Starting phenix.real_space_refine on Sun Apr 7 19:10:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxf_40850/04_2024/8sxf_40850.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxf_40850/04_2024/8sxf_40850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxf_40850/04_2024/8sxf_40850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxf_40850/04_2024/8sxf_40850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxf_40850/04_2024/8sxf_40850.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxf_40850/04_2024/8sxf_40850.pdb" } resolution = 3.92 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= 0.000 sd= 0.045 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 17 5.16 5 C 7074 2.51 5 N 2013 2.21 5 O 2217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 385": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11321 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2733 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 20, 'TRANS': 343} Chain breaks: 1 Chain: "B" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2707 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 20, 'TRANS': 340} Chain breaks: 1 Chain: "C" Number of atoms: 4248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4248 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 512} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1603 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 2 Time building chain proxies: 6.42, per 1000 atoms: 0.57 Number of scatterers: 11321 At special positions: 0 Unit cell: (91.908, 132.894, 182.574, 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 17 16.00 O 2217 8.00 N 2013 7.00 C 7074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.01 Conformation dependent library (CDL) restraints added in 2.1 seconds 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2716 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 14 sheets defined 56.2% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 42 through 60 Processing helix chain 'A' and resid 65 through 82 removed outlier: 4.086A pdb=" N ASP A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.814A pdb=" N ARG A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 214 through 230 Processing helix chain 'A' and resid 248 through 259 removed outlier: 3.519A pdb=" N ALA A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 removed outlier: 3.577A pdb=" N VAL A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.793A pdb=" N ARG A 340 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 removed outlier: 4.231A pdb=" N SER A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 435 Processing helix chain 'B' and resid 42 through 59 Processing helix chain 'B' and resid 65 through 80 removed outlier: 3.548A pdb=" N LEU B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.548A pdb=" N GLU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 214 through 231 Processing helix chain 'B' and resid 248 through 260 Processing helix chain 'B' and resid 272 through 276 removed outlier: 3.601A pdb=" N GLU B 276 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 314 Processing helix chain 'B' and resid 412 through 417 removed outlier: 4.063A pdb=" N ASP B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 435 Processing helix chain 'C' and resid 49 through 65 Processing helix chain 'C' and resid 67 through 83 removed outlier: 3.535A pdb=" N ALA C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 99 Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 118 through 132 removed outlier: 3.641A pdb=" N GLN C 122 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 148 Processing helix chain 'C' and resid 153 through 164 removed outlier: 4.263A pdb=" N LEU C 157 " --> pdb=" O HIS C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 183 Processing helix chain 'C' and resid 187 through 201 Processing helix chain 'C' and resid 203 through 213 removed outlier: 3.556A pdb=" N ASN C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 220 through 234 Processing helix chain 'C' and resid 235 through 250 removed outlier: 3.611A pdb=" N ALA C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Proline residue: C 241 - end of helix Processing helix chain 'C' and resid 253 through 268 removed outlier: 4.377A pdb=" N ARG