Starting phenix.real_space_refine on Fri Feb 6 05:00:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cup_45938/02_2026/9cup_45938_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cup_45938/02_2026/9cup_45938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cup_45938/02_2026/9cup_45938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cup_45938/02_2026/9cup_45938.map" model { file = "/net/cci-nas-00/data/ceres_data/9cup_45938/02_2026/9cup_45938_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cup_45938/02_2026/9cup_45938_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 31 5.49 5 Mg 1 5.21 5 S 43 5.16 5 C 7144 2.51 5 N 1702 2.21 5 O 2027 1.98 5 H 10017 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20965 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 10750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 10750 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 13, 'TRANS': 654} Chain: "C" Number of atoms: 9146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 9146 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 19, 'TRANS': 557} Chain: "D" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 472 Unusual residues: {' MG': 1, 'ATP': 1, 'POV': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 5, 'POV:plan-2': 1, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 597 Unusual residues: {'ATP': 1, 'HT1': 2, 'POV': 13} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 5, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 3.30, per 1000 atoms: 0.16 Number of scatterers: 20965 At special positions: 0 Unit cell: (79.581, 102.873, 155.927, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 43 16.00 P 31 15.00 Mg 1 11.99 O 2027 8.00 N 1702 7.00 C 7144 6.00 H 10017 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: 1.97 Conformation dependent library (CDL) restraints added in 561.4 milliseconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 6 sheets defined 65.5% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.628A pdb=" N LEU D 13 " --> pdb=" O ARG D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 45 removed outlier: 3.890A pdb=" N LEU D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) Proline residue: D 36 - end of helix Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 145 through 195 Processing helix chain 'D' and resid 197 through 204 removed outlier: 3.629A pdb=" N PHE D 201 " --> pdb=" O PRO D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 231 removed outlier: 3.568A pdb=" N VAL D 209 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR D 217 " --> pdb=" O ILE D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 249 removed outlier: 3.634A pdb=" N ILE D 241 " --> pdb=" O TYR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 297 removed outlier: 3.830A pdb=" N PHE D 254 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N CYS D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Proline residue: D 261 - end of helix removed outlier: 3.843A pdb=" N TYR D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 310 through 362 removed outlier: 4.644A pdb=" N ASN D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU D 340 " --> pdb=" O MET D 336 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN D 362 " --> pdb=" O GLY D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 383 removed outlier: 3.587A pdb=" N LEU D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG D 381 " --> pdb=" O ASP D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 411 removed outlier: 5.280A pdb=" N GLU D 397 " --> pdb=" O PHE D 393 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 477 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 505 Processing helix chain 'D' and resid 519 through 526 Processing helix chain 'D' and resid 534 through 540 removed outlier: 3.515A pdb=" N LEU D 540 " --> pdb=" O ILE D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 550 Processing helix chain 'D' and resid 559 through 563 removed outlier: 3.576A pdb=" N GLU D 562 " --> pdb=" O PRO D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 584 removed outlier: 3.573A pdb=" N PHE D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP D 584 " --> pdb=" O ALA D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 614 removed outlier: 4.706A pdb=" N ALA D 608 " --> pdb=" O VAL D 604 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 614 " --> pdb=" O ASP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 629 removed outlier: 3.656A pdb=" N ILE D 628 " --> pdb=" O ARG D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 655 Processing helix chain 'D' and resid 657 through 669 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 8 through 15 Processing helix chain 'C' and resid 16 through 33 Processing helix chain 'C' and resid 34 through 49 removed outlier: 3.952A pdb=" N LYS C 38 " --> pdb=" O MET C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 104 Processing helix chain 'C' and resid 105 through 112 removed outlier: 3.659A pdb=" N TYR C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 123 through 144 removed outlier: 4.051A pdb=" N ILE C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 157 Processing helix chain 'C' and resid 160 through 165 Processing helix chain 'C' and resid 167 through 207 removed outlier: 3.961A pdb=" N VAL C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 218 through 243 removed outlier: 3.895A pdb=" N ILE C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 269 removed outlier: 3.787A pdb=" N SER C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 267 " --> pdb=" O TYR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 289 Processing helix chain 'C' and resid 290 through 317 removed outlier: 3.868A pdb=" N GLY