Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 07:40:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8o_21576/10_2023/6w8o_21576.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8o_21576/10_2023/6w8o_21576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8o_21576/10_2023/6w8o_21576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8o_21576/10_2023/6w8o_21576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8o_21576/10_2023/6w8o_21576.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8o_21576/10_2023/6w8o_21576.pdb" } resolution = 3.4 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= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4184 2.51 5 N 1018 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "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 ARG 231": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ASP 371": "OD1" <-> "OD2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 233": "NH1" <-> "NH2" Residue "B ASP 251": "OD1" <-> "OD2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B ASP 283": "OD1" <-> "OD2" Residue "B TYR 313": "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 372": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 6332 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3166 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain breaks: 4 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3166 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain breaks: 4 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 46 Time building chain proxies: 4.20, per 1000 atoms: 0.66 Number of scatterers: 6332 At special positions: 0 Unit cell: (78.375, 84.15, 77.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1090 8.00 N 1018 7.00 C 4184 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.0 seconds 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 0 sheets defined 83.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.573A pdb=" N SER A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 67 through 101 Processing helix chain 'A' and resid 106 through 122 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 136 through 164 removed outlier: 4.052A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 180 through 204 removed outlier: 3.993A pdb=" N GLY A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Proline residue: A 193 - end of helix removed outlier: 3.614A pdb=" N CYS A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 223 removed outlier: 3.516A pdb=" N THR A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 257 through 284 removed outlier: 3.755A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS A 281 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.690A pdb=" N VAL A 291 " --> pdb=" O PRO A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.943A 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: 3.665A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 374 through 395 removed outlier: 4.145A pdb=" N ILE A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 436 removed outlier: 5.154A 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 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 444 through 469 Proline residue: A 456 - end of helix removed outlier: 4.120A pdb=" N LEU A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU A 461 " --> pdb=" O CYS A 457 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.583A pdb=" N SER B 38 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 67 through 101 Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 136 through 164 removed outlier: 4.046A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 150 " --> pdb=" O CYS B 146 " (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 205 removed outlier: 4.063A pdb=" N GLY B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Proline residue: B 193 - end of helix removed outlier: 3.637A pdb=" N CYS B 196 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 223 Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 257 through 284 removed outlier: 3.798A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.955A pdb=" N ALA B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.824A pdb=" N ALA B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 363 removed outlier: 3.649A pdb=" N LEU B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 373 through 395 removed outlier: 4.261A pdb=" N ARG B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 4.718A 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 406 through 410 Processing helix chain 'B' and resid 415 through 435 removed outlier: 5.226A 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 444 through 458 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 463 through 469 447 hydrogen bonds defined for protein. 