C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 284 Processing helix chain 'C' and resid 287 through 301 Processing helix chain 'C' and resid 303 through 318 Processing helix chain 'C' and resid 320 through 336 Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.503A pdb=" N TYR C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 368 Processing helix chain 'C' and resid 370 through 385 removed outlier: 3.874A pdb=" N GLN C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 404 removed outlier: 3.903A pdb=" N GLN C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 420 Processing helix chain 'C' and resid 423 through 438 Processing helix chain 'C' and resid 439 through 454 removed outlier: 4.626A pdb=" N MET C 443 " --> pdb=" O ASP C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 472 Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'C' and resid 492 through 507 removed outlier: 3.544A pdb=" N LEU C 496 " --> pdb=" O ASP C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 Processing helix chain 'C' and resid 525 through 540 Processing helix chain 'C' and resid 541 through 556 removed outlier: 4.211A pdb=" N ALA C 545 " --> pdb=" O ARG C 541 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR C 552 " --> pdb=" O ILE C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 570 Processing helix chain 'E' and resid 214 through 230 removed outlier: 4.002A pdb=" N GLU E 218 " --> pdb=" O ASN E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 260 Processing helix chain 'E' and resid 302 through 314 Processing helix chain 'E' and resid 412 through 417 Processing helix chain 'E' and resid 417 through 434 Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 106 Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 114 removed outlier: 6.632A pdb=" N GLY A 112 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N VAL A 120 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU A 114 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 147 removed outlier: 5.145A pdb=" N ILE A 140 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL A 173 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 200 removed outlier: 5.459A pdb=" N SER A 196 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ARG A 207 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL A 198 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR A 205 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 204 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ASP A 240 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A 206 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU A 292 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N MET A 320 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 294 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 280 removed outlier: 3.759A pdb=" N TYR A 267 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 330 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 374 Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.505A pdb=" N ALA B 341 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.505A pdb=" N ALA B 341 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL B 330 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.859A pdb=" N GLY B 162 " --> pdb=" O GLY B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 109 through 114 removed outlier: 6.891A pdb=" N GLU B 110 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 143 Processing sheet with id=AB3, first strand: chain 'B' and resid 166 through 170 Processing sheet with id=AB4, first strand: chain 'B' and resid 194 through 200 removed outlier: 5.132A pdb=" N SER B 196 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG B 207 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL B 198 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TYR B 205 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU B 200 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 204 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP B 240 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 208 " --> pdb=" O ASP B 240 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 293 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N MET B 320 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 294 