Starting phenix.real_space_refine on Sun Feb 18 00:41:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3k_41004/02_2024/8t3k_41004_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3k_41004/02_2024/8t3k_41004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3k_41004/02_2024/8t3k_41004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3k_41004/02_2024/8t3k_41004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3k_41004/02_2024/8t3k_41004_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3k_41004/02_2024/8t3k_41004_trim_updated.pdb" } resolution = 3.33 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= 0.014 sd= 0.031 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 41 5.16 5 C 6537 2.51 5 N 1630 2.21 5 O 1818 1.98 5 H 9730 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19768 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 10675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 10675 Classifications: {'peptide': 663} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 649} Chain breaks: 1 Chain: "C" Number of atoms: 8634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 8634 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 19, 'TRANS': 521} Chain breaks: 4 Chain: "D" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 268 Unusual residues: {'ATP': 1, 'POV': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 3, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 191 Unusual residues: {'ATP': 1, 'POV': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 4} Unresolved non-hydrogen planarities: 34 Time building chain proxies: 8.85, per 1000 atoms: 0.45 Number of scatterers: 19768 At special positions: 0 Unit cell: (76.346, 98.991, 157.221, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 12 15.00 O 1818 8.00 N 1630 7.00 C 6537 6.00 H 9730 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: 16.13 Conformation dependent library (CDL) restraints added in 1.7 seconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2234 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 8 sheets defined 57.6% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 15 through 44 removed outlier: 3.878A pdb=" N GLY D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) Proline residue: D 36 - end of helix Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 136 through 194 Proline residue: D 144 - end of helix removed outlier: 4.298A pdb=" N LYS D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLY D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN D 170 " --> pdb=" O PHE D 166 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS D 171 " --> pdb=" O GLN D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 206 through 213 Processing helix chain 'D' and resid 215 through 229 Processing helix chain 'D' and resid 231 through 248 Processing helix chain 'D' and resid 251 through 294 removed outlier: 3.984A pdb=" N ILE D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) Proline residue: D 261 - end of helix removed outlier: 4.227A pdb=" N TYR D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE D 281 " --> pdb=" O TYR D 277 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 334 removed outlier: 3.971A pdb=" N SER D 321 " --> pdb=" O GLU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 360 Processing helix chain 'D' and resid 369 through 384 removed outlier: 3.829A pdb=" N GLN D 384 " --> pdb=" O ASN D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 409 removed outlier: 4.940A pdb=" N GLU D 397 " --> pdb=" O PHE D 393 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LEU D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 476 removed outlier: 3.731A pdb=" N LEU D 473 " --> pdb=" O LYS D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 534 through 543 removed outlier: 4.701A pdb=" N GLN D 542 " --> pdb=" O ASN D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 548 No H-bonds generated for 'chain 'D' and resid 546 through 548' Processing helix chain 'D' and resid 569 through 583 Processing helix chain 'D' and resid 599 through 613 removed outlier: 4.065A pdb=" N GLU D 602 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 604 " --> pdb=" O THR D 601 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP D 610 " --> pdb=" O LYS D 607 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS D 613 " --> pdb=" O ASP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 654 removed outlier: 3.568A pdb=" N LEU D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 650 through 654' Processing helix chain 'D' and resid 656 through 664 removed outlier: 3.577A pdb=" N LEU D 664 " --> pdb=" O GLN D 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 13 removed outlier: 6.513A pdb=" N PHE C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE C 12 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 48 removed outlier: 3.553A pdb=" N ALA C 22 " --> pdb=" O ARG C 18 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE C 23 " --> pdb=" O TYR C 19 