Starting phenix.real_space_refine on Tue Jul 23 02:43:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3k_41004/07_2024/8t3k_41004_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3k_41004/07_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_41004/07_2024/8t3k_41004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3k_41004/07_2024/8t3k_41004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3k_41004/07_2024/8t3k_41004_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3k_41004/07_2024/8t3k_41004_trim.cif" } 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-5388/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: 12.54, per 1000 atoms: 0.63 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: 17.43 Conformation dependent library (CDL) restraints added in 2.2 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... Secondary structure from input PDB file: 47 helices and 8 sheets defined 63.8% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.507A pdb=" N THR D 6 " --> pdb=" O LYS D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 45 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 48 through 52 removed outlier: 3.656A pdb=" N GLU D 51 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 142 through 195 removed outlier: 3.575A pdb=" N ILE D 146 " --> pdb=" O TYR D 142 " (cutoff:3.500A) 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 197 through 203 removed outlier: 3.975A pdb=" N PHE D 201 " --> pdb=" O PRO D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 removed outlier: 3.520A pdb=" N VAL D 209 " --> pdb=" O PRO D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 230 Processing helix chain 'D' and resid 230 through 249 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 259 through 295 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 310 through 335 removed outlier: 3.924A pdb=" N GLU D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER D 321 " --> pdb=" O GLU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 361 Processing helix chain 'D' and resid 368 through 383 Processing helix chain 'D' and resid 385 through 412 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 468 through 477 removed outlier: 3.731A pdb=" N LEU D 473 " --> pdb=" O LYS D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'D' and resid 498 through 504 Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 533 through 544 removed outlier: 3.540A pdb=" N LYS D 537 " --> pdb=" O GLU D 533 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN D 542 " --> pdb=" O ASN D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 549 Processing helix chain 'D' and resid 568 through 584 Processing helix chain 'D' and resid 598 through 600 No H-bonds generated for 'chain 'D' and resid 598 through 600' Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.639A pdb=" N ILE D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D 611 " --> pdb=" O LYS D 607 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN D 614 " --> pdb=" O ASP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 655 removed outlier: 3.568A pdb=" N LEU D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 664 removed outlier: 3.849A pdb=" N TYR D 659 " --> pdb=" O GLU D 655 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 664 " --> pdb=" O GLN D 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 14 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) removed outlier: 3.858A pdb=" N ALA C 14 " --> pdb=" O TRP C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 33 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) Processing helix chain 'C' and resid 34 through 49 removed outlier: 4.058A pdb=" N LYS C 38 " --> pdb=" O MET C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 103 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 113 through 144 removed outlier: 3.528A pdb=" N LEU C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) 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 144 through 156 Processing helix chain 'C' and resid 160 through 167 Processing helix chain 'C' and resid 167 through 207 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 207 through 214 Processing helix chain 'C' and resid 216 through 243 removed outlier: 4.255A pdb=" N ILE C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 270 removed outlier: 3.576A pdb=" N THR C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.511A pdb=" N LEU C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 315 removed outlier: 4.293A pdb=" N MET C 292 " --> pdb=" O MET C 288 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) 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) removed outlier: 3.604A pdb=" N ASP C 310 " --> pdb=" O ASN C 306 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 385 removed outlier: 4.517A pdb=" N ILE C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 427 through 433 Processing helix chain 'C' and resid 452 through 458 removed outlier: 3.997A pdb=" N ASP C 456 " --> pdb=" O HIS C 452 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) 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 506 through 521 Processing helix chain 'C' and resid 555 through 561 removed outlier: 3.844A pdb=" N ALA C 561 " --> pdb=" O GLN C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 571 removed outlier: 3.545A pdb=" N TYR C 570 " --> pdb=" O ARG C 567 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'D' and resid 110 through 111 removed outlier: 4.074A pdb=" N ILE D 119 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG D 126 " --> pdb=" O ILE D 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 430 through 433 Processing sheet with id=AA4, first strand: chain 'D' and resid 506 through 508 Processing sheet with id=AA5, 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=AA6, first strand: chain 'C' and resid 360 through 361 removed outlier: 4.223A pdb=" N VAL C 342 " --> pdb=" O GLU C 392 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU C 392 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 366 through 369 removed outlier: 7.385A pdb=" N LEU C 496 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU C 529 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU C 498 " --> pdb=" O LEU C 529 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 544 through 546 removed outlier: 7.123A pdb=" N VAL C 544 " --> pdb=" O ALA C 551 " (cutoff:3.500A) 565 hydrogen bonds defined for protein. 