Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 08:22:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8p_21577/04_2023/6w8p_21577.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8p_21577/04_2023/6w8p_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_21577/04_2023/6w8p_21577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8p_21577/04_2023/6w8p_21577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8p_21577/04_2023/6w8p_21577.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8p_21577/04_2023/6w8p_21577.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 4.17, per 1000 atoms: 0.64 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: 2.76 Conformation dependent library (CDL) restraints added in 1.2 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: 0.28 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: 1.73 Time building geometry restraints manager: 2.94 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: 0.690 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: 3.800 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 21.720 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.500 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.835 Fit side-chains revert: symmetry clash outliers start: 76 outliers final: 53 residues processed: 217 average time/residue: 0.1712 time to fit residues: 49.9018 Evaluate side-chains 178 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 125 time to evaluate : 0.783 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 53 outliers final: 1 residues processed: 53 average time/residue: 0.0687 time to fit residues: 7.5650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0370 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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: 0.7785 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 6669 Z= 0.251 Angle : 0.749 7.866 9106 Z= 0.368 Chirality : 0.043 0.202 1119 Planarity : 0.005 0.053 1117 Dihedral : 5.063 22.605 894 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer Outliers : 6.59 % 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: -1.91 (0.28), residues: 836 helix: -0.48 (0.20), residues: 614 sheet: None (None), residues: 0 loop : -3.33 (0.39), residues: 222 *********************** 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 199 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 0.744 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 23 residues processed: 182 average time/residue: 0.1455 time to fit residues: 37.1477 Evaluate side-chains 159 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.0776 time to fit residues: 4.2641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0970 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- 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 : 0.004 0.067 6669 Z= 0.257 Angle : 0.729 8.802 9106 Z= 0.362 Chirality : 0.043 0.170 1119 Planarity : 0.005 0.059 1117 Dihedral : 4.928 20.279 894 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer Outliers : 4.30 % 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: -1.33 (0.29), residues: 836 helix: -0.02 (0.21), residues: 609 sheet: None (None), residues: 0 loop : -3.15 (0.40), residues: 227 *********************** 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 175 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 0.721 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 163 average time/residue: 0.1600 time to fit residues: 36.4158 Evaluate side-chains 152 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0712 time to fit residues: 3.2149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 6669 Z= 0.308 Angle : 0.749 8.121 9106 Z= 0.372 Chirality : 0.044 0.184 1119 Planarity : 0.005 0.056 1117 Dihedral : 4.926 21.202 894 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.81 % Favored : 90.07 % Rotamer Outliers : 5.01 % 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: -0.98 (0.29), residues: 836 helix: 0.18 (0.21), residues: 619 sheet: None (None), residues: 0 loop : -2.98 (0.42), residues: 217 *********************** 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 181 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 0.814 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 20 residues processed: 164 average time/residue: 0.1407 time to fit residues: 33.0537 Evaluate side-chains 162 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0685 time to fit residues: 3.4623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 284 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 6669 Z= 0.239 Angle : 0.726 7.278 9106 Z= 0.358 Chirality : 0.042 0.223 1119 Planarity : 0.005 0.052 1117 Dihedral : 4.811 22.572 894 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.97 % Favored : 90.91 % Rotamer Outliers : 3.30 % 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: -0.78 (0.30), residues: 836 helix: 0.25 (0.21), residues: 628 sheet: None (None), residues: 0 loop : -2.77 (0.44), residues: 208 *********************** 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 172 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 0.717 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 166 average time/residue: 0.1415 time to fit residues: 33.5699 Evaluate side-chains 147 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0693 time to fit residues: 2.3505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 80 optimal weight: 0.0970 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 77 optimal weight: 0.0770 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 6669 Z= 0.224 Angle : 0.734 9.238 9106 Z= 0.356 Chirality : 0.042 0.208 1119 Planarity : 0.005 0.050 1117 Dihedral : 4.737 22.035 894 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.33 % Favored : 90.55 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.30), residues: 836 helix: 0.38 (0.21), residues: 625 sheet: None (None), residues: 0 loop : -2.60 (0.45), residues: 211 *********************** 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 168 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 157 average time/residue: 0.1463 time to fit residues: 32.4374 Evaluate side-chains 141 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 0.760 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0675 time to fit residues: 2.0963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 0.0070 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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: 0.7743 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 6669 Z= 0.255 Angle : 0.761 8.149 9106 Z= 0.372 Chirality : 0.043 0.232 1119 Planarity : 0.005 0.048 1117 Dihedral : 4.695 22.494 894 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.21 % Favored : 90.67 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.30), residues: 836 helix: 0.41 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -2.55 (0.45), residues: 210 *********************** 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 151 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 0.798 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 141 average time/residue: 0.1581 time to fit residues: 31.4309 Evaluate side-chains 143 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 0.670 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0647 time to fit residues: 2.3772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 50 optimal weight: 0.0970 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 6669 Z= 0.235 Angle : 0.759 9.378 9106 Z= 0.368 Chirality : 0.043 0.251 1119 Planarity : 0.005 0.043 1117 Dihedral : 4.644 22.615 894 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer Outliers : 1.15 % 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: -0.48 (0.30), residues: 836 helix: 0.48 (0.21), residues: 622 sheet: None (None), residues: 0 loop : -2.61 (0.44), residues: 214 *********************** 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 144 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 0.771 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 141 average time/residue: 0.1436 time to fit residues: 29.0503 Evaluate side-chains 136 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0710 time to fit residues: 1.6589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 6669 Z= 0.256 Angle : 0.769 8.896 9106 Z= 0.375 Chirality : 0.043 0.276 1119 Planarity : 0.004 0.040 1117 Dihedral : 4.576 21.727 894 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.57 % Favored : 90.31 % Rotamer Outliers : 0.72 % 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: -0.41 (0.30), residues: 836 helix: 0.53 (0.21), residues: 623 sheet: None (None), residues: 0 loop : -2.61 (0.44), residues: 213 *********************** 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 141 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 0.770 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 138 average time/residue: 0.1542 time to fit residues: 29.9513 Evaluate side-chains 133 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0647 time to fit residues: 1.4283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 6669 Z= 0.256 Angle : 0.781 8.378 9106 Z= 0.381 Chirality : 0.043 0.280 1119 Planarity : 0.005 0.038 1117 Dihedral : 4.577 21.911 894 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.30), residues: 836 helix: 0.59 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -2.52 (0.45), residues: 212 ********************** 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 144 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 0.720 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 139 average time/residue: 0.1531 time to fit residues: 29.7412 Evaluate side-chains 137 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0644 time to fit residues: 1.8686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 67 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 GLN ** 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 = 0.4197 r_free = 0.4197 target = 0.174870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.139442 restraints weight = 9760.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.143619 restraints weight = 5511.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.146357 restraints weight = 3941.516| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3435 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= 0.248 Angle : 0.777 11.567 9106 Z= 0.377 Chirality : 0.044 0.251 1119 Planarity : 0.004 0.036 1117 Dihedral : 4.532 21.053 894 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer Outliers : 0.86 % 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: 0.67 (0.21), residues: 621 sheet: None (None), residues: 0 loop : -2.52 (0.45), residues: 215 =============================================================================== Job complete usr+sys time: 1494.87 seconds wall clock time: 27 minutes 42.02 seconds (1662.02 seconds total)