Starting phenix.real_space_refine on Sun Mar 17 11:02:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by2_16319/03_2024/8by2_16319_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by2_16319/03_2024/8by2_16319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by2_16319/03_2024/8by2_16319.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by2_16319/03_2024/8by2_16319.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by2_16319/03_2024/8by2_16319_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8by2_16319/03_2024/8by2_16319_trim_updated.pdb" } resolution = 3.18 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= 0.017 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 56 5.16 5 C 5572 2.51 5 N 1433 2.21 5 O 1487 1.98 5 H 8802 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17356 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 8598 Classifications: {'peptide': 548} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 529} Chain breaks: 1 Chain: "B" Number of atoms: 8568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 8568 Classifications: {'peptide': 546} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 527} Chain breaks: 1 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 95 Unusual residues: {' K': 1, 'GSH': 1, 'PGW': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna2p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 95 Unusual residues: {' K': 1, 'GSH': 1, 'PGW': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna2p': 1} Link IDs: {None: 3} Time building chain proxies: 9.56, per 1000 atoms: 0.55 Number of scatterers: 17356 At special positions: 0 Unit cell: (93.03, 73.538, 110.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 56 16.00 P 4 15.00 O 1487 8.00 N 1433 7.00 C 5572 6.00 H 8802 1.00 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: 13.93 Conformation dependent library (CDL) restraints added in 2.8 seconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 2 sheets defined 69.4% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 4 through 25 Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 30 through 41 Processing helix chain 'A' and resid 54 through 73 removed outlier: 3.878A pdb=" N GLU A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 83 through 108 removed outlier: 4.369A pdb=" N ALA A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.727A pdb=" N GLU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 143 through 164 removed outlier: 4.362A pdb=" N ILE A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.818A pdb=" N THR A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 179 through 182 No H-bonds generated for 'chain 'A' and resid 179 through 182' Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.533A pdb=" N ARG A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.590A pdb=" N VAL A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 237 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 256 through 283 removed outlier: 4.232A pdb=" N HIS A 259 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE A 265 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU A 266 " --> pdb=" O SER A 263 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 4.336A pdb=" N GLY A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 282 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 314 removed outlier: 3.681A pdb=" N LEU A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 354 through 369 Processing helix chain 'A' and resid 371 through 381 Processing helix chain 'A' and resid 409 through 420 removed outlier: 3.558A pdb=" N ILE A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 removed outlier: 4.128A pdb=" N GLU A 436 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 500 through 509 Processing helix chain 'A' and resid 520 through 533 Processing helix chain 'A' and resid 537 through 559 Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 20 through 26 Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 54 through 73 removed outlier: 3.752A pdb=" N GLU B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 90 through 108 removed outlier: 3.646A pdb=" N GLY B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 122 removed outlier: 3.860A pdb=" N GLU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 143 through 164 removed outlier: 4.265A pdb=" N ILE B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 166 through 169 No H-bonds generated for 'chain 'B' and resid 166 