Starting phenix.real_space_refine on Wed May 21 02:24:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3k_41004/05_2025/8t3k_41004_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3k_41004/05_2025/8t3k_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/cci-nas-00/data/ceres_data/8t3k_41004/05_2025/8t3k_41004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3k_41004/05_2025/8t3k_41004.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3k_41004/05_2025/8t3k_41004_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3k_41004/05_2025/8t3k_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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.67, per 1000 atoms: 0.54 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.23 Conformation dependent library (CDL) restraints added in 1.4 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: 1.45 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: 7.89 Time building geometry restraints manager: 6.32 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: 0.00 - 13.01: 35754 13.01 - 26.02: 12 26.02 - 39.03: 2 39.03 - 52.04: 1 52.04 - 65.05: 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 2.450 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 Time spend for trying shortcut: 0.00 ========== 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: 10.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.310 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 44.500 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.900 ------------------------------------------------------------------------------- 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= 0.396 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 Details of bonding type rmsd hydrogen bonds : bond 0.13763 ( 565) hydrogen bonds : angle 6.78620 ( 1653) covalent geometry : bond 0.00755 (10215) covalent geometry : angle 1.05875 (13715) *********************** 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 to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 1.563 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: 0.5312 time to fit residues: 93.5395 Evaluate side-chains 111 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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: 0.7980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 271 ASN C 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.130142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.107637 restraints weight = 63958.417| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.10 r_work: 0.3940 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1176 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= 0.150 Angle : 0.563 5.721 13715 Z= 0.307 Chirality : 0.038 0.148 1511 Planarity : 0.004 0.045 1694 Dihedral : 16.308 171.952 1681 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.78 % Allowed : 24.44 % 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: -1.04 (0.25), residues: 1190 helix: 0.35 (0.19), residues: 731 sheet: -2.35 (0.58), residues: 73 loop : -2.29 (0.32), residues: 386 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 0.023 0.001 PHE D 323 TYR 0.015 0.001 TYR C 19 ARG 0.005 0.000 ARG D 616 Details of bonding type rmsd hydrogen bonds : bond 0.04802 ( 565) hydrogen bonds : angle 5.06743 ( 1653) covalent geometry : bond 0.00322 (10215) covalent geometry : angle 0.56266 (13715) *********************** 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 122 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 1.505 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 254 PHE cc_start: 0.6798 (t80) cc_final: 0.6562 (m-80) REVERT: C 2 PHE cc_start: 0.5992 (p90) cc_final: 0.5711 (p90) outliers start: 8 outliers final: 2 residues processed: 121 average time/residue: 0.4999 time to fit residues: 84.1308 Evaluate side-chains 112 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 15 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 HIS D 523 ASN C 87 ASN C 282 ASN C 557 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.128164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.105264 restraints weight = 63551.954| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.14 r_work: 0.3889 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10215 Z= 0.243 Angle : 0.610 5.733 13715 Z= 0.336 Chirality : 0.040 0.144 1511 Planarity : 0.005 0.049 1694 Dihedral : 15.865 175.640 1680 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.25 % Allowed : 23.46 % 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: -1.56 (0.24), residues: 1190 helix: -0.12 (0.19), residues: 732 sheet: -2.72 (0.56), residues: 73 loop : -2.35 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 78 HIS 0.005 0.001 HIS D 68 PHE 0.030 0.002 PHE D 323 TYR 0.024 0.002 TYR C 76 ARG 0.005 0.001 ARG D 616 Details of bonding type rmsd hydrogen bonds : bond 0.04873 ( 565) hydrogen bonds : angle 5.06132 ( 1653) covalent geometry : bond 0.00542 (10215) covalent geometry : angle 0.60973 (13715) *********************** 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 134 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 254 PHE cc_start: 0.6828 (t80) cc_final: 0.6570 (m-80) REVERT: D 323 PHE cc_start: 0.5951 (OUTLIER) cc_final: 0.5677 (t80) REVERT: C 2 PHE cc_start: 0.6330 (p90) cc_final: 0.6124 (p90) outliers start: 23 outliers final: 16 residues processed: 130 average time/residue: 0.5050 time to fit residues: 90.8526 Evaluate side-chains 122 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 323 PHE Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 368 SER 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 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 256 SER Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 396 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.0770 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- 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 = 0.4412 r_free = 0.4412 target = 0.129940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.107167 restraints weight = 63988.945| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.18 r_work: 0.3930 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1677 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= 0.131 Angle : 0.526 5.615 13715 Z= 0.288 Chirality : 0.037 0.147 1511 Planarity : 0.004 0.044 1694 Dihedral : 14.941 174.082 1680 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 1.17 % Allowed : 24.05 % 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: -0.95 (0.25), residues: 1190 helix: 0.43 (0.19), residues: 732 sheet: -2.66 (0.56), residues: 78 loop : -2.21 (0.33), residues: 380 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 0.014 0.001 TYR C 76 ARG 0.002 0.000 ARG C 222 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 565) hydrogen bonds : angle 4.68564 ( 1653) covalent geometry : bond 0.00289 (10215) covalent geometry : angle 0.52619 (13715) *********************** 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 124 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 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: D 254 PHE cc_start: 0.6691 (t80) cc_final: 0.6458 (m-80) outliers start: 12 outliers final: 9 residues processed: 122 average time/residue: 0.5337 time to fit residues: 89.6885 Evaluate side-chains 118 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 C residue 76 TYR Chi-restraints excluded: chain C residue 197 LEU 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 538 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 38 optimal weight: 0.0050 chunk 13 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 overall best weight: 1.0398 ------------------------------------------------------------------------------- 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 = 0.4406 r_free = 0.4406 target = 0.129608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.106896 restraints weight = 64034.337| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.16 r_work: 0.3923 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1801 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= 0.145 Angle : 0.523 5.648 13715 Z= 0.286 Chirality : 0.037 0.146 1511 Planarity : 0.004 0.043 1694 Dihedral : 14.528 174.666 1680 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.86 % Allowed : 23.26 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1190 helix: 0.46 (0.19), residues: 735 sheet: -2.71 (0.56), residues: 78 loop : -2.23 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.002 0.001 HIS C 100 PHE 0.024 0.001 PHE D 323 TYR 0.017 0.002 TYR C 19 ARG 0.002 0.000 ARG C 362 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 565) hydrogen bonds : angle 4.61139 ( 1653) covalent geometry : bond 0.00321 (10215) covalent geometry : angle 0.52321 (13715) *********************** 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 127 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 323 PHE cc_start: 0.5903 (OUTLIER) cc_final: 0.5660 (t80) REVERT: D 540 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7233 (tp) outliers start: 19 outliers final: 12 residues processed: 124 average time/residue: 0.5383 time to fit residues: 92.5366 Evaluate side-chains 119 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 323 PHE 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 540 LEU 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 274 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4411 r_free = 0.4411 target = 0.129862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.107272 restraints weight = 63617.968| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.15 r_work: 0.3933 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1918 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= 0.129 Angle : 0.510 5.661 13715 Z= 0.278 Chirality : 0.037 0.145 1511 Planarity : 0.004 0.043 1694 Dihedral : 13.764 174.186 1680 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.15 % Allowed : 23.66 % 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: -0.69 (0.25), residues: 1190 helix: 0.66 (0.20), residues: 737 sheet: -2.68 (0.56), residues: 78 loop : -2.16 (0.33), residues: 375 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 0.021 0.001 PHE D 323 TYR 0.014 0.001 TYR C 19 ARG 0.005 0.000 ARG D 572 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 565) hydrogen bonds : angle 4.48226 ( 1653) covalent geometry : bond 0.00285 (10215) covalent geometry : angle 0.50966 (13715) *********************** 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 132 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 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: symmetry clash REVERT: D 540 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7272 (tp) outliers start: 22 outliers final: 15 residues processed: 130 average time/residue: 0.5318 time to fit residues: 94.9792 Evaluate side-chains 123 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 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 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 538 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 117 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 111 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.4416 r_free = 0.4416 target = 0.130225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.107599 restraints weight = 63441.188| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.16 r_work: 0.3936 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1978 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= 0.122 Angle : 0.499 5.698 13715 Z= 0.273 Chirality : 0.037 0.150 1511 Planarity : 0.004 0.042 1694 Dihedral : 13.482 174.048 1680 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.25 % Allowed : 23.56 % 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: -0.57 (0.25), residues: 1190 helix: 0.78 (0.20), residues: 735 sheet: -2.63 (0.56), residues: 78 loop : -2.14 (0.33), residues: 377 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 0.020 0.001 PHE D 323 TYR 0.014 0.001 TYR C 19 ARG 0.004 0.000 ARG D 572 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 565) hydrogen bonds : angle 4.39998 ( 1653) covalent geometry : bond 0.00269 (10215) covalent geometry : angle 0.49886 (13715) *********************** 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 132 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 196 MET cc_start: 0.8774 (mmt) cc_final: 0.8390 (mmt) REVERT: D 484 LYS cc_start: 0.8377 (tppt) cc_final: 0.8169 (tppt) REVERT: D 540 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7280 (tp) outliers start: 23 outliers final: 18 residues processed: 130 average time/residue: 0.5307 time to fit residues: 95.0848 Evaluate side-chains 124 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 C residue 76 TYR Chi-restraints excluded: chain C residue 123 ASN 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 538 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 12 