C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 385 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 427 through 433 Processing helix chain 'C' and resid 442 through 451 Processing helix chain 'C' and resid 453 through 460 removed outlier: 3.692A pdb=" N MET C 459 " --> pdb=" O LYS C 455 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 491 Processing helix chain 'C' and resid 506 through 521 Processing helix chain 'C' and resid 555 through 562 Processing helix chain 'C' and resid 566 through 578 removed outlier: 3.569A pdb=" N GLN C 573 " --> pdb=" O GLN C 569 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 574 " --> pdb=" O TYR C 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AA2, first strand: chain 'D' and resid 110 through 111 Processing sheet with id=AA3, first strand: chain 'D' and resid 444 through 453 removed outlier: 7.026A pdb=" N VAL D 445 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA D 438 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS D 447 " --> pdb=" O SER D 436 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N SER D 436 " --> pdb=" O LYS D 447 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE D 449 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP D 434 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 430 " --> pdb=" O ALA D 453 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N PHE D 432 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU D 488 " --> pdb=" O PHE D 432 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP D 434 " --> pdb=" O ASP D 486 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 506 through 509 removed outlier: 3.783A pdb=" N VAL D 509 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA D 460 " --> pdb=" O LEU D 635 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU D 637 " --> pdb=" O ALA D 460 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL D 462 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 636 " --> pdb=" O GLU D 644 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU D 644 " --> pdb=" O VAL D 636 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 339 removed outlier: 3.569A pdb=" N VAL C 338 " --> pdb=" O THR C 396 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 400 " --> pdb=" O PHE C 397 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 414 through 417 removed outlier: 6.406A pdb=" N LEU C 496 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU C 529 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU C 498 " --> pdb=" O LEU C 529 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY C 368 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET C 545 " --> pdb=" O GLY C 368 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA C 370 " --> pdb=" O MET C 545 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1821 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: 4.98 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10014 1.03 - 1.23: 62 1.23 - 1.42: 4372 1.42 - 1.62: 6570 1.62 - 1.81: 129 Bond restraints: 21147 Sorted by residual: bond pdb=" NZ LYS D 613 " pdb=" HZ2 LYS D 613 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS D 291 " pdb=" HZ1 LYS D 291 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS C 13 " pdb=" HZ2 LYS C 13 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS D 41 " pdb=" HZ3 LYS D 41 " ideal model delta sigma weight residual 0.890 0.970 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS D 469 " pdb=" HZ1 LYS D 469 " ideal model delta sigma weight residual 0.890 0.970 -0.080 2.00e-02 2.50e+03 1.62e+01 ... (remaining 21142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 35558 2.57 - 5.13: 2017 5.13 - 7.70: 44 7.70 - 10.27: 1 10.27 - 12.83: 1 Bond angle restraints: 37621 Sorted by residual: angle pdb=" PB ATP D 714 " pdb=" O3B ATP D 714 " pdb=" PG ATP D 714 " ideal model delta sigma weight residual 139.87 127.04 12.83 1.00e+00 1.00e+00 1.65e+02 angle pdb=" PA ATP D 714 " pdb=" O3A ATP D 714 " pdb=" PB ATP D 714 " ideal model delta sigma weight residual 136.83 130.29 6.54 1.00e+00 1.00e+00 4.27e+01 angle pdb=" N SER D 470 " pdb=" CA SER D 470 " pdb=" C SER D 470 " ideal model delta sigma weight residual 112.38 106.97 5.41 1.22e+00 6.72e-01 1.96e+01 angle pdb=" CA TYR D 276 " pdb=" C TYR D 276 " pdb=" O TYR D 276 " ideal model delta sigma weight residual 120.82 116.42 4.40 1.05e+00 9.07e-01 1.76e+01 angle pdb=" C ASN C 235 " pdb=" CA ASN C 235 " pdb=" CB ASN C 235 " ideal model delta sigma weight residual 110.67 118.63 -7.96 1.92e+00 2.71e-01 1.72e+01 ... (remaining 37616 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.90: 9348 28.90 - 57.80: 740 57.80 - 86.70: 82 86.70 - 115.60: 17 115.60 - 144.50: 8 Dihedral angle restraints: 10195 sinusoidal: 5917 harmonic: 4278 Sorted by residual: dihedral pdb=" CA SER D 337 " pdb=" C SER D 337 " pdb=" N HIS D 338 " pdb=" CA HIS D 338 " ideal model delta harmonic sigma weight residual -180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" C29 POV C 608 " pdb="C210 POV C 608 " pdb="C211 POV C 608 " pdb="C212 POV C 608 " ideal model delta sinusoidal sigma weight residual 112.25 -103.25 -144.50 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C27 POV D 707 " pdb=" C28 POV D 707 " pdb=" C29 POV D 707 " pdb="C210 POV D 707 " ideal model delta sinusoidal sigma weight residual 127.48 -95.63 -136.89 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 10192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1351 0.059 - 0.118: 199 0.118 - 0.177: 21 0.177 - 0.236: 1 0.236 - 0.295: 3 Chirality restraints: 1575 Sorted by residual: chirality pdb=" C2' ATP C 614 " pdb=" C1' ATP C 614 " pdb=" C3' ATP C 614 " pdb=" O2' ATP C 614 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.29 