through 169' Processing helix chain 'B' and resid 177 through 201 removed outlier: 3.795A pdb=" N ALA B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 211 Processing helix chain 'B' and resid 218 through 235 Processing helix chain 'B' and resid 241 through 254 Processing helix chain 'B' and resid 258 through 268 Proline residue: B 267 - end of helix Processing helix chain 'B' and resid 271 through 283 removed outlier: 4.252A pdb=" N PHE B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 293 through 314 removed outlier: 3.807A pdb=" N LEU B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 332 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 354 through 382 removed outlier: 3.710A pdb=" N THR B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 409 through 421 removed outlier: 3.865A pdb=" N ILE B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 414 " --> pdb=" O PHE B 410 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 453 through 459 removed outlier: 4.010A pdb=" N GLU B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N SER B 458 " --> pdb=" O ASP B 454 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 459' Processing helix chain 'B' and resid 474 through 487 Processing helix chain 'B' and resid 500 through 509 removed outlier: 3.600A pdb=" N ARG B 505 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 533 Processing helix chain 'B' and resid 537 through 559 Processing sheet with id= A, first strand: chain 'A' and resid 492 through 494 removed outlier: 6.018A pdb=" N LYS A 444 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASP A 429 " --> pdb=" O LYS A 444 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE A 446 " --> pdb=" O ASP A 429 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 467 through 469 removed outlier: 8.186A pdb=" N ILE B 468 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 403 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS B 424 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE B 404 " --> pdb=" O LYS B 424 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL B 426 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS B 444 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ASP B 429 " --> pdb=" O LYS B 444 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N PHE B 446 " --> pdb=" O ASP B 429 " (cutoff:3.500A) No H-bonds generated for sheet with id= B 488 hydrogen bonds defined for protein. 1344 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: 6.13 Time building geometry restraints manager: 13.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8796 1.03 - 1.23: 14 1.23 - 1.42: 3426 1.42 - 1.62: 5156 1.62 - 1.81: 108 Bond restraints: 17500 Sorted by residual: bond pdb=" C1 GSH B 603 " pdb=" O11 GSH B 603 " ideal model delta sigma weight residual 1.213 1.247 -0.034 1.00e-02 1.00e+04 1.16e+01 bond pdb=" C1 GSH A 603 " pdb=" O11 GSH A 603 " ideal model delta sigma weight residual 1.213 1.247 -0.034 1.00e-02 1.00e+04 1.15e+01 bond pdb=" C1 GSH B 603 " pdb=" O12 GSH B 603 " ideal model delta sigma weight residual 1.307 1.247 0.060 1.90e-02 2.77e+03 1.00e+01 bond pdb=" C1 GSH A 603 " pdb=" O12 GSH A 603 " ideal model delta sigma weight residual 1.307 1.247 0.060 1.90e-02 2.77e+03 9.98e+00 bond pdb=" C3 GSH A 603 " pdb=" O32 GSH A 603 " ideal model delta sigma weight residual 1.308 1.246 0.062 2.00e-02 2.50e+03 9.56e+00 ... (remaining 17495 not shown) Histogram of bond angle deviations from ideal: 98.62 - 106.19: 195 106.19 - 113.77: 21333 113.77 - 121.34: 7129 121.34 - 128.91: 3002 128.91 - 136.49: 50 Bond angle restraints: 31709 Sorted by residual: angle pdb=" N VAL B 86 " pdb=" CA VAL B 86 " pdb=" C VAL B 86 " ideal model delta sigma weight residual 113.53 109.10 4.43 9.80e-01 1.04e+00 2.04e+01 angle pdb=" CA3 GSH B 603 " pdb=" C3 GSH B 603 " pdb=" O31 GSH B 603 " ideal model delta sigma weight residual 123.68 117.02 6.66 2.25e+00 1.97e-01 8.75e+00 angle pdb=" CA3 GSH A 603 " pdb=" C3 GSH A 603 " pdb=" O31 GSH A 603 " ideal model delta sigma weight residual 123.68 117.11 6.57 2.25e+00 1.97e-01 8.51e+00 angle pdb=" CA3 GSH B 603 " pdb=" C3 GSH B 603 " pdb=" O32 GSH B 603 " ideal model delta sigma weight residual 111.89 117.33 -5.44 2.43e+00 1.69e-01 5.00e+00 angle pdb=" CA VAL B 86 " pdb=" C VAL B 86 " pdb=" N PHE B 87 " ideal model delta sigma weight residual 119.31 116.80 2.51 1.15e+00 7.56e-01 4.76e+00 ... (remaining 31704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.00: 7709 35.00 - 70.00: 393 70.00 - 105.01: 22 105.01 - 140.01: 3 140.01 - 175.01: 4 Dihedral angle restraints: 8131 sinusoidal: 4559 harmonic: 3572 Sorted by residual: dihedral pdb=" C5' AMP B 602 " pdb=" O5' AMP B 602 " pdb=" P AMP B 602 " pdb=" O3P AMP B 602 " ideal model delta sinusoidal sigma weight residual -60.00 66.55 -126.54 1 2.00e+01 2.50e-03 3.83e+01 dihedral pdb=" O01 PGW B 604 " pdb=" C01 PGW B 604 " pdb=" C02 PGW B 604 " pdb=" O03 PGW B 604 " ideal model delta sinusoidal sigma weight residual 59.30 -115.71 175.01 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C03 PGW B 604 " pdb=" C01 PGW B 604 " pdb=" C02 PGW B 604 " pdb=" O03 PGW B 604 " ideal model delta sinusoidal sigma weight residual 295.35 120.45 174.90 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 975 0.026 - 0.052: 246 0.052 - 0.078: 106 0.078 - 0.105: 52 0.105 - 0.131: 17 Chirality restraints: 1396 Sorted by residual: chirality pdb=" CA ILE A 494 " pdb=" N ILE A 494 " pdb=" C ILE A 494 " pdb=" CB ILE A 494 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA VAL A 320 " pdb=" N VAL A 320 " pdb=" C VAL A 320 " pdb=" CB VAL A 320 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1393 not shown) Planarity restraints: 2512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 GSH A 603 " -0.003 2.00e-02 2.50e+03 2.41e-02 7.25e+00 pdb=" CA2 GSH A 603 " 0.021 2.00e-02 2.50e+03 pdb=" CA3 GSH A 603 " 0.029 2.00e-02 2.50e+03 pdb=" N3 GSH A 603 " -0.039 2.00e-02 2.50e+03 pdb=" O2 GSH A 603 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 316 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO B 317 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 302 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C GLY A 302 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY A 302 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE A 303 " -0.012 2.00e-02 2.50e+03 ... (remaining 2509 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.32: 4204 2.32 - 3.02: 47128 3.02 - 3.73: 60662 3.73 - 4.43: 91529 4.43 - 5.14: 145156 Nonbonded interactions: 348679 Sorted by model distance: nonbonded pdb=" OE1 GLN A 93 " pdb="HE22 GLN A 155 " model vdw 1.609 1.850 nonbonded pdb=" OD1 ASP A 51 " pdb=" H SER A 54 " model vdw 1.634 1.850 nonbonded pdb=" O ARG B 212 " pdb=" HE ARG B 212 " model vdw 1.651 1.850 nonbonded pdb=" OD1 ASP B 429 " pdb=" H HIS B 430 " model vdw 1.656 1.850 nonbonded pdb=" OE1 GLU A 512 " pdb=" H GLU A 512 " model vdw 1.662 1.850 ... (remaining 348674 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 1 through 385 or resid 400 through 560 or resid 601 throug \ h 604)) selection = (chain 'B' and (resid 1 through 126 or (resid 127 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 128 through 560 or resid 601 t \ hrough 604)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 0.270 Extract box with map and model: 6.540 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 60.970 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8698 Z= 0.173 Angle : 0.541 6.658 11751 Z= 0.271 Chirality : 0.034 0.131 1396 Planarity : 0.004 0.066 1457 Dihedral : 19.610 175.012 3240 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 24.83 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.27), residues: 1086 helix: 2.27 (0.19), residues: 799 sheet: -0.61 (0.64), residues: 60 loop : -2.29 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 44 HIS 0.003 0.001 HIS B 259 PHE 0.008 0.001 PHE A 410 TYR 0.019 0.001 TYR A 538 ARG 0.002 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.307 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.4202 time to fit residues: 79.7732 Evaluate side-chains 131 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.0408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8698 Z= 0.220 Angle : 0.523 5.831 11751 Z= 0.265 Chirality : 0.035 0.136 1396 Planarity : 0.004 0.056 1457 Dihedral : 14.845 175.107 1318 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.38 % Allowed : 23.68 % Favored : 74.94 % 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: 1.46 (0.27), residues: 1086 helix: 1.93 (0.19), residues: 804 sheet: -0.61 (0.65), residues: 60 loop : -2.26 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 44 HIS 0.003 0.001 HIS B 259 PHE 0.010 0.001 PHE B 328 TYR 0.016 0.001 TYR B 257 ARG 0.001 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.422 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 136 average time/residue: 0.4520 time to fit residues: 85.1593 