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET C 34 " --> pdb=" O ASN C 30 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Proline residue: C 36 - end of helix Processing helix chain 'C' and resid 54 through 102 removed outlier: 3.862A pdb=" N HIS C 80 " --> pdb=" O TYR C 76 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 143 removed outlier: 3.599A pdb=" N GLY C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 122 " --> pdb=" O MET C 118 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N LEU C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 155 Processing helix chain 'C' and resid 161 through 206 Proline residue: C 168 - end of helix removed outlier: 4.207A pdb=" N VAL C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU C 189 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 217 through 270 removed outlier: 4.255A pdb=" N ILE C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU C 244 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLU C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) Proline residue: C 247 - end of helix removed outlier: 3.708A pdb=" N SER C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 290 through 308 removed outlier: 3.992A pdb=" N GLY C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN C 306 " --> pdb=" O MET C 302 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA C 307 " --> pdb=" O GLN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 314 Processing helix chain 'C' and resid 379 through 385 removed outlier: 3.603A pdb=" N LEU C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 428 through 432 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 477 through 491 removed outlier: 3.824A pdb=" N ALA C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 520 Processing helix chain 'C' and resid 556 through 560 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing sheet with id= A, first strand: chain 'D' and resid 54 through 56 Processing sheet with id= B, first strand: chain 'D' and resid 89 through 93 Processing sheet with id= C, first strand: chain 'D' and resid 430 through 433 Processing sheet with id= D, first strand: chain 'D' and resid 506 through 508 removed outlier: 6.890A pdb=" N ILE D 587 " --> pdb=" O GLY D 507 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N THR D 617 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU D 590 " --> pdb=" O THR D 617 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE D 619 " --> pdb=" O LEU D 590 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'D' and resid 634 through 638 removed outlier: 3.695A pdb=" N GLU D 644 " --> pdb=" O VAL D 636 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP D 638 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 338 through 340 Processing sheet with id= G, first strand: chain 'C' and resid 366 through 369 removed outlier: 5.688A pdb=" N THR C 526 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE C 369 " --> pdb=" O THR C 526 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 528 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 498 " --> pdb=" O PHE C 527 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 544 through 546 removed outlier: 3.765A pdb=" N GLU C 552 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ASP C 546 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE C 550 " --> pdb=" O ASP C 546 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1425 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: 6.49 Time building geometry restraints manager: 16.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 3229 1.04 - 1.23: 6734 1.23 - 1.43: 3923 1.43 - 1.62: 5969 1.62 - 1.81: 90 Bond restraints: 19945 Sorted by residual: bond pdb=" NE1 TRP C 413 " pdb=" HE1 TRP C 413 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP C 16 " pdb=" HE1 TRP C 16 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP D 266 " pdb=" HE1 TRP D 266 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP C 290 " pdb=" HE1 TRP C 290 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP D 354 " pdb=" HE1 TRP D 354 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 19940 not shown) Histogram of bond angle deviations from ideal: 80.75 - 100.41: 11 100.41 - 120.07: 29826 120.07 - 139.73: 5929 139.73 - 159.39: 3 159.39 - 179.05: 1 Bond angle restraints: 35770 Sorted by residual: angle pdb=" CA GLU C 465 " pdb=" N GLU C 465 " pdb=" H GLU C 465 " ideal model delta sigma weight residual 114.00 179.05 -65.05 3.00e+00 1.11e-01 4.70e+02 angle pdb=" CA ASN C 353 " pdb=" N ASN C 353 " pdb=" H ASN C 353 " ideal model delta sigma weight residual 114.00 153.47 -39.47 3.00e+00 1.11e-01 1.73e+02 angle pdb=" CA ALA C 451 " pdb=" N ALA C 451 " pdb=" H ALA C 451 " ideal model delta sigma weight residual 114.00 151.05 -37.05 3.00e+00 1.11e-01 1.53e+02 angle pdb=" CA SER C 476 " pdb=" N SER C 476 " pdb=" H SER C 476 " ideal model delta sigma weight residual 114.00 80.75 33.25 3.00e+00 1.11e-01 1.23e+02 angle pdb=" O13 POV D 701 " pdb=" P POV