Starting phenix.real_space_refine on Sun Feb 18 12:13:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh1_12185/02_2024/7bh1_12185_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh1_12185/02_2024/7bh1_12185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh1_12185/02_2024/7bh1_12185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh1_12185/02_2024/7bh1_12185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh1_12185/02_2024/7bh1_12185_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bh1_12185/02_2024/7bh1_12185_trim_updated.pdb" } resolution = 3.38 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= 0.002 sd= 0.088 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 1 8.98 5 P 1 5.49 5 S 61 5.16 5 C 6977 2.51 5 N 1818 2.21 5 O 1964 1.98 5 H 11139 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 208": "OE1" <-> "OE2" Residue "B ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21961 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8444 Classifications: {'peptide': 557} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 10201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 10201 Classifications: {'peptide': 674} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 647} Chain: "C" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2827 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 13, 'TRANS': 172} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 421 Classifications: {'peptide': 27} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'9Y0': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 12 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 9.72, per 1000 atoms: 0.44 Number of scatterers: 21961 At special positions: 0 Unit cell: (78.66, 114.885, 157.32, 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 1 19.00 S 61 16.00 P 1 15.00 O 1964 8.00 N 1818 7.00 C 6977 6.00 H 11139 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: 19.32 Conformation dependent library (CDL) restraints added in 2.1 seconds 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 6 sheets defined 57.5% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 133 through 156 Processing helix chain 'A' and resid 166 through 192 removed outlier: 4.180A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.408A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 304 removed outlier: 3.501A pdb=" N MET A 287 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 298 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.749A pdb=" N LEU A 312 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 341 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.545A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 378 through 398 Processing helix chain 'A' and resid 411 through 437 removed outlier: 3.784A pdb=" N LEU A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.685A pdb=" N VAL A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 507 Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 525 through 548 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'B' and resid 11 through 24 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 34 through 54 Processing helix chain 'B' and resid 62 through 101 removed outlier: 3.642A pdb=" N LYS B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 Processing helix chain 'B' and resid 216 through 246 removed outlier: 4.508A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 285 removed outlier: 5.037A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 308 through 311 No H-bonds generated for 'chain 'B' and resid 308 through 311' Processing helix chain 'B' and resid 330 through 343 removed outlier: 4.574A pdb=" N ALA B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'B' and resid 398 through 407 Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 454 through 463 Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'B' and resid 496 through 508 Processing helix chain 'B' and resid 520 through 528 Proline residue: B 524 - end of helix Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.648A pdb=" N ALA B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 594 removed outlier: 3.527A pdb=" N LEU B 569 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 581 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 