Evaluate side-chains 134 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8698 Z= 0.300 Angle : 0.565 5.908 11751 Z= 0.288 Chirality : 0.036 0.137 1396 Planarity : 0.004 0.052 1457 Dihedral : 14.551 177.158 1318 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.84 % Allowed : 23.10 % Favored : 75.06 % 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: 0.86 (0.27), residues: 1086 helix: 1.51 (0.19), residues: 801 sheet: -0.79 (0.66), residues: 60 loop : -2.54 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 44 HIS 0.004 0.001 HIS B 430 PHE 0.013 0.001 PHE B 328 TYR 0.014 0.002 TYR A 503 ARG 0.002 0.000 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 288 THR cc_start: 0.6963 (OUTLIER) cc_final: 0.6579 (m) REVERT: A 289 LEU cc_start: 0.4452 (OUTLIER) cc_final: 0.3557 (mt) outliers start: 16 outliers final: 12 residues processed: 140 average time/residue: 0.4186 time to fit residues: 82.2173 Evaluate side-chains 139 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8698 Z= 0.272 Angle : 0.554 5.803 11751 Z= 0.279 Chirality : 0.035 0.142 1396 Planarity : 0.004 0.050 1457 Dihedral : 14.197 176.396 1318 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.84 % Allowed : 23.68 % Favored : 74.48 % 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: 0.70 (0.27), residues: 1086 helix: 1.38 (0.19), residues: 807 sheet: -0.81 (0.66), residues: 60 loop : -2.63 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 44 HIS 0.003 0.001 HIS B 430 PHE 0.011 0.001 PHE B 328 TYR 0.013 0.001 TYR A 503 ARG 0.001 0.000 ARG B 496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.7582 (tt) cc_final: 0.7254 (tp) REVERT: A 232 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8459 (mm) REVERT: A 289 LEU cc_start: 0.4571 (OUTLIER) cc_final: 0.3650 (mt) REVERT: B 243 MET cc_start: 0.8547 (mmp) cc_final: 0.8277 (mmp) outliers start: 16 outliers final: 14 residues processed: 136 average time/residue: 0.4571 time to fit residues: 87.5223 Evaluate side-chains 141 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8698 Z= 0.158 Angle : 0.509 5.829 11751 Z= 0.250 Chirality : 0.034 0.143 1396 Planarity : 0.004 0.047 1457 Dihedral : 13.558 174.533 1318 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.07 % Allowed : 23.79 % Favored : 74.14 % 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 (0.27), residues: 1086 helix: 1.62 (0.20), residues: 802 sheet: -0.74 (0.66), residues: 60 loop : -2.43 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 44 HIS 0.002 0.001 HIS B 487 PHE 0.008 0.001 PHE A 154 TYR 0.008 0.001 TYR A 503 ARG 0.001 0.000 ARG B 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8398 (mm) REVERT: B 216 ARG cc_start: 0.7721 (ptm160) cc_final: 0.7496 (ptm160) REVERT: B 243 MET cc_start: 0.8504 (mmp) cc_final: 0.8203 (mmp) outliers start: 18 outliers final: 16 residues processed: 143 average time/residue: 0.4445 time to fit residues: 88.3882 Evaluate side-chains 145 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8698 Z= 0.167 Angle : 0.510 5.798 11751 Z= 0.251 Chirality : 0.034 0.140 1396 Planarity : 0.004 0.046 1457 Dihedral : 12.986 174.585 1318 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.18 % Allowed : 23.79 % Favored : 74.02 % 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 (0.27), residues: 1086 helix: 1.68 (0.20), residues: 802 sheet: -0.73 (0.66), residues: 60 loop : -2.41 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 44 HIS 0.002 0.001 HIS B 487 PHE 0.007 0.001 PHE B 328 TYR 0.008 0.001 TYR B 503 ARG 0.004 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8377 (mm) REVERT: B 243 MET cc_start: 0.8531 (mmp) cc_final: 0.8214 (mmp) REVERT: B 255 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8435 (t) outliers start: 19 outliers final: 16 residues processed: 144 average time/residue: 0.4404 time to fit residues: 88.5568 Evaluate side-chains 147 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.0070 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8698 Z= 0.201 Angle : 0.520 5.687 11751 Z= 0.257 Chirality : 0.034 0.140 1396 Planarity : 0.004 0.046 1457 Dihedral : 12.776 175.067 1318 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.53 % Allowed : 23.45 % Favored : 74.02 % 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: 1.01 (0.27), residues: 1086 helix: 1.63 (0.20), residues: 801 sheet: -0.76 (0.66), residues: 60 loop : -2.49 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 44 HIS 0.002 0.001 HIS B 