D 701 " pdb=" O14 POV D 701 " ideal model delta sigma weight residual 121.11 101.06 20.05 3.00e+00 1.11e-01 4.46e+01 ... (remaining 35765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.75: 8690 26.75 - 53.51: 636 53.51 - 80.26: 107 80.26 - 107.02: 16 107.02 - 133.77: 11 Dihedral angle restraints: 9460 sinusoidal: 5307 harmonic: 4153 Sorted by residual: dihedral pdb=" CA GLU D 558 " pdb=" C GLU D 558 " pdb=" N PRO D 559 " pdb=" CA PRO D 559 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" C29 POV D 704 " pdb="C210 POV D 704 " pdb="C211 POV D 704 " pdb="C212 POV D 704 " ideal model delta sinusoidal sigma weight residual 112.25 -113.98 -133.77 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" C29 POV D 707 " pdb="C210 POV D 707 " pdb="C211 POV D 707 " pdb="C212 POV D 707 " ideal model delta sinusoidal sigma weight residual 112.25 -114.83 -132.92 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 9457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1306 0.060 - 0.121: 173 0.121 - 0.181: 22 0.181 - 0.242: 5 0.242 - 0.302: 5 Chirality restraints: 1511 Sorted by residual: chirality pdb=" C3' ATP C 607 " pdb=" C2' ATP C 607 " pdb=" C4' ATP C 607 " pdb=" O3' ATP C 607 " both_signs ideal model delta sigma weight residual False -2.63 -2.94 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C3' ATP D 708 " pdb=" C2' ATP D 708 " pdb=" C4' ATP D 708 " pdb=" O3' ATP D 708 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C2' ATP C 607 " pdb=" C1' ATP C 607 " pdb=" C3' ATP C 607 " pdb=" O2' ATP C 607 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1508 not shown) Planarity restraints: 2859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D 707 " 0.088 2.00e-02 2.50e+03 2.55e-01 6.49e+02 pdb=" C29 POV D 707 " -0.329 2.00e-02 2.50e+03 pdb="C210 POV D 707 " 0.360 2.00e-02 2.50e+03 pdb="C211 POV D 707 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 605 " 0.135 2.00e-02 2.50e+03 2.33e-01 5.45e+02 pdb=" C29 POV C 605 " -0.301 2.00e-02 2.50e+03 pdb="C210 POV C 605 " 0.301 2.00e-02 2.50e+03 pdb="C211 POV C 605 " -0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 701 " -0.126 2.00e-02 2.50e+03 2.14e-01 4.60e+02 pdb=" C29 POV D 701 " 0.275 2.00e-02 2.50e+03 pdb="C210 POV D 701 " -0.276 2.00e-02 2.50e+03 pdb="C211 POV D 701 " 0.127 2.00e-02 2.50e+03 ... (remaining 2856 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 914 2.09 - 2.71: 31414 2.71 - 3.34: 56509 3.34 - 3.97: 75231 3.97 - 4.60: 112503 Nonbonded interactions: 276571 Sorted by model distance: nonbonded pdb="HD12 ILE D 302 " pdb=" HH TYR C 434 " model vdw 1.458 2.270 nonbonded pdb=" HE2 MET D 185 " pdb=" HE1 PHE D 407 " model vdw 1.546 2.270 nonbonded pdb=" OE1 GLU D 314 " pdb=" H GLU D 314 " model vdw 1.560 1.850 nonbonded pdb=" HB2 PRO C 334 " pdb="HD11 ILE C 495 " model vdw 1.588 2.440 nonbonded pdb="HH11 ARG D 629 " pdb=" HH TYR D 658 " model vdw 1.597 2.100 ... (remaining 276566 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: 4.750 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: 0.280 Extract box with map and model: 22.940 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 61.490 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 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 : 0.008 0.198 10215 Z= 0.538 Angle : 1.059 20.046 13715 Z= 0.519 Chirality : 0.046 0.302 1511 Planarity : 0.012 0.255 1694 Dihedral : 20.306 133.770 3961 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.20 % Allowed : 22.97 % Favored : 76.83 % 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: -1.55 (0.24), residues: 1190 helix: -0.10 (0.19), residues: 727 sheet: -2.12 (0.56), residues: 77 loop : -2.50 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.003 0.001 HIS D 307 PHE 0.018 0.002 PHE C 59 TYR 0.023 0.002 TYR C 434 ARG 0.005 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.416 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: D 99 PHE cc_start: 0.7681 (t80) cc_final: 0.7426 (t80) REVERT: D 652 MET cc_start: 0.2693 (mmp) cc_final: 0.2206 (mmm) outliers start: 2 outliers final: 1 residues processed: 128 average time/residue: 0.5162 time to fit residues: 91.1052 Evaluate side-chains 111 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 427 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 523 ASN C 271 ASN C 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10215 Z= 0.197 Angle : 0.538 5.784 13715 Z= 0.290 Chirality : 0.037 0.161 1511 Planarity : 0.004 0.046 1694 Dihedral : 16.360 171.833 1681 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.88 % Allowed : 23.75 % Favored : 75.37 % 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: -1.00 (0.25), residues: 1190 helix: 0.40 (0.19), residues: 727 sheet: -2.23 (0.58), residues: 72 loop : -2.34 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 78 HIS 0.005 0.001 HIS C 80 PHE 0.021 0.001 PHE D 323 TYR 0.015 0.001 TYR C 19 ARG 0.003 0.000 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 PHE cc_start: 0.5647 (p90) cc_final: 0.5368 (p90) outliers start: 9 outliers final: 3 residues processed: 120 average time/residue: 0.5600 time to fit residues: 93.1549 Evaluate side-chains 115 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 108 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN C 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10215 Z= 0.245 Angle : 0.536 5.686 13715 Z= 0.292 Chirality : 0.038 0.156 1511 Planarity : 0.004 0.044 1694 Dihedral : 15.408 175.336 1680 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 1.27 % Allowed : 24.14 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.25), residues: 1190 helix: 0.36 (0.19), residues: 726 sheet: -2.30 (0.58), residues: 72 loop : -2.36 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 78 HIS 0.003 0.001 HIS C 80 PHE 0.023 0.002 PHE D 323 TYR 0.019 0.002 TYR C 19 ARG 0.002 0.000 ARG D 616 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.498 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: C 2 PHE cc_start: 0.5966 (p90) cc_final: 0.5689 (p90) outliers start: 13 outliers final: 8 residues processed: 126 average time/residue: 0.5132 time to fit residues: 90.3093 Evaluate side-chains 120 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 538 HIS Chi-restraints excluded: chain C residue 544 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 56 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10215 Z= 0.244 Angle : 0.530 5.754 13715 Z= 0.289 Chirality : 0.038 0.153 1511 Planarity : 0.004 0.044 1694 Dihedral : 14.810 174.547 1680 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 1.96 % Allowed : 23.46 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.25), residues: 1190 helix: 0.32 (0.19), residues: 730 sheet: -2.41 (0.58), residues: 72 loop : -2.40 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.003 0.001 HIS D 307 PHE 0.022 0.001 PHE D 323 TYR 0.019 0.002 TYR C 19 ARG 0.002 0.000 ARG D 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.527 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: C 2 PHE cc_start: 0.6126 (p90) cc_final: 0.5916 (p90) REVERT: C 275 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6887 (mp) outliers start: 20 outliers final: 13 residues processed: 130 average time/residue: 0.5224 time to fit residues: 95.3729 Evaluate side-chains 123 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 538 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10215 Z= 0.159 Angle : 0.489 5.693 13715 Z= 0.265 Chirality : 0.036 0.153 1511 Planarity : 0.004 0.043 1694 Dihedral : 13.882 174.644 1680 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 2.05 % Allowed : 23.17 % Favored : 74.78 % 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: -0.65 (0.25), residues: 1190 helix: 0.73 (0.20), residues: 730 sheet: -2.34 (0.58), residues: 72 loop : -2.29 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.003 0.001 HIS C 80 PHE 0.019 0.001 PHE D 315 TYR 0.013 0.001 TYR C 76 ARG 0.003 0.000 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 1.795 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: D 540 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7160 (tp) outliers start: 21 outliers final: 15 residues processed: 132 average time/residue: 0.5039 time to fit residues: 93.5329 Evaluate side-chains 127 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 538 HIS Chi-restraints excluded: chain C residue 552 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.3980 chunk 104 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 116 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10215 Z= 0.183 Angle : 0.490 5.720 13715 Z= 0.266 Chirality : 0.037 0.151 1511 Planarity : 0.004 0.042 1694 Dihedral : 13.633 175.033 1680 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.35 % Allowed : 23.07 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1190 helix: 0.79 (0.20), residues: 725 sheet: -2.34 (0.59), residues: 72 loop : -2.29 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.002 0.001 HIS D 307 PHE 0.016 0.001 PHE D 323 TYR 0.016 0.001 TYR C 19 ARG 0.002 0.000 ARG D 429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.510 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: D 540 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7188 (tp) outliers start: 24 outliers final: 20 residues processed: 129 average time/residue: 0.5231 time to fit residues: 95.0061 Evaluate side-chains 130 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 538 HIS Chi-restraints excluded: chain C residue 552 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10215 Z= 0.253 Angle : 0.524 5.765 13715 Z= 0.286 Chirality : 0.038 0.148 1511 Planarity : 0.004 0.042 1694 Dihedral : 13.765 174.511 1680 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 3.42 % Allowed : 22.39 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.25), residues: 1190 helix: 0.46 (0.19), residues: 733 sheet: -2.49 (0.57), residues: 72 loop : -2.40 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.003 0.001 HIS D 307 PHE 0.019 0.001 PHE D 