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 194 through 198 removed outlier: 3.836A pdb=" N ILE E 208 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU E 237 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU E 295 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU E 239 " --> pdb=" O LEU E 295 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1884 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: 3.45 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3946 1.34 - 1.46: 1735 1.46 - 1.57: 5769 1.57 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 11483 Sorted by residual: bond pdb=" N GLY B 247 " pdb=" CA GLY B 247 " ideal model delta sigma weight residual 1.458 1.447 0.010 9.20e-03 1.18e+04 1.28e+00 bond pdb=" N VAL B 290 " pdb=" CA VAL B 290 " ideal model delta sigma weight residual 1.468 1.460 0.008 1.05e-02 9.07e+03 5.84e-01 bond pdb=" N ILE B 140 " pdb=" CA ILE B 140 " ideal model delta sigma weight residual 1.474 1.463 0.012 1.57e-02 4.06e+03 5.59e-01 bond pdb=" C ILE A 74 " pdb=" O ILE A 74 " ideal model delta sigma weight residual 1.237 1.245 -0.008 1.13e-02 7.83e+03 5.30e-01 bond pdb=" N ALA E 301 " pdb=" CA ALA E 301 " ideal model delta sigma weight residual 1.459 1.468 -0.009 1.20e-02 6.94e+03 5.28e-01 ... (remaining 11478 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.35: 341 107.35 - 114.01: 6475 114.01 - 120.66: 4869 120.66 - 127.32: 3758 127.32 - 133.97: 92 Bond angle restraints: 15535 Sorted by residual: angle pdb=" C GLN B 358 " pdb=" N ALA B 359 " pdb=" CA ALA B 359 " ideal model delta sigma weight residual 121.54 125.61 -4.07 1.91e+00 2.74e-01 4.54e+00 angle pdb=" CA TYR B 205 " pdb=" CB TYR B 205 " pdb=" CG TYR B 205 " ideal model delta sigma weight residual 113.90 117.64 -3.74 1.80e+00 3.09e-01 4.31e+00 angle pdb=" C ASN A 338 " pdb=" N ASP A 339 " pdb=" CA ASP A 339 " ideal model delta sigma weight residual 121.54 124.93 -3.39 1.91e+00 2.74e-01 3.15e+00 angle pdb=" CA VAL A 141 " pdb=" C VAL A 141 " pdb=" N GLN A 142 " ideal model delta sigma weight residual 116.60 119.08 -2.48 1.45e+00 4.76e-01 2.92e+00 angle pdb=" N VAL A 141 " pdb=" CA VAL A 141 " pdb=" C VAL A 141 " ideal model delta sigma weight residual 109.34 112.63 -3.29 2.08e+00 2.31e-01 2.51e+00 ... (remaining 15530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6297 17.76 - 35.52: 607 35.52 - 53.28: 128 53.28 - 71.04: 24 71.04 - 88.80: 17 Dihedral angle restraints: 7073 sinusoidal: 2848 harmonic: 4225 Sorted by residual: dihedral pdb=" CA PHE C 48 " pdb=" C PHE C 48 " pdb=" N SER C 49 " pdb=" CA SER C 49 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA SER E 300 " pdb=" C SER E 300 " pdb=" N ALA E 301 " pdb=" CA ALA E 301 " ideal model delta harmonic sigma weight residual -180.00 -163.19 -16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASP B 115 " pdb=" CB ASP B 115 " pdb=" CG ASP B 115 " pdb=" OD1 ASP B 115 " ideal model delta sinusoidal sigma weight residual -30.00 -86.94 56.94 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 7070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1158 0.027 - 0.054: 390 0.054 - 0.081: 88 0.081 - 0.108: 85 0.108 - 0.135: 42 Chirality restraints: 1763 Sorted by residual: chirality pdb=" CA ILE E 318 " pdb=" N ILE E 318 " pdb=" C ILE E 318 " pdb=" CB ILE E 318 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE E 296 " pdb=" N ILE E 296 " pdb=" C ILE E 296 " pdb=" CB ILE E 296 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE A 109 " pdb=" N ILE A 109 " pdb=" C ILE A 109 " pdb=" CB ILE A 109 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1760 not shown) Planarity restraints: 2074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 285 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO E 286 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO E 286 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 286 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 127 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO B 128 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 128 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 128 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 205 " 0.012 2.00e-02 2.50e+03 8.30e-03 1.38e+00 pdb=" CG TYR B 205 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 205 