1311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.54: 6408 1.54 - 1.90: 72 1.90 - 2.25: 0 2.25 - 2.60: 0 2.60 - 2.96: 2 Bond restraints: 6482 Sorted by residual: bond pdb=" C ARG B 294 " pdb=" N SER B 296 " ideal model delta sigma weight residual 1.332 2.956 -1.623 1.40e-02 5.10e+03 1.34e+04 bond pdb=" C ARG A 294 " pdb=" N SER A 296 " ideal model delta sigma weight residual 1.332 2.914 -1.582 1.40e-02 5.10e+03 1.28e+04 bond pdb=" C ILE B 277 " pdb=" O ILE B 277 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.32e-02 5.74e+03 1.32e+01 bond pdb=" C ILE A 46 " pdb=" O ILE A 46 " ideal model delta sigma weight residual 1.237 1.196 0.041 1.17e-02 7.31e+03 1.24e+01 bond pdb=" C LEU B 278 " pdb=" O LEU B 278 " ideal model delta sigma weight residual 1.237 1.197 0.039 1.19e-02 7.06e+03 1.10e+01 ... (remaining 6477 not shown) Histogram of bond angle deviations from ideal: 71.85 - 85.34: 2 85.34 - 98.83: 0 98.83 - 112.33: 3624 112.33 - 125.82: 5117 125.82 - 139.31: 105 Bond angle restraints: 8848 Sorted by residual: angle pdb=" O ARG A 294 " pdb=" C ARG A 294 " pdb=" N SER A 296 " ideal model delta sigma weight residual 122.59 71.85 50.74 1.33e+00 5.65e-01 1.46e+03 angle pdb=" O ARG B 294 " pdb=" C ARG B 294 " pdb=" N SER B 296 " ideal model delta sigma weight residual 122.59 76.84 45.75 1.33e+00 5.65e-01 1.18e+03 angle pdb=" CA ARG A 294 " pdb=" C ARG A 294 " pdb=" N SER A 296 " ideal model delta sigma weight residual 116.84 135.75 -18.91 1.71e+00 3.42e-01 1.22e+02 angle pdb=" C ARG A 294 " pdb=" N SER A 296 " pdb=" CA SER A 296 " ideal model delta sigma weight residual 121.54 139.31 -17.77 1.91e+00 2.74e-01 8.66e+01 angle pdb=" N ASP A 279 " pdb=" CA ASP A 279 " pdb=" C ASP A 279 " ideal model delta sigma weight residual 113.88 103.08 10.80 1.23e+00 6.61e-01 7.71e+01 ... (remaining 8843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.16: 3417 22.16 - 44.31: 293 44.31 - 66.47: 67 66.47 - 88.62: 5 88.62 - 110.78: 4 Dihedral angle restraints: 3786 sinusoidal: 1356 harmonic: 2430 Sorted by residual: dihedral pdb=" CA ARG B 294 " pdb=" C ARG B 294 " pdb=" N SER B 296 " pdb=" CA SER B 296 " ideal model delta harmonic sigma weight residual -180.00 -69.22 -110.78 0 5.00e+00 4.00e-02 4.91e+02 dihedral pdb=" CA ARG A 294 " pdb=" C ARG A 294 " pdb=" N SER A 296 " pdb=" CA SER A 296 " ideal model delta harmonic sigma weight residual -180.00 -69.36 -110.64 0 5.00e+00 4.00e-02 4.90e+02 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 93.00 156.86 -63.86 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 3783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1064 0.112 - 0.224: 28 0.224 - 0.336: 2 0.336 - 0.448: 0 0.448 - 0.559: 2 Chirality restraints: 1096 Sorted by residual: chirality pdb=" CB ILE A 277 " pdb=" CA ILE A 277 " pdb=" CG1 ILE A 277 " pdb=" CG2 ILE A 277 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.56 2.00e-01 2.50e+01 7.83e+00 chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 1.92 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" CA TYR A 222 " pdb=" N TYR A 222 " pdb=" C TYR A 222 " pdb=" CB TYR A 222 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1093 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 294 " 0.179 2.00e-02 2.50e+03 2.24e-01 5.00e+02 pdb=" C ARG B 294 " -0.380 2.00e-02 2.50e+03 pdb=" O ARG B 294 " 0.144 2.00e-02 2.50e+03 pdb=" N SER B 296 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 294 " 0.179 2.00e-02 2.50e+03 2.17e-01 4.72e+02 pdb=" C ARG A 294 " -0.369 2.00e-02 2.50e+03 pdb=" O ARG A 294 " 0.130 2.00e-02 2.50e+03 pdb=" N SER A 296 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 276 " 0.039 2.00e-02 2.50e+03 7.70e-02 5.93e+01 pdb=" C LEU A 276 " -0.133 2.00e-02 2.50e+03 pdb=" O LEU A 276 " 0.051 2.00e-02 2.50e+03 pdb=" N ILE A 277 " 0.044 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 3 1.91 - 2.66: 153 2.66 - 3.40: 10405 3.40 - 4.15: 14728 4.15 - 4.90: 26316 Nonbonded interactions: 51605 Sorted by model distance: nonbonded pdb=" CG2 ILE A 277 " pdb=" CE1 TYR A 313 " model vdw 1.161 3.760 nonbonded pdb=" CG2 ILE A 277 " pdb=" CZ TYR A 313 " model vdw 1.582 3.680 nonbonded pdb=" CG2 ILE A 277 " pdb=" CD1 TYR A 313 " model vdw 1.655 3.760 nonbonded pdb=" O LEU A 213 " pdb=" OG1 THR A 216 " model vdw 2.223 2.440 nonbonded pdb=" O LEU B 213 " pdb=" OG1 THR B 216 " model vdw 2.226 2.440 ... (remaining 51600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.000 Extract box with map and model: 3.720 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.830 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.029 1.623 6482 Z= 1.217 Angle : 1.198 50.741 8848 Z= 0.795 Chirality : 0.050 0.559 1096 Planarity : 0.011 0.224 1080 Dihedral : 17.622 110.781 2192 Min Nonbonded Distance : 1.161 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 11.79 % Allowed : 21.49 % Favored : 66.72 % Cbeta Deviations : 0.38 % 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: -3.22 (0.26), residues: 808 helix: -1.66 (0.18), residues: 626 sheet: None (None), residues: 0 loop : -3.25 (0.44), residues: 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 236 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 52 residues processed: 284 average time/residue: 0.1708 time to fit residues: 64.6836 Evaluate side-chains 243 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 191 time to evaluate : 0.660 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.0650 time to fit residues: 6.9422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 166 HIS B 154 GLN B 166 HIS B 390 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 6482 Z= 0.278 Angle : 0.809 16.050 8848 Z= 0.391 Chirality : 0.046 0.462 1096 Planarity : 0.005 0.044 1080 Dihedral : 5.007 26.351 872 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.03 % Favored : 93.35 % Rotamer: Outliers : 5.07 % Allowed : 31.34 % Favored : 63.58 % 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: -1.10 (0.29), residues: 812 helix: -0.23 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -2.26 (0.49), residues: 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 257 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 271 average time/residue: 0.1350 time to fit residues: 50.8690 Evaluate side-chains 237 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 218 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0660 time to fit residues: 3.0477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS B 416 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 6482 Z= 0.297 Angle : 0.821 14.831 8848 Z= 0.395 Chirality : 0.043 0.270 1096 Planarity : 0.004 0.045 1080 Dihedral : 4.862 22.867 872 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.53 % Favored : 92.98 % Rotamer: Outliers : 6.72 % Allowed : 31.04 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.30), residues: 812 helix: 0.26 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.76 (0.51), residues: 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 247 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 23 residues processed: 263 average time/residue: 0.1402 time to fit residues: 51.0536 Evaluate side-chains 256 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 233 time to evaluate : 0.695 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.0630 time to fit residues: 3.5126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.0070 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN B 449 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6482 Z= 0.258 Angle : 0.820 15.660 8848 Z= 0.390 Chirality : 0.042 0.211 1096 Planarity : 0.004 0.042 1080 Dihedral : 4.804 22.601 872 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.65 % Favored : 92.98 % Rotamer: Outliers : 6.42 % Allowed : 32.39 % Favored : 61.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.30), residues: 812 helix: 0.43 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.76 (0.50), residues: 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 255 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 22 residues processed: 275 average time/residue: 0.1431 time to fit residues: 54.8970 Evaluate side-chains 266 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 244 time to evaluate : 0.703 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.0663 time to fit residues: 3.4995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 54 optimal weight: 0.0370 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS B 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6482 Z= 0.247 Angle : 0.808 14.811 8848 Z= 0.388 Chirality : 0.044 0.216 1096 Planarity : 0.004 0.037 1080 Dihedral : 4.755 22.612 872 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.16 % Favored : 93.60 % Rotamer: Outliers : 4.63 % Allowed : 35.07 % Favored : 60.30 % 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: -0.07 (0.30), residues: 812 helix: 0.52 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -1.76 (0.47), residues: 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 267 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 276 average time/residue: 0.1416 time to fit residues: 54.4678 Evaluate side-chains 271 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 253 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0664 time to fit residues: 3.0372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 0.0870 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 79 optimal weight: 0.0470 chunk 65 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6482 Z= 0.240 Angle : 0.833 13.636 8848 Z= 0.397 Chirality : 0.044 0.230 1096 Planarity : 0.004 0.037 1080 Dihedral : 4.749 23.014 872 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.53 % Favored : 93.23 % Rotamer: Outliers : 3.58 % Allowed : 37.76 % Favored : 58.66 % 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: -0.09 (0.30), residues: 