585 " --> pdb=" O ASN B 582 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 587 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ILE B 591 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 4.050A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 630 Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 646 through 679 Proline residue: B 665 - end of helix Processing helix chain 'C' and resid 5 through 19 Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 118 through 121 No H-bonds generated for 'chain 'C' and resid 118 through 121' Processing helix chain 'C' and resid 134 through 148 removed outlier: 3.530A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE C 141 " --> pdb=" O ALA C 137 " (cutoff:3.500A) Proline residue: C 142 - end of helix Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'D' and resid 3 through 23 Processing sheet with id= A, first strand: chain 'A' and resid 202 through 204 Processing sheet with id= B, first strand: chain 'B' and resid 107 through 109 removed outlier: 3.557A pdb=" N ASP B 119 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 131 through 135 removed outlier: 3.653A pdb=" N VAL B 188 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 148 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 150 through 153 Processing sheet with id= E, first strand: chain 'B' and resid 513 through 515 removed outlier: 6.485A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL B 468 " --> pdb=" O LEU B 306 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 383 through 386 removed outlier: 5.447A pdb=" N GLU B 435 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VAL B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 321 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LYS B 446 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALA B 319 " --> pdb=" O LYS B 446 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1575 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: 8.27 Time building geometry restraints manager: 19.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11127 1.03 - 1.22: 106 1.22 - 1.42: 4295 1.42 - 1.62: 6513 1.62 - 1.81: 112 Bond restraints: 22153 Sorted by residual: bond pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " ideal model delta sigma weight residual 1.333 1.532 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" ND2 ASN B 582 " pdb="HD21 ASN B 582 " ideal model delta sigma weight residual 0.860 0.972 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C5 9Y0 B 801 " pdb=" O5 9Y0 B 801 " ideal model delta sigma weight residual 1.326 1.433 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" ND2 ASN B 582 " pdb="HD22 ASN B 582 " ideal model delta sigma weight residual 0.860 0.966 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C21 9Y0 B 801 " pdb=" O7 9Y0 B 801 " ideal model delta sigma weight residual 1.330 1.417 -0.087 2.00e-02 2.50e+03 1.89e+01 ... (remaining 22148 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.20: 313 105.20 - 112.50: 26327 112.50 - 119.79: 6348 119.79 - 127.08: 7064 127.08 - 134.38: 135 Bond angle restraints: 40187 Sorted by residual: angle pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " pdb=" C15 9Y0 B 801 " ideal model delta sigma weight residual 127.64 104.93 22.71 3.00e+00 1.11e-01 5.73e+01 angle pdb=" C12 9Y0 B 801 " pdb=" C13 9Y0 B 801 " pdb=" C14 9Y0 B 801 " ideal model delta sigma weight residual 127.16 114.64 12.52 3.00e+00 1.11e-01 1.74e+01 angle pdb=" O 9Y0 B 801 " pdb=" P 9Y0 B 801 " pdb=" O2 9Y0 B 801 " ideal model delta sigma weight residual 120.70 108.37 12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C6 9Y0 B 801 " pdb=" C5 9Y0 B 801 " pdb=" O5 9Y0 B 801 " ideal model delta sigma weight residual 111.26 122.17 -10.91 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C2 9Y0 B 801 " pdb=" O3 9Y0 B 801 " pdb=" P 9Y0 B 801 " ideal model delta sigma weight residual 119.47 108.60 10.87 3.00e+00 1.11e-01 1.31e+01 ... (remaining 40182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.35: 9766 27.35 - 54.71: 518 54.71 - 82.06: 86 82.06 - 109.42: 4 109.42 - 136.77: 1 Dihedral angle restraints: 10375 sinusoidal: 5715 harmonic: 4660 Sorted by residual: dihedral pdb=" CA LEU A 36 " pdb=" C LEU A 36 " pdb=" N PRO A 37 " pdb=" CA PRO A 37 " ideal model delta harmonic sigma weight residual -180.00 -151.28 -28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ALA A 238 " pdb=" C ALA A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual -180.00 -157.76 -22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" C 9Y0 B 801 " pdb=" C5 9Y0 B 801 " pdb=" O5 9Y0 B 801 " pdb=" C6 9Y0 B 801 " ideal model delta sinusoidal sigma weight residual 183.38 46.61 136.77 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 10372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1471 0.076 - 0.153: 300 0.153 - 0.229: 27 0.229 - 0.305: 3 0.305 - 0.382: 1 Chirality restraints: 1802 Sorted by residual: chirality pdb=" C1 9Y0 B 801 " pdb=" C 9Y0 B 801 " pdb=" C2 9Y0 B 801 " pdb=" O7 9Y0 B 801 " both_signs ideal model delta sigma weight residual False 2.36 2.74 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CB ILE B 580 " pdb=" CA ILE B 580 " pdb=" CG1 ILE B 580 " pdb=" CG2 ILE B 580 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA PRO B 34 " pdb=" N PRO B 34 " pdb=" C PRO B 34 " pdb=" CB PRO B 34 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1799 not shown) Planarity restraints: 3275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 582 " -0.236 2.00e-02 2.50e+03 2.46e-01 9.06e+02 pdb=" CG ASN B 582 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN B 582 " 0.224 2.00e-02 2.50e+03 pdb=" ND2 ASN B 582 " 0.005 2.00e-02 2.50e+03 pdb="HD21 ASN B 582 " 0.352 2.00e-02 2.50e+03 pdb="HD22 ASN B 582 " -0.363 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 624 " -0.039 2.00e-02 2.50e+03 7.11e-02 7.58e+01 pdb=" CG ASN B 624 " 0.070 2.00e-02 2.50e+03 pdb=" OD1 ASN B 624 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 624 " -0.124 2.00e-02 2.50e+03 pdb="HD21 ASN B 624 " -0.011 2.00e-02 2.50e+03 pdb="HD22 ASN B 624 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 9Y0 B 801 " 0.045 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C13 9Y0 B 801 " -0.053 2.00e-02 2.50e+03 pdb=" C14 9Y0 B 801 " -0.035 2.00e-02 2.50e+03 pdb=" C15 9Y0 B 801 " 0.043 2.00e-02 2.50e+03 ... (remaining 3272 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.34: 7481 2.34 - 3.04: 65569 3.04 - 3.74: 82073 3.74 - 4.44: 129815 4.44 - 5.14: 200812 Nonbonded interactions: 485750 Sorted by model distance: nonbonded pdb=" OD1 ASN A 447 " pdb=" H ALA C 88 " model vdw 1.640 1.850 nonbonded pdb=" OD1 ASP B 335 " pdb="HE21 GLN B 338 " model vdw 1.660 1.850 nonbonded pdb=" HE ARG B 365 " pdb=" OG SER B 369 " model vdw 1.666 1.850 nonbonded pdb="HH11 ARG B 167 " pdb=" O PHE B 173 " model vdw 1.683 1.850 nonbonded pdb=" OD1 ASP B 550 " pdb=" H LEU B 551 " model vdw 1.692 1.850 ... (remaining 485745 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.320 Extract box with map and model: 8.080 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 79.610 Find NCS groups from input model: 0.410 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.014 0.199 11014 Z= 0.914 Angle : 1.148 22.705 14980 Z= 0.617 Chirality : 0.060 0.382 1802 Planarity : 0.007 0.075 1899 Dihedral : 14.321 136.773 3937 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.35 % Allowed : 11.32 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.18), residues: 1436 helix: -1.56 (0.15), residues: 852 sheet: -3.20 (0.48), residues: 67 loop : -3.44 (0.23), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 32 HIS 0.008 0.002 HIS C 66 PHE 0.041 0.004 PHE A 260 TYR 0.046 0.004 TYR A 381 ARG 0.012 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 ASP cc_start: 0.8974 (t0) cc_final: 0.8430 (t70) outliers start: 4 outliers final: 1 residues processed: 127 average time/residue: 0.4445 time to fit residues: 85.8011 Evaluate side-chains 98 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 582 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN B 582 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11014 Z= 0.218 Angle : 0.616 6.693 14980 Z= 0.328 Chirality : 0.040 0.171 1802 Planarity : 0.005 0.052 1899 Dihedral : 9.522 86.132 1565 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.53 % Allowed : 13.26 % Favored : 86.21 % 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: -2.17 (0.20), residues: 1436 helix: -0.39 (0.16), residues: 851 sheet: -2.40 (0.46), residues: 84 loop : -3.08 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 32 HIS 0.003 0.001 HIS A 451 PHE 0.022 0.002 PHE A 327 TYR 0.029 0.002 TYR A 381 ARG 0.002 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8694 (tp) cc_final: 0.8491 (tp) REVERT: A 310 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8838 (tt) REVERT: A 489 MET cc_start: 0.8690 (mtm) cc_final: 0.8480 (mtm) REVERT: B 463 MET cc_start: 0.8183 (mtm) cc_final: 0.7982 (ttm) outliers start: 6 outliers final: 4 residues processed: 119 average time/residue: 0.4573 time to fit residues: 83.9628 Evaluate side-chains 107 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 129 optimal weight: 0.4980 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 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 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11014 Z= 0.241 Angle : 0.575 6.436 14980 Z= 0.304 Chirality : 0.039 0.151 1802 Planarity : 0.004 0.053 1899 Dihedral : 8.037 86.770 1563 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.71 % Allowed : 13.79 % Favored : 85.50 % 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: -1.61 (0.21), residues: 1436 helix: 0.13 (0.17), residues: 852 sheet: -2.28 (0.48), residues: 84 loop : -2.97 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 32 HIS 0.002 0.000 HIS A 451 PHE 0.015 0.001 PHE A 260 TYR 0.026 0.002 TYR A 381 ARG 0.002 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8863 (tt) REVERT: A 489 MET cc_start: 0.8754 (mtm) cc_final: 0.8508 (mtm) REVERT: B 463 MET cc_start: 0.8162 (mtm) cc_final: 0.7962 (ttm) REVERT: B 490 PHE cc_start: 0.8015 (p90) cc_final: 0.7779 (p90) outliers start: 8 outliers final: 6 residues processed: 109 average time/residue: 0.4563 time to fit residues: 75.9185 Evaluate side-chains 108 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 chunk 137 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 114 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN C 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11014 Z= 0.189 Angle : 0.535 6.096 14980 Z= 0.280 Chirality : 0.038 0.148 1802 Planarity : 0.004 0.053 1899 Dihedral : 7.335 82.875 1563 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.80 % Allowed : 14.15 % Favored : 85.06 % 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: -1.03 (0.21), residues: 1436 helix: 0.59 (0.17), residues: 848 sheet: -2.13 (0.49), residues: 84 loop : -2.67 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 245 HIS 0.003 0.000 HIS A 451 PHE 0.013 0.001 PHE A 260 TYR 0.024 0.001 TYR A 381 ARG 0.002 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8853 (tt) REVERT: A 489 MET cc_start: 0.8785 (mtm) cc_final: 0.8543 (mtm) REVERT: B 203 MET cc_start: 0.6769 (tmm) cc_final: 0.6380 (tpt) REVERT: B 490 PHE cc_start: 0.7979 (p90) cc_final: 0.7759 (p90) REVERT: B 568 MET cc_start: 0.7634 (ttm) cc_final: 0.7367 (mtp) REVERT: C 129 ASP cc_start: 0.8788 (t0) cc_final: 0.8304 (t70) outliers start: 9 outliers final: 4 residues processed: 112 average time/residue: 0.4381 time to fit residues: 74.5137 Evaluate side-chains 101 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 117 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 70 optimal weight: 30.0000 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN C 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11014 Z= 0.243 Angle : 0.538 6.139 14980 Z= 0.282 Chirality : 0.039 0.147 1802 Planarity : 0.004 0.056 1899 Dihedral : 7.163 82.021 1563 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.06 % Allowed : 14.06 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1436 helix: 0.64 (0.17), residues: 862 sheet: -2.57 (0.45), residues: 98 loop : -2.44 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 PHE 0.011 0.001 PHE A 260 TYR 0.022 0.001 TYR A 381 ARG 0.002 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7304 (mmp) REVERT: A 310 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8879 (tt) REVERT: A 471 PHE cc_start: 0.7412 (m-80) cc_final: 0.7211 (m-80) REVERT: A 489 MET cc_start: 0.8814 (mtm) cc_final: 0.8572 (mtm) REVERT: B 203 MET cc_start: 0.6865 (tmm) cc_final: 0.6580 (tpt) REVERT: C 77 TYR cc_start: 0.8396 (m-80) cc_final: 0.8161 (m-80) REVERT: C 129 ASP cc_start: 0.8817 (t0) cc_final: 0.8203 (t70) outliers start: 12 outliers final: 5 residues processed: 108 average time/residue: 0.5079 time to fit residues: 83.7843 Evaluate side-chains 107 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 513 GLN Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 30.0000 chunk 132 optimal weight: 1.