Starting phenix.real_space_refine on Wed Jun 18 05:14:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t3k_41004/06_2025/8t3k_41004_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t3k_41004/06_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_41004/06_2025/8t3k_41004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t3k_41004/06_2025/8t3k_41004.map" model { file = "/net/cci-nas-00/data/ceres_data/8t3k_41004/06_2025/8t3k_41004_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t3k_41004/06_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-5710/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: 10.76, 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: 5.71 Conformation dependent library (CDL) restraints added in 1.5 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: 1.55 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: 6.67 Time building geometry restraints manager: 6.79 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: 0.010 Normalize map: mean=0, sd=1: 9.310 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: 0.380 Extract box with map and model: 0.910 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 44.680 Find NCS groups from input model: 0.130 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.760 ------------------------------------------------------------------------------- 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 : 1.764 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: 0.5270 time to fit residues: 93.3265 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 : 1.433 ------------------------------------------------------------------------------- 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 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.130145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.107588 restraints weight = 63952.880| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.11 r_work: 0.3938 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1170 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= 0.149 Angle : 0.563 5.717 13715 Z= 0.307 Chirality : 0.038 0.148 1511 Planarity : 0.004 0.045 1694 Dihedral : 16.312 171.956 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 : 0.68 % Allowed : 24.54 % 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 0.04804 ( 565) hydrogen bonds : angle 5.06838 ( 1653) covalent geometry : bond 0.00323 (10215) covalent geometry : angle 0.56279 (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 121 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 1.426 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: 0.6820 (t80) cc_final: 0.6579 (m-80) REVERT: C 2 PHE cc_start: 0.6011 (p90) cc_final: 0.5731 (p90) outliers start: 7 outliers final: 2 residues processed: 120 average time/residue: 0.5074 time to fit residues: 85.1473 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 : 1.450 ------------------------------------------------------------------------------- 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: 3.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 271 ASN C 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.128829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.106281 restraints weight = 63844.925| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.09 r_work: 0.3913 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10215 Z= 0.186 Angle : 0.561 5.608 13715 Z= 0.308 Chirality : 0.039 0.144 1511 Planarity : 0.004 0.044 1694 Dihedral : 15.518 175.361 1680 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.37 % Allowed : 23.95 % Favored : 74.68 % 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: -1.17 (0.24), residues: 1190 helix: 0.22 (0.19), residues: 732 sheet: -2.59 (0.58), residues: 73 loop : -2.26 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.004 0.001 HIS D 68 PHE 0.027 0.002 PHE D 323 TYR 0.020 0.002 TYR C 19 ARG 0.004 0.000 ARG D 616 Details of bonding type rmsd hydrogen bonds : bond 0.04508 ( 565) hydrogen bonds : angle 4.88282 ( 1653) covalent geometry : bond 0.00413 (10215) covalent geometry : angle 0.56128 (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 124 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 254 PHE cc_start: 0.6735 (t80) cc_final: 0.6480 (m-80) REVERT: C 2 PHE cc_start: 0.6201 (p90) cc_final: 0.5996 (p90) outliers start: 14 outliers final: 9 residues processed: 122 average time/residue: 0.5304 time to fit residues: 89.9294 Evaluate side-chains 115 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 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: 1.9990 chunk 45 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 HIS C 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.127818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.104957 restraints weight = 64372.668| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.15 r_work: 0.3885 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10215 Z= 0.241 Angle : 0.606 5.775 13715 Z= 0.333 Chirality : 0.040 0.144 1511 Planarity : 0.005 0.048 1694 Dihedral : 15.294 173.841 1680 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 3.13 % Allowed : 22.29 % 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: -1.59 (0.24), residues: 1190 helix: -0.14 (0.19), residues: 733 sheet: -2.88 (0.54), residues: 78 loop : -2.33 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 78 HIS 0.004 0.001 HIS D 307 PHE 0.029 0.002 PHE D 323 TYR 0.024 0.002 TYR C 76 ARG 0.006 0.001 ARG D 572 Details of bonding type rmsd hydrogen bonds : bond 0.04742 ( 565) hydrogen bonds : angle 4.96372 ( 1653) covalent geometry : bond 0.00541 (10215) covalent geometry : angle 0.60597 (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 145 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 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: 0.6751 (t80) cc_final: 0.6517 (m-80) REVERT: D 323 PHE cc_start: 0.6053 (OUTLIER) cc_final: 0.5723 (t80) REVERT: D 540 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7282 (tp) outliers start: 32 outliers final: 22 residues