90) cc_final: 0.7912 (t70) REVERT: B 196 CYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7138 (t) REVERT: B 374 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: B 414 ARG cc_start: 0.8034 (tpm170) cc_final: 0.7721 (tpm170) outliers start: 87 outliers final: 65 residues processed: 200 average time/residue: 0.1394 time to fit residues: 39.2017 Evaluate side-chains 207 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 135 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 470 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6669 Z= 0.235 Angle : 0.715 8.776 9106 Z= 0.346 Chirality : 0.043 0.227 1119 Planarity : 0.004 0.053 1117 Dihedral : 9.916 58.622 960 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.33 % Favored : 90.55 % Rotamer: Outliers : 11.60 % Allowed : 32.23 % Favored : 56.16 % 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: -0.39 (0.30), residues: 836 helix: 0.57 (0.21), residues: 625 sheet: None (None), residues: 0 loop : -2.72 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 324 HIS 0.005 0.001 HIS A 449 PHE 0.012 0.001 PHE B 85 TYR 0.020 0.002 TYR B 125 ARG 0.005 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 141 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8291 (pm20) cc_final: 0.7944 (pm20) REVERT: A 112 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8771 (mm) REVERT: A 196 CYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6583 (t) REVERT: A 206 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.6719 (m-10) REVERT: A 254 GLU cc_start: 0.7526 (pm20) cc_final: 0.7153 (pm20) REVERT: A 257 SER cc_start: 0.8676 (t) cc_final: 0.8397 (m) REVERT: A 359 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7300 (t80) REVERT: A 377 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8051 (tpp80) REVERT: A 415 GLU cc_start: 0.8617 (pm20) cc_final: 0.8098 (pm20) REVERT: B 163 HIS cc_start: 0.8122 (t-90) cc_final: 0.7906 (t70) REVERT: B 282 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7332 (tm-30) REVERT: B 372 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6297 (mt-10) REVERT: B 374 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: B 414 ARG cc_start: 0.8055 (tpm170) cc_final: 0.7776 (tpm170) outliers start: 81 outliers final: 62 residues processed: 201 average time/residue: 0.1457 time to fit residues: 41.1972 Evaluate side-chains 200 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 132 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 462 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 31 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6669 Z= 0.222 Angle : 0.720 8.988 9106 Z= 0.348 Chirality : 0.043 0.227 1119 Planarity : 0.004 0.051 1117 Dihedral : 9.599 59.794 955 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 11.46 % Allowed : 32.66 % Favored : 55.87 % 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: -0.27 (0.30), residues: 836 helix: 0.65 (0.21), residues: 625 sheet: None (None), residues: 0 loop : -2.65 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 324 HIS 0.005 0.001 HIS A 449 PHE 0.027 0.001 PHE B 197 TYR 0.016 0.002 TYR A 313 ARG 0.007 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 132 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8741 (mm) REVERT: A 196 CYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6588 (t) REVERT: A 206 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6607 (m-10) REVERT: A 254 GLU cc_start: 0.7552 (pm20) cc_final: 0.7129 (pm20) REVERT: A 257 SER cc_start: 0.8670 (t) cc_final: 0.8388 (m) REVERT: A 289 LYS cc_start: 0.9415 (mmmt) cc_final: 0.9210 (ttmm) REVERT: A 359 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7438 (t80) REVERT: A 377 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8023 (tpp80) REVERT: A 415 GLU cc_start: 0.8601 (pm20) cc_final: 0.8123 (pm20) REVERT: B 211 TYR cc_start: 0.5770 (OUTLIER) cc_final: 0.5540 (t80) REVERT: B 372 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6218 (mt-10) REVERT: B 374 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: B 415 GLU cc_start: 0.8830 (pt0) cc_final: 0.8617 (pt0) outliers start: 80 outliers final: 60 residues processed: 194 average time/residue: 0.1449 time to fit residues: 40.0569 Evaluate side-chains 200 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 133 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 462 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6669 Z= 0.242 Angle : 0.734 8.763 9106 Z= 0.355 Chirality : 0.043 0.239 1119 Planarity : 0.004 0.048 1117 Dihedral : 9.425 60.902 951 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.45 % Favored : 90.43 % Rotamer: Outliers : 10.17 % Allowed : 34.24 % Favored : 55.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.30), residues: 836 helix: 0.68 (0.21), residues: 625 sheet: None (None), residues: 0 loop : -2.61 (0.44), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 92 HIS 0.005 0.001 HIS B 449 PHE 0.020 0.001 PHE B 197 TYR 0.015 0.002 TYR A 313 ARG 0.004 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 134 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8720 (mm) REVERT: A 196 CYS cc_start: 0.6805 (OUTLIER) cc_final: 0.6409 (t) REVERT: A 206 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6589 (m-10) REVERT: A 252 LEU cc_start: 0.7606 (tt) cc_final: 0.7164 (mm) REVERT: A 254 GLU cc_start: 0.7553 (pm20) cc_final: 0.7158 (pm20) REVERT: A 257 SER cc_start: 0.8720 (t) cc_final: 0.8435 (m) REVERT: A 359 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7444 (t80) REVERT: A 377 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7993 (tpp80) REVERT: A 415 GLU cc_start: 0.8547 (pm20) cc_final: 0.8055 (pm20) REVERT: B 211 TYR cc_start: 0.5772 (OUTLIER) cc_final: 0.5426 (t80) REVERT: B 372 GLU cc_start: 0.6745 (mt-10) cc_final: 0.6171 (mt-10) REVERT: B 374 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: B 414 ARG cc_start: 0.8097 (tpm170) cc_final: 0.7855 (tpm170) outliers start: 71 outliers final: 59 residues processed: 189 average time/residue: 0.1416 time to fit residues: 37.6001 Evaluate side-chains 195 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 129 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 211 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 462 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6669 Z= 0.250 Angle : 0.744 8.840 9106 Z= 0.359 Chirality : 0.044 0.242 1119 Planarity : 0.004 0.042 1117 Dihedral : 9.239 60.498 949 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 10.03 % Allowed : 34.81 % Favored : 55.16 % 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: -0.23 (0.30), residues: 836 helix: 0.68 (0.21), residues: 623 sheet: None (None), residues: 0 loop : -2.59 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 92 HIS 0.005 0.001 HIS A 449 PHE 0.021 0.001 PHE B 197 TYR 0.014 0.002 TYR A 313 ARG 0.004 0.000 ARG B 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 134 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8722 (mm) REVERT: A 196 CYS cc_start: 0.6784 (OUTLIER) cc_final: 0.6378 (t) REVERT: A 206 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6547 (m-10) REVERT: A 252 LEU cc_start: 0.7614 (tt) cc_final: 0.7173 (mm) REVERT: A 254 GLU cc_start: 0.7572 (pm20) cc_final: 0.7172 (pm20) REVERT: A 257 SER cc_start: 0.8728 (t) cc_final: 0.8436 (m) REVERT: A 289 LYS cc_start: 0.9410 (mmmt) cc_final: 0.9186 (ttmm) REVERT: A 359 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.7420 (t80) REVERT: A 377 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7975 (tpp80) REVERT: A 415 GLU cc_start: 0.8536 (pm20) cc_final: 0.8044 (pm20) REVERT: B 372 GLU cc_start: 0.6747 (mt-10) cc_final: 0.6165 (mt-10) REVERT: B 374 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: B 414 ARG cc_start: 0.8123 (tpm170) cc_final: 0.7898 (tpm170) REVERT: B 432 LEU cc_start: 0.8841 (tp) cc_final: 0.8638 (tt) outliers start: 70 outliers final: 59 residues processed: 186 average time/residue: 0.1479 time to fit residues: 38.4684 Evaluate side-chains 199 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 134 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 462 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.4980 chunk 82 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.0370 chunk 52 optimal weight: 0.0870 chunk 70 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6669 Z= 0.217 Angle : 0.750 8.982 9106 Z= 0.361 Chirality : 0.043 0.262 1119 Planarity : 0.004 0.045 1117 Dihedral : 9.050 61.236 946 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.69 % Favored : 90.19 % Rotamer: Outliers : 8.88 % Allowed : 36.25 % Favored : 54.87 % 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: -0.12 (0.30), residues: 836 helix: 0.71 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -2.49 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 92 HIS 0.005 0.001 HIS A 449 PHE 0.020 0.001 PHE B 197 TYR 0.016 0.002 TYR A 313 ARG 0.004 0.000 ARG B 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1672 Ramachandran restraints generated. 836 Oldfield, 0 Emsley, 836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 137 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8708 (mm) REVERT: A 196 CYS cc_start: 0.6563 (OUTLIER) cc_final: 0.6167 (t) REVERT: A 206 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.6472 (m-10) REVERT: A 252 LEU cc_start: 0.7536 (tt) cc_final: 0.7145 (mm) REVERT: A 254 GLU cc_start: 0.7570 (pm20) cc_final: 0.7166 (pm20) REVERT: A 289 LYS cc_start: 0.9404 (mmmt) cc_final: 0.9170 (ttmm) REVERT: A 359 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.7517 (t80) REVERT: A 415 GLU cc_start: 0.8460 (pm20) cc_final: 0.8017 (pm20) REVERT: B 374 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: B 414 ARG cc_start: 0.8096 (tpm170) cc_final: 0.7830 (tpm170) outliers start: 62 outliers final: 53 residues processed: 181 average time/residue: 0.1378 time to fit residues: 35.3314 Evaluate side-chains 189 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 131 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 310 PHE Chi-restraints excluded: chain B residue 314 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 462 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.186221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.149486 restraints weight = 10216.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.154225 restraints weight = 4982.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.157312 restraints weight = 3378.231| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6669 Z= 0.249 Angle : 0.764 8.933 9106 Z= 0.371 Chirality : 0.044 0.263 1119 Planarity : 0.004 0.038 1117 Dihedral : 8.344 56.083 936 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 8.74 % Allowed : 36.96 % Favored : 54.30 % 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: -0.10 (0.30), residues: 836 helix: 0.75 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -2.49 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 92 HIS 0.005 0.001 HIS A 449 PHE 0.020 0.001 PHE B 197 TYR 0.014 0.002 TYR A 313 ARG 0.004 0.000 ARG B 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1679.21 seconds wall clock time: 31 minutes 32.17 seconds (1892.17 seconds total)