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4395 r_free = 0.4395 target = 0.128881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.106037 restraints weight = 63966.928| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.17 r_work: 0.3907 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10215 Z= 0.180 Angle : 0.541 5.748 13715 Z= 0.296 Chirality : 0.038 0.142 1511 Planarity : 0.004 0.041 1694 Dihedral : 13.710 173.277 1680 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.64 % Allowed : 23.75 % Favored : 73.61 % 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: -0.88 (0.25), residues: 1190 helix: 0.50 (0.19), residues: 736 sheet: -2.73 (0.56), residues: 78 loop : -2.21 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.003 0.001 HIS D 505 PHE 0.024 0.002 PHE D 323 TYR 0.020 0.002 TYR C 76 ARG 0.003 0.000 ARG D 572 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 565) hydrogen bonds : angle 4.54222 ( 1653) covalent geometry : bond 0.00406 (10215) covalent geometry : angle 0.54086 (13715) *********************** 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 138 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 196 MET cc_start: 0.8796 (mmt) cc_final: 0.8423 (mmt) REVERT: D 323 PHE cc_start: 0.5971 (OUTLIER) cc_final: 0.5763 (t80) REVERT: D 540 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7284 (tp) outliers start: 27 outliers final: 20 residues processed: 135 average time/residue: 0.5273 time to fit residues: 98.1850 Evaluate side-chains 130 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.444 ------------------------------------------------------------------------------- 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 323 PHE 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 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 519 GLU 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 9 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4407 r_free = 0.4407 target = 0.129623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.106899 restraints weight = 63858.767| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.16 r_work: 0.3924 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2119 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= 0.143 Angle : 0.517 6.022 13715 Z= 0.282 Chirality : 0.037 0.144 1511 Planarity : 0.004 0.041 1694 Dihedral : 13.439 170.940 1680 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.35 % Allowed : 23.95 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.25), residues: 1190 helix: 0.67 (0.19), residues: 736 sheet: -2.72 (0.56), residues: 78 loop : -2.16 (0.33), residues: 376 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 0.020 0.001 PHE D 323 TYR 0.016 0.002 TYR C 76 ARG 0.002 0.000 ARG D 579 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 565) hydrogen bonds : angle 4.45387 ( 1653) covalent geometry : bond 0.00319 (10215) covalent geometry : angle 0.51742 (13715) *********************** 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 133 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 196 MET cc_start: 0.8781 (mmt) cc_final: 0.8415 (mmt) REVERT: D 540 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7269 (tp) outliers start: 24 outliers final: 19 residues processed: 130 average time/residue: 0.5502 time to fit residues: 99.1143 Evaluate side-chains 128 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 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 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 519 GLU 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 65 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4402 r_free = 0.4402 target = 0.129293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.106487 restraints weight = 63740.244| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.15 r_work: 0.3918 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10215 Z= 0.162 Angle : 0.530 6.030 13715 Z= 0.290 Chirality : 0.038 0.143 1511 Planarity : 0.004 0.042 1694 Dihedral : 13.406 168.224 1680 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.25 % Allowed : 24.24 % Favored : 73.51 % 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: -0.77 (0.25), residues: 1190 helix: 0.60 (0.19), residues: 736 sheet: -2.72 (0.56), residues: 78 loop : -2.18 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.002 0.001 HIS C 100 PHE 0.014 0.001 PHE D 315 TYR 0.018 0.002 TYR C 76 ARG 0.002 0.000 ARG D 572 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 565) hydrogen bonds : angle 4.48640 ( 1653) covalent geometry : bond 0.00363 (10215) covalent geometry : angle 0.53006 (13715) ********************** 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 134 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 196 MET cc_start: 0.8772 (mmt) cc_final: 0.8430 (mmt) REVERT: D 540 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7295 (tp) outliers start: 23 outliers final: 20 residues processed: 131 average time/residue: 0.5229 time to fit residues: 94.4435 Evaluate side-chains 131 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.523 ------------------------------------------------------------------------------- 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 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 519 GLU 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 14 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.129494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.106770 restraints weight = 64093.111| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.17 r_work: 0.3921 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2222 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= 0.145 Angle : 0.519 6.063 13715 Z= 0.283 Chirality : 0.037 0.153 1511 Planarity : 0.004 0.042 1694 Dihedral : 13.209 162.734 1680 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.35 % Allowed : 24.34 % 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: -0.64 (0.25), residues: 1190 helix: 0.71 (0.20), residues: 736 sheet: -2.71 (0.56), residues: 78 loop : -2.15 (0.33), residues: 376 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 315 TYR 0.016 0.002 TYR C 76 ARG 0.002 0.000 ARG D 433 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 565) hydrogen bonds : angle 4.43224 ( 1653) covalent geometry : bond 0.00322 (10215) covalent geometry : angle 0.51885 (13715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10968.38 seconds wall clock time: 188 minutes 57.75 seconds (11337.75 seconds total)