1653 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: 7.72 Time building geometry restraints manager: 18.13 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: 888 2.09 - 2.71: 31354 2.71 - 3.34: 56439 3.34 - 3.97: 75125 3.97 - 4.60: 112389 Nonbonded interactions: 276195 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 276190 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.270 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 71.120 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.200 ------------------------------------------------------------------------------- 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= 0.481 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 : 1.590 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: 0.5187 time to fit residues: 91.7782 Evaluate side-chains 111 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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: 2.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 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 ** 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: 0.6601 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10215 Z= 0.203 Angle : 0.552 5.730 13715 Z= 0.300 Chirality : 0.038 0.152 1511 Planarity : 0.004 0.045 1694 Dihedral : 16.261 172.677 1681 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.68 % Allowed : 24.24 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.25), residues: 1190 helix: 0.38 (0.19), residues: 731 sheet: -2.43 (0.59), residues: 72 loop : -2.31 (0.32), residues: 387 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 0.022 0.001 PHE D 323 TYR 0.015 0.001 TYR C 76 ARG 0.003 0.000 ARG D 572 *********************** 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 118 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 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: C 2 PHE cc_start: 0.5649 (p90) cc_final: 0.5353 (p90) outliers start: 7 outliers final: 2 residues processed: 117 average time/residue: 0.5258 time to fit residues: 85.5114 Evaluate side-chains 112 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain C residue 210 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 523 ASN C 87 ASN C 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10215 Z= 0.299 Angle : 0.572 5.723 13715 Z= 0.315 Chirality : 0.039 0.147 1511 Planarity : 0.004 0.044 1694 Dihedral : 15.649 175.331 1680 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 1.66 % Allowed : 23.75 % 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: -1.31 (0.24), residues: 1190 helix: 0.11 (0.19), residues: 733 sheet: -2.67 (0.59), residues: 73 loop : -2.33 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.004 0.001 HIS C 80 PHE 0.025 0.002 PHE D 323 TYR 0.022 0.002 TYR C 76 ARG 0.005 0.001 ARG C 362 *********************** 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 129 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.392 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: 0.6013 (p90) cc_final: 0.5720 (p90) REVERT: C 275 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6843 (mp) outliers start: 17 outliers final: 12 residues processed: 126 average time/residue: 0.5473 time to fit residues: 97.3275 Evaluate side-chains 123 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 430 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 248 THR Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 538 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10215 Z= 0.224 Angle : 0.528 5.680 13715 Z= 0.289 Chirality : 0.037 0.147 1511 Planarity : 0.004 0.044 1694 Dihedral : 14.674 174.053 1680 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.35 % Allowed : 23.66 % 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: -1.03 (0.25), residues: 1190 helix: 0.37 (0.19), residues: 733 sheet: -2.71 (0.59), residues: 73 loop : -2.26 (0.32), residues: 384 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 0.021 0.001 PHE D 323 TYR 0.016 0.002 TYR C 76 ARG 0.003 0.000 ARG C 362 *********************** 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 140 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 136 average time/residue: 0.5260 time to fit residues: 101.8159 Evaluate side-chains 127 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 623 HIS 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 149 ILE 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 275 LEU Chi-restraints excluded: chain C residue 298 LEU 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: 2.9990 chunk 1 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 98 optimal weight: 0.0570 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- 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: 0.6642 moved from start: 0.1757 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= 0.216 Angle : 0.521 5.635 13715 Z= 0.286 Chirality : 0.037 0.146 1511 Planarity : 0.004 0.043 1694 Dihedral : 14.125 174.339 1680 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.74 % Allowed : 23.07 % 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: -0.95 (0.25), residues: 1190 helix: 0.45 (0.19), residues: 733 sheet: -2.80 (0.57), residues: 73 loop : -2.24 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.003 0.001 HIS D 448 PHE 0.011 0.001 PHE C 424 TYR 0.017 0.002 TYR C 19 ARG 0.004 0.000 ARG D 572 *********************** 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 139 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 1.728 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: D 540 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7138 (tp) outliers start: 28 outliers final: 22 residues processed: 135 average time/residue: 0.5222 time to fit residues: 98.9472 Evaluate side-chains 133 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 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 331 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 430 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 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 396 THR Chi-restraints excluded: chain C residue 538 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 116 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.6655 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10215 Z= 0.239 Angle : 0.525 5.656 13715 Z= 0.289 Chirality : 0.038 0.150 1511 Planarity : 0.004 0.043 1694 Dihedral : 13.848 173.679 1680 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.52 % Allowed : 23.17 % Favored : 73.31 % 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: -1.04 (0.25), residues: 1190 helix: 0.40 (0.19), residues: 735 sheet: -2.82 (0.58), residues: 73 loop : -2.35 (0.32), residues: 382 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 0.001 PHE D 323 TYR 0.019 0.002 TYR C 76 ARG 0.002 0.000 ARG D 616 *********************** 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 147 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 1.465 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 540 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7152 (tp) outliers start: 36 outliers final: 29 residues processed: 141 average