812 helix: 0.48 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -1.66 (0.47), residues: 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 266 time to evaluate : 0.727 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 14 residues processed: 276 average time/residue: 0.1437 time to fit residues: 55.5862 Evaluate side-chains 263 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 249 time to evaluate : 0.641 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0711 time to fit residues: 2.6466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 47 optimal weight: 0.4980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6482 Z= 0.275 Angle : 0.845 12.570 8848 Z= 0.407 Chirality : 0.045 0.231 1096 Planarity : 0.004 0.037 1080 Dihedral : 4.659 22.707 872 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.13 % Allowed : 40.30 % Favored : 56.57 % 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: -0.04 (0.30), residues: 812 helix: 0.44 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -1.47 (0.50), residues: 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 259 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 268 average time/residue: 0.1402 time to fit residues: 52.3733 Evaluate side-chains 263 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 250 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0634 time to fit residues: 2.3909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.0030 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.0050 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6482 Z= 0.256 Angle : 0.877 11.851 8848 Z= 0.421 Chirality : 0.047 0.251 1096 Planarity : 0.004 0.036 1080 Dihedral : 4.782 23.061 872 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.94 % Allowed : 40.60 % Favored : 57.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.30), residues: 812 helix: 0.47 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.57 (0.49), residues: 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 265 time to evaluate : 0.791 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 270 average time/residue: 0.1378 time to fit residues: 52.0178 Evaluate side-chains 267 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 259 time to evaluate : 0.632 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0705 time to fit residues: 1.8046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6482 Z= 0.276 Angle : 0.913 15.623 8848 Z= 0.435 Chirality : 0.049 0.285 1096 Planarity : 0.004 0.039 1080 Dihedral : 4.684 23.566 872 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.79 % Allowed : 41.49 % Favored : 56.72 % 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: 0.04 (0.30), residues: 812 helix: 0.53 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.60 (0.50), residues: 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 261 time to evaluate : 0.682 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 265 average time/residue: 0.1403 time to fit residues: 51.7358 Evaluate side-chains 272 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 262 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0627 time to fit residues: 2.0417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 81 optimal weight: 0.6980 chunk 75 optimal weight: 0.0970 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6482 Z= 0.293 Angle : 0.952 14.751 8848 Z= 0.452 Chirality : 0.050 0.237 1096 Planarity : 0.004 0.034 1080 Dihedral : 4.698 23.644 872 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.19 % Allowed : 42.84 % Favored : 55.97 % 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: -0.08 (0.30), residues: 812 helix: 0.43 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -1.56 (0.50), residues: 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 259 time to evaluate : 0.747 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 260 average time/residue: 0.1461 time to fit residues: 53.1745 Evaluate side-chains 261 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 253 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0676 time to fit residues: 1.9221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.111080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.088056 restraints weight = 15901.968| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 4.97 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 6482 Z= 0.293 Angle : 0.927 14.484 8848 Z= 0.446 Chirality : 0.048 0.280 1096 Planarity : 0.004 0.033 1080 Dihedral : 4.705 23.587 872 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.60 % Allowed : 43.28 % Favored : 56.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.30), residues: 812 helix: 0.47 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.58 (0.50), residues: 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1660.87 seconds wall clock time: 30 minutes 39.35 seconds (1839.35 seconds total)