487 PHE 0.009 0.001 PHE B 328 TYR 0.019 0.001 TYR B 538 ARG 0.002 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8393 (mm) REVERT: A 289 LEU cc_start: 0.4606 (OUTLIER) cc_final: 0.4374 (mt) REVERT: B 243 MET cc_start: 0.8536 (mmp) cc_final: 0.8209 (mmp) REVERT: B 255 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8453 (t) outliers start: 22 outliers final: 18 residues processed: 145 average time/residue: 0.4425 time to fit residues: 89.2785 Evaluate side-chains 150 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 129 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8698 Z= 0.179 Angle : 0.515 5.609 11751 Z= 0.253 Chirality : 0.034 0.141 1396 Planarity : 0.004 0.045 1457 Dihedral : 12.661 174.822 1318 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.53 % Allowed : 23.33 % Favored : 74.14 % 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: 1.02 (0.27), residues: 1086 helix: 1.63 (0.20), residues: 807 sheet: -0.75 (0.66), residues: 60 loop : -2.55 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 44 HIS 0.002 0.001 HIS B 434 PHE 0.008 0.001 PHE B 328 TYR 0.015 0.001 TYR B 538 ARG 0.002 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8413 (mm) REVERT: A 289 LEU cc_start: 0.4547 (OUTLIER) cc_final: 0.4322 (mt) REVERT: B 243 MET cc_start: 0.8536 (mmp) cc_final: 0.8198 (mmp) REVERT: B 255 SER cc_start: 0.8654 (OUTLIER) cc_final: 0.8446 (t) outliers start: 22 outliers final: 19 residues processed: 144 average time/residue: 0.4022 time to fit residues: 82.6044 Evaluate side-chains 152 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8698 Z= 0.183 Angle : 0.515 5.622 11751 Z= 0.254 Chirality : 0.034 0.141 1396 Planarity : 0.004 0.045 1457 Dihedral : 12.591 174.863 1318 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.76 % Allowed : 22.87 % Favored : 74.37 % 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: 1.06 (0.27), residues: 1086 helix: 1.67 (0.20), residues: 800 sheet: -0.72 (0.67), residues: 60 loop : -2.50 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 44 HIS 0.002 0.001 HIS B 487 PHE 0.008 0.001 PHE B 328 TYR 0.015 0.002 TYR A 257 ARG 0.002 0.000 ARG B 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8413 (mm) REVERT: A 289 LEU cc_start: 0.4552 (OUTLIER) cc_final: 0.4330 (mt) REVERT: B 243 MET cc_start: 0.8539 (mmp) cc_final: 0.8198 (mmp) outliers start: 24 outliers final: 22 residues processed: 142 average time/residue: 0.4106 time to fit residues: 83.2799 Evaluate side-chains 153 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8698 Z= 0.211 Angle : 0.526 5.697 11751 Z= 0.260 Chirality : 0.035 0.140 1396 Planarity : 0.004 0.045 1457 Dihedral : 12.604 175.188 1318 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.76 % Allowed : 23.10 % Favored : 74.14 % 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: 0.95 (0.27), residues: 1086 helix: 1.59 (0.20), residues: 806 sheet: -0.73 (0.67), residues: 60 loop : -2.63 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 44 HIS 0.002 0.001 HIS B 434 PHE 0.009 0.001 PHE B 328 TYR 0.020 0.002 TYR A 257 ARG 0.002 0.000 ARG B 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 127 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8437 (mm) REVERT: A 289 LEU cc_start: 0.4441 (OUTLIER) cc_final: 0.4203 (mt) REVERT: B 243 MET cc_start: 0.8553 (mmp) cc_final: 0.8209 (mmp) outliers start: 24 outliers final: 21 residues processed: 145 average time/residue: 0.4426 time to fit residues: 91.0710 Evaluate side-chains 153 residues out of total 870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 560 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111100 restraints weight = 36119.227| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.75 r_work: 0.3218 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8698 Z= 0.149 Angle : 0.509 5.578 11751 Z= 0.248 Chirality : 0.034 0.142 1396 Planarity : 0.004 0.045 1457 Dihedral : 12.458 174.400 1318 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.41 % Allowed : 23.33 % Favored : 74.25 % 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 (0.28), residues: 1086 helix: 1.75 (0.20), residues: 800 sheet: -0.66 (0.68), residues: 60 loop : -2.47 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 44 HIS 0.002 0.001 HIS B 487 PHE 0.007 0.001 PHE A 328 TYR 0.015 0.002 TYR A 257 ARG 0.002 0.000 ARG B 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3851.96 seconds wall clock time: 68 minutes 19.91 seconds (4099.91 seconds total)