323 TYR 0.021 0.002 TYR C 19 ARG 0.003 0.000 ARG D 572 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 109 time to evaluate : 1.593 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: D 540 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7164 (tp) outliers start: 35 outliers final: 28 residues processed: 140 average time/residue: 0.5091 time to fit residues: 100.7296 Evaluate side-chains 136 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 538 HIS Chi-restraints excluded: chain C residue 552 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10215 Z= 0.244 Angle : 0.519 5.788 13715 Z= 0.283 Chirality : 0.037 0.151 1511 Planarity : 0.004 0.042 1694 Dihedral : 13.604 172.593 1680 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.13 % Allowed : 22.78 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.25), residues: 1190 helix: 0.45 (0.19), residues: 733 sheet: -2.48 (0.57), residues: 72 loop : -2.39 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 159 HIS 0.002 0.001 HIS D 307 PHE 0.018 0.001 PHE D 323 TYR 0.019 0.002 TYR C 76 ARG 0.003 0.000 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 1.423 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: D 540 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7152 (tp) outliers start: 32 outliers final: 26 residues processed: 138 average time/residue: 0.4858 time to fit residues: 95.1004 Evaluate side-chains 137 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 538 HIS Chi-restraints excluded: chain C residue 552 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 64 optimal weight: 0.3980 chunk 46 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10215 Z= 0.158 Angle : 0.483 5.757 13715 Z= 0.262 Chirality : 0.037 0.152 1511 Planarity : 0.004 0.041 1694 Dihedral : 13.182 169.597 1680 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.74 % Allowed : 23.26 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1190 helix: 0.81 (0.20), residues: 733 sheet: -2.43 (0.56), residues: 72 loop : -2.30 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 HIS 0.002 0.001 HIS D 46 PHE 0.015 0.001 PHE D 323 TYR 0.013 0.001 TYR C 76 ARG 0.004 0.000 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 1.440 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: D 540 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7160 (tp) outliers start: 28 outliers final: 24 residues processed: 137 average time/residue: 0.4945 time to fit residues: 94.3401 Evaluate side-chains 136 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 538 HIS Chi-restraints excluded: chain C residue 552 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10215 Z= 0.200 Angle : 0.501 6.172 13715 Z= 0.271 Chirality : 0.037 0.148 1511 Planarity : 0.004 0.041 1694 Dihedral : 13.108 165.529 1680 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.64 % Allowed : 23.07 % Favored : 74.29 % 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: -0.62 (0.25), residues: 1190 helix: 0.80 (0.20), residues: 727 sheet: -2.43 (0.57), residues: 72 loop : -2.33 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.002 0.001 HIS D 448 PHE 0.017 0.001 PHE D 323 TYR 0.017 0.001 TYR C 19 ARG 0.005 0.000 ARG C 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 1.517 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: D 540 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7153 (tp) REVERT: C 433 LEU cc_start: 0.7601 (mt) cc_final: 0.7373 (mt) outliers start: 27 outliers final: 25 residues processed: 135 average time/residue: 0.5094 time to fit residues: 95.7533 Evaluate side-chains 136 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 110 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 563 LYS Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 630 ASN Chi-restraints excluded: chain D residue 661 MET Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 98 MET Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 538 HIS Chi-restraints excluded: chain C residue 552 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 95 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.129997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.107555 restraints weight = 63458.602| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.16 r_work: 0.3935 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10215 Z= 0.165 Angle : 0.483 5.844 13715 Z= 0.261 Chirality : 0.036 0.152 1511 Planarity : 0.004 0.040 1694 Dihedral : 12.812 156.727 1680 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.64 % Allowed : 23.56 % Favored : 73.80 % 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: -0.38 (0.25), residues: 1190 helix: 1.03 (0.20), residues: 721 sheet: -2.43 (0.55), residues: 77 loop : -2.24 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 HIS 0.002 0.001 HIS D 448 PHE 0.029 0.001 PHE C 266 TYR 0.014 0.001 TYR C 19 ARG 0.006 0.000 ARG C 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4741.18 seconds wall clock time: 84 minutes 47.68 seconds (5087.68 seconds total)