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 ASN C 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11014 Z= 0.278 Angle : 0.548 6.054 14980 Z= 0.289 Chirality : 0.039 0.147 1802 Planarity : 0.004 0.057 1899 Dihedral : 7.118 81.802 1563 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.06 % Allowed : 14.68 % Favored : 84.26 % 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: -0.81 (0.22), residues: 1436 helix: 0.68 (0.17), residues: 863 sheet: -2.51 (0.45), residues: 98 loop : -2.35 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 71 HIS 0.002 0.001 HIS A 451 PHE 0.011 0.001 PHE A 373 TYR 0.021 0.001 TYR A 381 ARG 0.002 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7309 (mmp) REVERT: A 310 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8963 (tt) REVERT: A 327 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.8182 (m-10) REVERT: A 489 MET cc_start: 0.8835 (mtm) cc_final: 0.8585 (mtm) REVERT: B 203 MET cc_start: 0.6892 (tmm) cc_final: 0.6628 (tpt) REVERT: B 296 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6755 (mt-10) REVERT: B 490 PHE cc_start: 0.8022 (p90) cc_final: 0.7805 (p90) outliers start: 12 outliers final: 5 residues processed: 112 average time/residue: 0.4536 time to fit residues: 77.3685 Evaluate side-chains 107 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11014 Z= 0.233 Angle : 0.529 5.979 14980 Z= 0.278 Chirality : 0.038 0.146 1802 Planarity : 0.004 0.056 1899 Dihedral : 6.898 77.534 1563 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.24 % Allowed : 14.24 % Favored : 84.53 % 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: -0.56 (0.22), residues: 1436 helix: 0.83 (0.18), residues: 856 sheet: -2.33 (0.46), residues: 98 loop : -2.13 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 PHE 0.020 0.001 PHE A 471 TYR 0.020 0.001 TYR A 381 ARG 0.001 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8896 (tt) REVERT: A 327 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8321 (m-10) REVERT: A 389 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8483 (tp) REVERT: A 489 MET cc_start: 0.8827 (mtm) cc_final: 0.8564 (mtm) REVERT: B 203 MET cc_start: 0.6786 (tmm) cc_final: 0.6541 (tpt) REVERT: B 490 PHE cc_start: 0.8028 (p90) cc_final: 0.7803 (p90) REVERT: B 568 MET cc_start: 0.7621 (ttm) cc_final: 0.7280 (mtp) outliers start: 14 outliers final: 7 residues processed: 114 average time/residue: 0.4462 time to fit residues: 77.2544 Evaluate side-chains 114 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain C residue 28 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 124 optimal weight: 0.4980 chunk 131 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11014 Z= 0.217 Angle : 0.524 5.870 14980 Z= 0.274 Chirality : 0.038 0.146 1802 Planarity : 0.004 0.056 1899 Dihedral : 6.704 78.118 1563 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.88 % Allowed : 14.59 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.22), residues: 1436 helix: 0.95 (0.18), residues: 844 sheet: -2.19 (0.46), residues: 98 loop : -1.97 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 71 HIS 0.003 0.000 HIS A 451 PHE 0.014 0.001 PHE A 471 TYR 0.020 0.001 TYR A 381 ARG 0.001 0.000 ARG B 382 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7147 (mmp) REVERT: A 310 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8889 (tt) REVERT: A 327 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8310 (m-10) REVERT: A 389 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8498 (tp) REVERT: A 489 MET cc_start: 0.8811 (mtm) cc_final: 0.8556 (mtm) REVERT: B 203 MET cc_start: 0.6771 (tmm) cc_final: 0.6545 (tpt) REVERT: B 296 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6739 (mt-10) REVERT: B 490 PHE cc_start: 0.8032 (p90) cc_final: 0.7809 (p90) REVERT: B 568 MET cc_start: 0.7594 (ttm) cc_final: 0.7279 (mtp) REVERT: C 129 ASP cc_start: 0.8761 (t0) cc_final: 0.8244 (t70) outliers start: 10 outliers final: 5 residues processed: 115 average time/residue: 0.4583 time to fit residues: 80.7428 Evaluate side-chains 117 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain C residue 28 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.0870 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11014 Z= 0.197 Angle : 0.509 5.801 14980 Z= 0.266 Chirality : 0.038 0.144 1802 Planarity : 0.004 0.055 1899 Dihedral : 6.292 76.362 1563 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.80 % Allowed : 14.50 % Favored : 84.70 % 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: -0.20 (0.22), residues: 1436 helix: 1.10 (0.18), residues: 841 sheet: -2.08 (0.47), residues: 98 loop : -1.87 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 245 HIS 0.002 0.000 HIS A 451 PHE 0.016 0.001 PHE A 471 TYR 0.020 0.001 TYR A 381 ARG 0.002 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7128 (mmp) REVERT: A 310 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8885 (tt) REVERT: A 327 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8115 (m-10) REVERT: A 389 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8485 (tp) REVERT: A 489 MET cc_start: 0.8813 (mtm) cc_final: 0.8558 (mtm) REVERT: B 203 MET cc_start: 0.6748 (tmm) cc_final: 0.6542 (tpt) REVERT: B 296 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6728 (mt-10) REVERT: B 490 PHE cc_start: 0.8000 (p90) cc_final: 0.7787 (p90) REVERT: C 129 ASP cc_start: 0.8742 (t0) cc_final: 0.8232 (t70) outliers start: 9 outliers final: 4 residues processed: 117 average time/residue: 0.4460 time to fit residues: 79.4639 Evaluate side-chains 116 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain C residue 28 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 69 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 chunk 120 optimal weight: 0.1980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11014 Z= 0.289 Angle : 0.545 5.851 14980 Z= 0.288 Chirality : 0.039 0.143 1802 Planarity : 0.004 0.054 1899 Dihedral : 6.314 72.259 1563 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.62 % Allowed : 14.94 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1436 helix: 0.94 (0.18), residues: 854 sheet: -2.05 (0.47), residues: 98 loop : -1.97 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 71 HIS 0.002 0.001 HIS A 451 PHE 0.014 0.001 PHE A 471 TYR 0.018 0.002 TYR A 381 ARG 0.002 0.000 ARG A 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2872 Ramachandran restraints generated. 1436 Oldfield, 0 Emsley, 1436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8974 (tt) REVERT: A 327 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8563 (m-10) REVERT: A 389 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8514 (tp) REVERT: A 489 MET cc_start: 0.8825 (mtm) cc_final: 0.8567 (mtm) REVERT: B 203 MET cc_start: 0.6825 (tmm) cc_final: 0.6594 (tpt) REVERT: B 296 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6771 (mt-10) REVERT: B 568 MET cc_start: 0.7662 (ttm) cc_final: 0.7233 (mtp) outliers start: 7 outliers final: 4 residues processed: 111 average time/residue: 0.4557 time to fit residues: 77.5269 Evaluate side-chains 112 residues out of total 1131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 99 optimal weight: 0.4980 chunk 6 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.168655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.114591 restraints weight = 41677.332| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.15 r_work: 0.3496 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11014 Z= 0.156 Angle : 0.498 5.746 14980 Z= 0.259 Chirality : 0.037 0.143 1802 Planarity : 0.004 0.052 1899 Dihedral : 5.924 59.240 1563 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.62 % Allowed : 14.68 % Favored : 84.70 % 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: -0.11 (0.22), residues: 1436 helix: 1.11 (0.18), residues: 858 sheet: -1.81 (0.48), residues: 91 loop : -1.87 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 245 HIS 0.003 0.000 HIS A 451 PHE 0.013 0.001 PHE A 471 TYR 0.021 0.001 TYR A 381 ARG 0.002 0.000 ARG A 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4571.15 seconds wall clock time: 82 minutes 8.15 seconds (4928.15 seconds total)