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 205 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 205 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 205 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 205 " 0.002 2.00e-02 2.50e+03 ... (remaining 2071 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 224 2.63 - 3.20: 11375 3.20 - 3.77: 18131 3.77 - 4.33: 23765 4.33 - 4.90: 38773 Nonbonded interactions: 92268 Sorted by model distance: nonbonded pdb=" O LEU C 229 " pdb=" OG SER C 232 " model vdw 2.063 2.440 nonbonded pdb=" O LEU C 468 " pdb=" OG1 THR C 472 " model vdw 2.066 2.440 nonbonded pdb=" OE2 GLU E 305 " pdb=" OG SER E 324 " model vdw 2.077 2.440 nonbonded pdb=" OG1 THR C 82 " pdb=" OD1 ASP C 84 " model vdw 2.091 2.440 nonbonded pdb=" OD1 ASP C 379 " pdb=" OH TYR C 393 " model vdw 2.098 2.440 ... (remaining 92263 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 38 through 371 or resid 411 through 436)) selection = (chain 'B' and (resid 38 through 371 or resid 411 through 436)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 7.410 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.030 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 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 : 0.002 0.021 11483 Z= 0.146 Angle : 0.482 5.022 15535 Z= 0.250 Chirality : 0.038 0.135 1763 Planarity : 0.003 0.039 2074 Dihedral : 15.077 88.795 4357 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % 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: 1.25 (0.22), residues: 1455 helix: 2.04 (0.19), residues: 754 sheet: -0.54 (0.42), residues: 161 loop : -0.43 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 537 HIS 0.004 0.001 HIS C 531 PHE 0.008 0.001 PHE A 325 TYR 0.020 0.001 TYR B 205 ARG 0.002 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 LEU cc_start: 0.8598 (tp) cc_final: 0.8079 (pp) REVERT: E 233 ARG cc_start: 0.6092 (tpm170) cc_final: 0.5743 (mmm160) REVERT: E 385 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6446 (mm-30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2624 time to fit residues: 42.4871 Evaluate side-chains 68 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 85 optimal weight: 0.0070 chunk 132 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 HIS C 486 HIS E 212 GLN E 230 ASN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11483 Z= 0.205 Angle : 0.569 7.714 15535 Z= 0.285 Chirality : 0.040 0.189 1763 Planarity : 0.004 0.043 2074 Dihedral : 4.045 19.992 1606 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.26 % Allowed : 10.64 % Favored : 87.10 % 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: 1.22 (0.22), residues: 1455 helix: 1.88 (0.18), residues: 777 sheet: -0.52 (0.43), residues: 153 loop : -0.33 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 501 HIS 0.005 0.001 HIS C 531 PHE 0.010 0.001 PHE A 325 TYR 0.019 0.001 TYR B 205 ARG 0.002 0.000 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 82 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 GLN cc_start: 0.7188 (tm-30) cc_final: 0.6938 (tm-30) REVERT: C 237 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6663 (p0) REVERT: C 376 GLN cc_start: 0.7192 (pp30) cc_final: 0.6905 (pp30) REVERT: E 214 ASN cc_start: 0.8579 (m-40) cc_final: 0.8331 (t0) REVERT: E 226 LEU cc_start: 0.7727 (tp) cc_final: 0.7251 (tt) REVERT: E 381 GLU cc_start: 0.7882 (tp30) cc_final: 0.7615 (tp30) REVERT: E 385 GLU cc_start: 0.7732 (mm-30) cc_final: 0.6524 (mm-30) outliers start: 27 outliers final: 13 residues processed: 101 average time/residue: 0.2534 time to fit residues: 37.0959 Evaluate side-chains 82 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 366 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 143 optimal weight: 0.0970 chunk 118 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11483 Z= 0.192 Angle : 0.539 7.502 15535 Z= 0.268 Chirality : 0.039 0.142 1763 Planarity : 0.003 0.046 2074 Dihedral : 3.984 20.200 1606 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.93 % Allowed : 14.24 % Favored : 83.84 % 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: 1.19 (0.22), residues: 1455 helix: 1.82 (0.18), residues: 782 sheet: -0.67 (0.41), residues: 171 loop : -0.23 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 501 HIS 