time/residue: 0.4960 time to fit residues: 99.1335 Evaluate side-chains 140 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 376 VAL Chi-restraints excluded: chain D residue 430 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 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 210 VAL 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 396 THR Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 538 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.6674 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10215 Z= 0.278 Angle : 0.542 5.665 13715 Z= 0.298 Chirality : 0.038 0.152 1511 Planarity : 0.004 0.042 1694 Dihedral : 13.859 172.363 1680 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.42 % Allowed : 23.46 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.24), residues: 1190 helix: 0.27 (0.19), residues: 737 sheet: -2.94 (0.56), residues: 73 loop : -2.38 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 HIS 0.003 0.001 HIS D 448 PHE 0.019 0.002 PHE D 323 TYR 0.021 0.002 TYR C 76 ARG 0.002 0.000 ARG D 616 *********************** 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 143 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 108 time to evaluate : 1.443 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: D 540 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7175 (tp) REVERT: C 81 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6552 (mm110) outliers start: 35 outliers final: 30 residues processed: 138 average time/residue: 0.5118 time to fit residues: 98.5637 Evaluate side-chains 140 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 108 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 376 VAL Chi-restraints excluded: chain D residue 430 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 81 GLN 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 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 396 THR Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 538 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.6638 moved from start: 0.2046 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= 0.190 Angle : 0.506 5.689 13715 Z= 0.277 Chirality : 0.037 0.154 1511 Planarity : 0.004 0.042 1694 Dihedral : 13.433 169.994 1680 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.74 % Allowed : 24.44 % Favored : 72.83 % 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: -0.82 (0.25), residues: 1190 helix: 0.61 (0.19), residues: 736 sheet: -2.99 (0.53), residues: 83 loop : -2.24 (0.33), residues: 371 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 0.016 0.001 PHE D 323 TYR 0.015 0.001 TYR C 76 ARG 0.002 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 140 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 1.539 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: D 540 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7187 (tp) outliers start: 28 outliers final: 22 residues processed: 135 average time/residue: 0.4966 time to fit residues: 93.2617 Evaluate side-chains 132 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 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 123 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 210 VAL 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 298 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 538 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 70 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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: 0.6653 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10215 Z= 0.224 Angle : 0.516 5.703 13715 Z= 0.283 Chirality : 0.037 0.153 1511 Planarity : 0.004 0.041 1694 Dihedral : 13.406 168.030 1680 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.74 % Allowed : 24.83 % Favored : 72.43 % 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 (0.25), residues: 1190 helix: 0.54 (0.19), residues: 736 sheet: -3.03 (0.52), residues: 83 loop : -2.24 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 HIS 0.003 0.001 HIS D 448 PHE 0.018 0.001 PHE D 323 TYR 0.018 0.002 TYR C 19 ARG 0.002 0.000 ARG D 572 *********************** 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 136 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 540 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7189 (tp) outliers start: 28 outliers final: 24 residues processed: 133 average time/residue: 0.4665 time to fit residues: 87.8605 Evaluate side-chains 133 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 396 THR Chi-restraints excluded: chain C residue 538 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 95 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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: 0.6613 moved from start: 0.2139 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= 0.156 Angle : 0.494 5.788 13715 Z= 0.269 Chirality : 0.037 0.154 1511 Planarity : 0.004 0.041 1694 Dihedral : 12.983 162.740 1680 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.25 % Allowed : 25.32 % Favored : 72.43 % 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: -0.51 (0.26), residues: 1190 helix: 0.88 (0.20), residues: 735 sheet: -2.95 (0.52), residues: 83 loop : -2.14 (0.34), residues: 372 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 0.012 0.001 TYR C 76 ARG 0.003 0.000 ARG D 572 ********************** 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 133 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 540 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7181 (tp) outliers start: 23 outliers final: 18 residues processed: 129 average time/residue: 0.4740 time to fit residues: 86.7474 Evaluate side-chains 125 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 123 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 538 HIS 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: 0.8980 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.129556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.106957 restraints weight = 63604.926| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.14 r_work: 0.3930 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10215 Z= 0.200 Angle : 0.505 5.907 13715 Z= 0.276 Chirality : 0.037 0.151 1511 Planarity : 0.004 0.040 1694 Dihedral : 12.925 154.464 1680 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.35 % Allowed : 25.71 % Favored : 71.95 % 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: -0.59 (0.25), residues: 1190 helix: 0.79 (0.19), residues: 736 sheet: -2.98 (0.50), residues: 88 loop : -2.10 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 78 HIS 0.002 0.001 HIS C 100 PHE 0.017 0.001 PHE D 323 TYR 0.018 0.001 TYR C 19 ARG 0.002 0.000 ARG D 616 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4763.59 seconds wall clock time: 84 minutes 50.26 seconds (5090.26 seconds total)