processed: 141 average time/residue: 0.5083 time to fit residues: 99.6812 Evaluate side-chains 132 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 321 SER 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 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 149 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.129055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.106151 restraints weight = 64184.161| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.18 r_work: 0.3912 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.1901 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= 0.148 Angle : 0.532 5.642 13715 Z= 0.292 Chirality : 0.038 0.147 1511 Planarity : 0.004 0.043 1694 Dihedral : 14.443 172.939 1680 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.35 % Allowed : 23.85 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.25), residues: 1190 helix: 0.29 (0.19), residues: 737 sheet: -2.81 (0.55), residues: 78 loop : -2.28 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 HIS 0.003 0.001 HIS D 46 PHE 0.020 0.001 PHE D 323 TYR 0.017 0.002 TYR C 76 ARG 0.003 0.000 ARG C 362 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 565) hydrogen bonds : angle 4.67910 ( 1653) covalent geometry : bond 0.00326 (10215) covalent geometry : angle 0.53232 (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 134 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.456 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: 0.6663 (t80) cc_final: 0.6453 (m-80) REVERT: D 323 PHE cc_start: 0.5934 (OUTLIER) cc_final: 0.5645 (t80) outliers start: 24 outliers final: 15 residues processed: 131 average time/residue: 0.5090 time to fit residues: 92.8655 Evaluate side-chains 124 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 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 435 VAL 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 240 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 538 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 49 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.128604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.105802 restraints weight = 63767.241| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.15 r_work: 0.3903 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10215 Z= 0.170 Angle : 0.540 5.656 13715 Z= 0.297 Chirality : 0.038 0.144 1511 Planarity : 0.004 0.043 1694 Dihedral : 14.077 172.643 1680 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.93 % Allowed : 23.46 % 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: -1.12 (0.25), residues: 1190 helix: 0.30 (0.19), residues: 737 sheet: -2.81 (0.55), residues: 78 loop : -2.30 (0.33), residues: 375 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 0.022 0.001 PHE D 323 TYR 0.019 0.002 TYR C 76 ARG 0.003 0.000 ARG C 362 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 565) hydrogen bonds : angle 4.63886 ( 1653) covalent geometry : bond 0.00381 (10215) covalent geometry : angle 0.53976 (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 138 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 1.478 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 323 PHE cc_start: 0.5976 (OUTLIER) cc_final: 0.5703 (t80) REVERT: D 484 LYS cc_start: 0.8415 (tppt) cc_final: 0.8209 (tppt) REVERT: D 540 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7269 (tp) outliers start: 30 outliers final: 22 residues processed: 132 average time/residue: 0.5208 time to fit residues: 95.7342 Evaluate side-chains 132 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 176 MET 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 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 D residue 540 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.129607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.107073 restraints weight = 63215.528| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.15 r_work: 0.3927 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2024 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= 0.126 Angle : 0.508 5.647 13715 Z= 0.278 Chirality : 0.037 0.152 1511 Planarity : 0.004 0.043 1694 Dihedral : 13.499 171.344 1680 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.35 % Allowed : 24.54 % 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: -0.77 (0.25), residues: 1190 helix: 0.61 (0.19), residues: 736 sheet: -2.73 (0.56), residues: 78 loop : -2.22 (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 46 PHE 0.018 0.001 PHE D 323 TYR 0.014 0.001 TYR C 76 ARG 0.001 0.000 ARG D 429 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 565) hydrogen bonds : angle 4.46001 ( 1653) covalent geometry : bond 0.00278 (10215) covalent geometry : angle 0.50826 (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 134 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.439 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 323 PHE cc_start: 0.5952 (OUTLIER) cc_final: 0.5730 (t80) REVERT: D 540 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7296 (tp) outliers start: 24 outliers final: 17 residues processed: 130 average time/residue: 0.5126 time to fit residues: 91.6446 Evaluate side-chains 125 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 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 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 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: 0.4980 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.128999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.106070 restraints weight = 64377.659| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.19 r_work: 0.3908 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10215 Z= 0.174 Angle : 0.538 6.002 13715 Z= 0.295 Chirality : 0.038 0.144 1511 Planarity : 0.004 0.042 1694 Dihedral : 13.616 170.469 1680 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.83 % Allowed : 24.34 % 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: -0.94 (0.25), residues: 1190 helix: 0.45 (0.19), residues: 736 sheet: -2.79 (0.55), residues: 78 loop : -2.23 (0.34), 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 448 PHE 0.022 0.001 PHE D 323 TYR 0.019 0.002 TYR C 19 ARG 0.002 0.000 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 565) hydrogen bonds : angle 4.55099 ( 1653) covalent geometry : bond 0.00390 (10215) covalent geometry : angle 0.53792 (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 141 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 323 PHE cc_start: 0.5982 (OUTLIER) cc_final: 0.5776 (t80) REVERT: D 540 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7299 (tp) outliers start: 29 outliers final: 21 residues processed: 137 average time/residue: 0.5188 time to fit residues: 98.0892 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 : 1.454 ------------------------------------------------------------------------------- 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 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 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 248 THR 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: 0.7980 chunk 76 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.129398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.106587 restraints weight = 64187.762| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.18 r_work: 0.3919 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2135 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= 0.146 Angle : 0.527 6.055 13715 Z= 0.287 Chirality : 0.037 0.144 1511 Planarity : 0.004 0.041 1694 Dihedral : 13.407 168.269 1680 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.54 % Allowed : 24.34 % 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: -0.79 (0.25), residues: 1190 helix: 0.58 (0.19), residues: 736 sheet: -2.75 (0.55), residues: 78 loop : -2.19 (0.34), 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 0.019 0.001 PHE D 323 TYR 0.016 0.001 TYR C 76 ARG 0.002 0.000 ARG C 362 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 565) hydrogen bonds : angle 4.48046 ( 1653) covalent geometry : bond 0.00326 (10215) covalent geometry : angle 0.52688 (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 134 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 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: symmetry clash REVERT: D 540 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7286 (tp) outliers start: 26 outliers final: 20 residues processed: 131 average time/residue: 0.5684 time to fit residues: 104.2376 Evaluate side-chains 127 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 368 SER 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 248 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 536 VAL 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: 1.9990 chunk 119 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 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: 3.9990 chunk 69 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.4393 r_free = 0.4393 target = 0.128807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.105875 restraints weight = 63902.497| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.17 r_work: 0.3906 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2210 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= 0.172 Angle : 0.543 6.037 13715 Z= 0.297 Chirality : 0.038 0.143 1511 Planarity : 0.004 0.041 1694 Dihedral : 13.453 165.448 1680 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.64 % Allowed : 24.63 % Favored : 72.73 % 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: -0.94 (0.25), residues: 1190 helix: 0.44 (0.19), residues: 736 sheet: -2.81 (0.55), residues: 78 loop : -2.20 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 78 HIS 0.003 0.001 HIS C 100 PHE 0.014 0.001 PHE D 516 TYR 0.019 0.002 TYR C 76 ARG 0.003 0.000 ARG C 362 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 565) hydrogen bonds : angle 4.54147 ( 1653) covalent geometry : bond 0.00385 (10215) covalent geometry : angle 0.54266 (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 133 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 323 PHE cc_start: 0.5911 (OUTLIER) cc_final: 0.5665 (t80) REVERT: D 540 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7291 (tp) outliers start: 27 outliers final: 23 residues processed: 129 average time/residue: 0.5326 time to fit residues: 95.2185 Evaluate side-chains 131 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.632 ------------------------------------------------------------------------------- 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 323 PHE Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 368 SER 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 248 THR 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 536 VAL 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: 0.0870 chunk 79 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 0.1980 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 = 0.4408 r_free = 0.4408 target = 0.129755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.107131 restraints weight = 64011.119| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.16 r_work: 0.3929 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2230 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= 0.124 Angle : 0.512 6.043 13715 Z= 0.278 Chirality : 0.037 0.152 1511 Planarity : 0.004 0.040 1694 Dihedral : 12.995 159.241 1680 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.86 % Allowed : 25.42 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.26), residues: 1190 helix: 0.77 (0.20), residues: 736 sheet: -2.70 (0.56), residues: 78 loop : -2.10 (0.34), 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 0.009 0.001 PHE D 323 TYR 0.014 0.001 TYR C 76 ARG 0.003 0.000 ARG C 362 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 565) hydrogen bonds : angle 4.37656 ( 1653) covalent geometry : bond 0.00273 (10215) covalent geometry : angle 0.51200 (13715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11439.33 seconds wall clock time: 194 minutes 33.54 seconds (11673.54 seconds total)