0.004 0.001 HIS C 531 PHE 0.009 0.001 PHE A 325 TYR 0.017 0.001 TYR B 205 ARG 0.003 0.000 ARG E 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8521 (tt) REVERT: A 77 MET cc_start: 0.8042 (ttm) cc_final: 0.7792 (ttp) REVERT: B 77 MET cc_start: 0.8709 (ttp) cc_final: 0.8082 (ptt) REVERT: B 197 GLN cc_start: 0.7094 (tm-30) cc_final: 0.6871 (tm-30) REVERT: C 237 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6429 (p0) REVERT: C 376 GLN cc_start: 0.6899 (pp30) cc_final: 0.6641 (pp30) REVERT: E 214 ASN cc_start: 0.8283 (m-40) cc_final: 0.7928 (t0) REVERT: E 226 LEU cc_start: 0.7685 (tp) cc_final: 0.7176 (tt) REVERT: E 385 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6346 (mm-30) outliers start: 23 outliers final: 9 residues processed: 95 average time/residue: 0.2182 time to fit residues: 31.9503 Evaluate side-chains 77 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11483 Z= 0.202 Angle : 0.531 7.445 15535 Z= 0.265 Chirality : 0.039 0.142 1763 Planarity : 0.003 0.049 2074 Dihedral : 3.994 20.803 1606 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.35 % Allowed : 16.42 % Favored : 81.24 % 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: 1.16 (0.22), residues: 1455 helix: 1.82 (0.18), residues: 781 sheet: -0.64 (0.43), residues: 157 loop : -0.33 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 501 HIS 0.004 0.001 HIS C 526 PHE 0.011 0.001 PHE C 191 TYR 0.018 0.002 TYR B 205 ARG 0.003 0.000 ARG E 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 77 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8508 (tt) REVERT: A 77 MET cc_start: 0.8052 (ttm) cc_final: 0.7755 (ttp) REVERT: B 77 MET cc_start: 0.8758 (ttp) cc_final: 0.8221 (ptt) REVERT: B 422 GLN cc_start: 0.8080 (mm110) cc_final: 0.7842 (mm110) REVERT: C 237 ASP cc_start: 0.6909 (OUTLIER) cc_final: 0.6370 (p0) REVERT: C 376 GLN cc_start: 0.6914 (pp30) cc_final: 0.6641 (pp30) REVERT: E 214 ASN cc_start: 0.8440 (m-40) cc_final: 0.8072 (t0) REVERT: E 385 GLU cc_start: 0.7838 (mm-30) cc_final: 0.6611 (mm-30) outliers start: 28 outliers final: 16 residues processed: 103 average time/residue: 0.2071 time to fit residues: 32.6790 Evaluate side-chains 85 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 366 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 58 optimal weight: 0.0980 chunk 120 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11483 Z= 0.215 Angle : 0.540 7.495 15535 Z= 0.270 Chirality : 0.039 0.142 1763 Planarity : 0.003 0.050 2074 Dihedral : 4.011 21.426 1606 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.35 % Allowed : 17.67 % Favored : 79.98 % 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: 1.12 (0.22), residues: 1455 helix: 1.79 (0.18), residues: 781 sheet: -0.66 (0.43), residues: 157 loop : -0.36 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 549 HIS 0.003 0.001 HIS C 531 PHE 0.016 0.001 PHE C 191 TYR 0.017 0.001 TYR B 205 ARG 0.002 0.000 ARG E 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 70 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8624 (tt) REVERT: A 77 MET cc_start: 0.8095 (ttm) cc_final: 0.7840 (ttp) REVERT: A 288 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7525 (t70) REVERT: B 77 MET cc_start: 0.8756 (ttp) cc_final: 0.8301 (ptt) REVERT: B 197 GLN cc_start: 0.7139 (tm-30) cc_final: 0.6882 (tm-30) REVERT: C 376 GLN cc_start: 0.6967 (pp30) cc_final: 0.6704 (pp30) REVERT: E 214 ASN cc_start: 0.8474 (m-40) cc_final: 0.8105 (t0) REVERT: E 385 GLU cc_start: 0.7796 (mm-30) cc_final: 0.6592 (mm-30) outliers start: 28 outliers final: 18 residues processed: 94 average time/residue: 0.2021 time to fit residues: 29.6414 Evaluate side-chains 83 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 366 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.0670 chunk 127 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 0.0060 chunk 141 optimal weight: 0.3980 chunk 117 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11483 Z= 0.158 Angle : 0.507 7.396 15535 Z= 0.256 Chirality : 0.039 0.141 1763 Planarity : 0.003 0.049 2074 Dihedral : 3.854 19.779 1606 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.68 % Allowed : 17.42 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.22), residues: 1455 helix: 1.87 (0.18), residues: 782 sheet: -0.65 (0.44), residues: 152 loop : -0.33 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 501 HIS 0.007 0.001 HIS C 526 PHE 0.015 0.001 PHE C 191 TYR 0.014 0.001 TYR B 418 ARG 0.007 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 77 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8574 (tt) REVERT: A 77 MET cc_start: 0.7952 (ttm) cc_final: 0.7728 (ttp) REVERT: A 288 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7478 (t70) REVERT: B 77 MET cc_start: 0.8728 (ttp) cc_final: 0.8251 (ptt) REVERT: B 197 GLN cc_start: 0.7139 (tm-30) cc_final: 0.6936 (tm-30) REVERT: C 237 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6634 (p0) REVERT: C 376 GLN cc_start: 0.7013 (pp30) cc_final: 0.6769 (pp30) REVERT: E 214 ASN cc_start: 0.8416 (m-40) cc_final: 0.8024 (t0) REVERT: E 385 GLU cc_start: 0.7761 (mm-30) cc_final: 0.6583 (mm-30) outliers start: 32 outliers final: 18 residues processed: 103 average time/residue: 0.2081 time to fit residues: 32.8990 Evaluate side-chains 89 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 394 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 85 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11483 Z= 0.256 Angle : 0.574 8.665 15535 Z= 0.285 Chirality : 0.040 0.203 1763 Planarity : 0.004 0.053 2074 Dihedral : 4.029 21.573 1606 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.68 % Allowed : 18.17 % Favored : 79.15 % 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: 1.03 (0.22), residues: 1455 helix: 1.73 (0.18), residues: 784 sheet: -0.63 (0.43), residues: 157 loop : -0.46 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 501 HIS 0.007 0.001 HIS C 526 PHE 0.015 0.001 PHE C 191 TYR 0.020 0.001 TYR B 205 ARG 0.005 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 66 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8470 (tt) REVERT: A 77 MET cc_start: 0.8156 (ttm) cc_final: 0.7932 (ttp) REVERT: A 203 TYR cc_start: 0.7582 (m-80) cc_final: 0.7366 (m-10) REVERT: A 288 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7513 (t0) REVERT: B 197 GLN cc_start: 0.7225 (tm-30) cc_final: 0.6973 (tm-30) REVERT: C 139 MET cc_start: 0.6112 (ttt) cc_final: 0.5727 (tmm) REVERT: C 376 GLN cc_start: 0.7028 (pp30) cc_final: 0.6761 (pp30) REVERT: E 214 ASN cc_start: 0.8583 (m-40) cc_final: 0.8207 (t0) REVERT: E 385 GLU cc_start: 0.7784 (mm-30) cc_final: 0.6542 (mm-30) outliers start: 32 outliers final: 26 residues processed: 93 average time/residue: 0.2014 time to fit residues: 29.5231 Evaluate side-chains 93 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 65 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 349 TYR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 394 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 69 optimal weight: 0.4980 chunk 13 optimal weight: 0.0670 chunk 110 optimal weight: 0.9990 chunk 128 optimal weight: 0.3980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11483 Z= 0.160 Angle : 0.527 10.834 15535 Z= 0.261 Chirality : 0.039 0.142 1763 Planarity : 0.003 0.049 2074 Dihedral : 3.843 19.644 1606 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.18 % Allowed : 18.43 % Favored : 79.40 % 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: 1.14 (0.22), residues: 1455 helix: 1.82 (0.18), residues: 784 sheet: -0.65 (0.44), residues: 154 loop : -0.38 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 501 HIS 0.005 0.001 HIS C 526 PHE 0.014 0.001 PHE C 191 TYR 0.022 0.001 TYR B 418 ARG 0.005 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 70 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8604 (tt) REVERT: A 77 MET cc_start: 0.7980 (ttm) cc_final: 0.7675 (ttp) REVERT: B 77 MET cc_start: 0.8490 (ttp) cc_final: 0.7949 (ptt) REVERT: C 237 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6681 (p0) REVERT: C 376 GLN cc_start: 0.7004 (pp30) cc_final: 0.6753 (pp30) REVERT: E 214 ASN cc_start: 0.8404 (m-40) cc_final: 0.8073 (t0) REVERT: E 385 GLU cc_start: 0.7771 (mm-30) cc_final: 0.6620 (mm-30) outliers start: 26 outliers final: 22 residues processed: 91 average time/residue: 0.1940 time to fit residues: 28.1268 Evaluate side-chains 88 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 64 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 394 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 118 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11483 Z= 0.174 Angle : 0.534 9.713 15535 Z= 0.266 Chirality : 0.039 0.186 1763 Planarity : 0.004 0.050 2074 Dihedral : 3.826 19.285 1606 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.43 % Allowed : 18.59 % Favored : 78.98 % 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: 1.16 (0.22), residues: 1455 helix: 1.83 (0.18), residues: 784 sheet: -0.61 (0.43), residues: 159 loop : -0.37 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 501 HIS 0.005 0.001 HIS C 526 PHE 0.015 0.001 PHE C 191 TYR 0.016 0.001 TYR B 205 ARG 0.004 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 64 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8621 (tt) REVERT: A 77 MET cc_start: 0.8020 (ttm) cc_final: 0.7756 (ttp) REVERT: B 77 MET cc_start: 0.8596 (ttp) cc_final: 0.8108 (ptt) REVERT: C 237 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6713 (p0) REVERT: E 214 ASN cc_start: 0.8431 (m-40) cc_final: 0.8083 (t0) REVERT: E 385 GLU cc_start: 0.7737 (mm-30) cc_final: 0.6623 (mm-30) outliers start: 29 outliers final: 25 residues processed: 88 average time/residue: 0.1914 time to fit residues: 26.9671 Evaluate side-chains 87 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 60 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 410 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.1980 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 chunk 96 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 438 ASN ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11483 Z= 0.172 Angle : 0.548 9.820 15535 Z= 0.274 Chirality : 0.039 0.163 1763 Planarity : 0.004 0.049 2074 Dihedral : 3.802 18.873 1606 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.51 % Allowed : 18.93 % Favored : 78.56 % 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: 1.15 (0.22), residues: 1455 helix: 1.81 (0.18), residues: 785 sheet: -0.66 (0.43), residues: 154 loop : -0.35 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 501 HIS 0.004 0.001 HIS C 526 PHE 0.015 0.001 PHE C 191 TYR 0.027 0.001 TYR B 418 ARG 0.004 0.000 ARG C 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2910 Ramachandran restraints generated. 1455 Oldfield, 0 Emsley, 1455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 62 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8609 (tt) REVERT: A 77 MET cc_start: 0.7997 (ttm) cc_final: 0.7733 (ttp) REVERT: B 77 MET cc_start: 0.8590 (ttp) cc_final: 0.8112 (ptt) REVERT: C 237 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6825 (p0) REVERT: E 214 ASN cc_start: 0.8424 (m-40) cc_final: 0.8078 (t0) REVERT: E 385 GLU cc_start: 0.7729 (mm-30) cc_final: 0.6648 (mm-30) outliers start: 30 outliers final: 24 residues processed: 87 average time/residue: 0.1987 time to fit residues: 27.3412 Evaluate side-chains 87 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 61 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 410 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 32 optimal weight: 0.2980 chunk 116 optimal weight: 0.2980 chunk 48 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 101 optimal weight: 0.0060 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 438 ASN ** E 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.137012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.112916 restraints weight = 33602.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.111296 restraints weight = 43431.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.112383 restraints weight = 39319.028| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11483 Z= 0.146 Angle : 0.529 9.816 15535 Z= 0.264 Chirality : 0.039 0.139 1763 Planarity : 0.004 0.048 2074 Dihedral : 3.678 16.706 1606 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.09 % Allowed : 19.43 % Favored : 78.48 % 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: 1.28 (0.22), residues: 1455 helix: 1.91 (0.18), residues: 783 sheet: -0.62 (0.42), residues: 163 loop : -0.25 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 501 HIS 0.004 0.001 HIS C 526 PHE 0.016 0.001 PHE C 191 TYR 0.014 0.001 TYR B 418 ARG 0.004 0.000 ARG C 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2094.02 seconds wall clock time: 39 minutes 23.01 seconds (2363.01 seconds total)