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C3' ATP C 614 " pdb=" C2' ATP C 614 " pdb=" C4' ATP C 614 " pdb=" O3' ATP C 614 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C4' ATP C 614 " pdb=" C3' ATP C 614 " pdb=" C5' ATP C 614 " pdb=" O4' ATP C 614 " both_signs ideal model delta sigma weight residual False -2.49 -2.76 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1572 not shown) Planarity restraints: 3011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 131 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.29e+00 pdb=" C THR C 131 " -0.047 2.00e-02 2.50e+03 pdb=" O THR C 131 " 0.018 2.00e-02 2.50e+03 pdb=" N THR C 132 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 35 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO D 36 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 36 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 36 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 538 " 0.003 2.00e-02 2.50e+03 1.31e-02 3.88e+00 pdb=" CG HIS C 538 " 0.027 2.00e-02 2.50e+03 pdb=" ND1 HIS C 538 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS C 538 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS C 538 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 538 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 HIS C 538 " -0.021 2.00e-02 2.50e+03 pdb=" HD2 HIS C 538 " -0.019 2.00e-02 2.50e+03 pdb=" HE1 HIS C 538 " 0.004 2.00e-02 2.50e+03 ... (remaining 3008 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 512 2.10 - 2.72: 35229 2.72 - 3.35: 59919 3.35 - 3.97: 75193 3.97 - 4.60: 119477 Nonbonded interactions: 290330 Sorted by model distance: nonbonded pdb="HD21 LEU D 18 " pdb=" HG SER D 177 " model vdw 1.471 2.270 nonbonded pdb=" OE1 GLU D 417 " pdb=" H GLU D 417 " model vdw 1.572 2.450 nonbonded pdb=" HH TYR D 270 " pdb=" OD1 ASN D 333 " model vdw 1.607 2.450 nonbonded pdb=" O MET D 196 " pdb="HH12 ARG C 212 " model vdw 1.611 2.450 nonbonded pdb=" HE1 MET D 299 " pdb="HD23 LEU C 102 " model vdw 1.614 2.440 ... (remaining 290325 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: 6.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.470 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 20.190 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.004 0.053 11130 Z= 0.227 Angle : 0.638 12.834 14902 Z= 0.373 Chirality : 0.042 0.295 1575 Planarity : 0.004 0.049 1800 Dihedral : 21.561 144.499 4533 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.28 % Allowed : 23.91 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.24), residues: 1241 helix: 0.99 (0.19), residues: 770 sheet: -1.27 (0.61), residues: 80 loop : -2.64 (0.27), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 487 TYR 0.011 0.001 TYR D 200 PHE 0.014 0.001 PHE C 145 TRP 0.013 0.001 TRP C 78 HIS 0.012 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00440 (11130) covalent geometry : angle 0.63777 (14902) hydrogen bonds : bond 0.14466 ( 616) hydrogen bonds : angle 6.13598 ( 1821) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 117 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 119 average time/residue: 0.2443 time to fit residues: 41.5048 Evaluate side-chains 113 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 432 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 117 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: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.118224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.090984 restraints weight = 55349.956| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.14 r_work: 0.3397 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.0555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11130 Z= 0.171 Angle : 0.565 6.652 14902 Z= 0.300 Chirality : 0.039 0.152 1575 Planarity : 0.004 0.050 1800 Dihedral : 20.006 138.602 2181 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.70 % Allowed : 23.35 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.24), residues: 1241 helix: 1.18 (0.18), residues: 798 sheet: -1.22 (0.62), residues: 76 loop : -2.79 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 212 TYR 0.017 0.001 TYR D 200 PHE 0.014 0.001 PHE D 323 TRP 0.013 0.001 TRP C 78 HIS 0.010 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00384 (11130) covalent geometry : angle 0.56545 (14902) hydrogen bonds : bond 0.05247 ( 616) hydrogen bonds : angle 5.02178 ( 1821) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.613 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: C 321 ASP cc_start: 0.6791 (p0) cc_final: 0.6540 (p0) outliers start: 18 outliers final: 14 residues processed: 127 average time/residue: 0.2499 time to fit residues: 45.3895 Evaluate side-chains 123 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 596 HIS Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 559 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 64 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 69 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.118753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.091184 restraints weight = 55603.114| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.20 r_work: 0.3404 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11130 Z= 0.135 Angle : 0.513 7.430 14902 Z= 0.272 Chirality : 0.038 0.153 1575 Planarity : 0.004 0.052 1800 Dihedral : 18.825 134.703 2179 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.98 % Allowed : 23.91 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.24), residues: 1241 helix: 1.43 (0.19), residues: 789 sheet: -1.35 (0.61), residues: 76 loop : -2.82 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 487 TYR 0.015 0.001 TYR D 200 PHE 0.011 0.001 PHE C 339 TRP 0.013 0.001 TRP C 78 HIS 0.009 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00300 (11130) covalent geometry : angle 0.51294 (14902) hydrogen bonds : bond 0.04726 ( 616) hydrogen bonds : angle 4.72675 ( 1821) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 321 ASP cc_start: 0.6741 (p0) cc_final: 0.6485 (p0) outliers start: 21 outliers final: 16 residues processed: 129 average time/residue: 0.2206 time to fit residues: 41.2143 Evaluate side-chains 126 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 427 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.118612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.091035 restraints weight = 55522.123| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.20 r_work: 0.3395 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11130 Z= 0.145 Angle : 0.516 8.900 14902 Z= 0.272 Chirality : 0.038 0.151 1575 Planarity : 0.004 0.052 1800 Dihedral : 18.445 133.225 2179 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.98 % Allowed : 24.29 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.24), residues: 1241 helix: 1.45 (0.19), residues: 792 sheet: -1.36 (0.60), residues: 76 loop : -2.81 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 553 TYR 0.014 0.001 TYR D 200 PHE 0.013 0.001 PHE D 323 TRP 0.013 0.001 TRP C 78 HIS 0.007 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00325 (11130) covalent geometry : angle 0.51553 (14902) hydrogen bonds : bond 0.04616 ( 616) hydrogen bonds : angle 4.66679 ( 1821) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 321 ASP cc_start: 0.6759 (p0) cc_final: 0.6481 (p0) outliers start: 21 outliers final: 18 residues processed: 128 average time/residue: 0.2062 time to fit residues: 38.7478 Evaluate side-chains 128 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 559 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 61 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 0.0040 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 0.0270 chunk 73 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.4252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.119606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.092212 restraints weight = 55146.638| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.20 r_work: 0.3422 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11130 Z= 0.107 Angle : 0.483 5.506 14902 Z= 0.257 Chirality : 0.037 0.151 1575 Planarity : 0.004 0.053 1800 Dihedral : 17.576 128.619 2179 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.55 % Allowed : 23.82 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.24), residues: 1241 helix: 1.71 (0.19), residues: 788 sheet: -1.33 (0.60), residues: 76 loop : -2.74 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 518 TYR 0.011 0.001 TYR D 200 PHE 0.010 0.001 PHE C 339 TRP 0.013 0.001 TRP C 78 HIS 0.012 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00231 (11130) covalent geometry : angle 0.48256 (14902) hydrogen bonds : bond 0.04287 ( 616) hydrogen bonds : angle 4.46184 ( 1821) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 321 ASP cc_start: 0.6670 (p0) cc_final: 0.6392 (p0) outliers start: 27 outliers final: 19 residues processed: 136 average time/residue: 0.2106 time to fit residues: 42.0111 Evaluate side-chains 131 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 596 HIS Chi-restraints excluded: chain D residue 648 HIS Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 559 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN C 431 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.119279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.091825 restraints weight = 55637.766| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.20 r_work: 0.3413 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11130 Z= 0.122 Angle : 0.484 5.478 14902 Z= 0.258 Chirality : 0.038 0.150 1575 Planarity : 0.004 0.053 1800 Dihedral : 17.365 125.897 2179 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.46 % Allowed : 23.82 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1241 helix: 1.73 (0.19), residues: 789 sheet: -1.28 (0.63), residues: 66 loop : -2.77 (0.27), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 518 TYR 0.012 0.001 TYR D 200 PHE 0.011 0.001 PHE D 323 TRP 0.013 0.001 TRP C 78 HIS 0.010 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00270 (11130) covalent geometry : angle 0.48430 (14902) hydrogen bonds : bond 0.04318 ( 616) hydrogen bonds : angle 4.43578 ( 1821) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 321 ASP cc_start: 0.6685 (p0) cc_final: 0.6403 (p0) REVERT: C 445 GLN cc_start: 0.8675 (tp40) cc_final: 0.8392 (tp40) outliers start: 26 outliers final: 24 residues processed: 133 average time/residue: 0.2129 time to fit residues: 41.1259 Evaluate side-chains 136 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 648 HIS Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 559 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.119102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.091800 restraints weight = 55429.605| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.18 r_work: 0.3412 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11130 Z= 0.128 Angle : 0.487 5.530 14902 Z= 0.261 Chirality : 0.038 0.151 1575 Planarity : 0.004 0.053 1800 Dihedral : 17.267 124.093 2179 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.55 % Allowed : 23.82 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.24), residues: 1241 helix: 1.73 (0.19), residues: 789 sheet: -1.28 (0.63), residues: 66 loop : -2.74 (0.27), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 518 TYR 0.012 0.001 TYR D 200 PHE 0.012 0.001 PHE D 323 TRP 0.013 0.001 TRP C 78 HIS 0.009 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00286 (11130) covalent geometry : angle 0.48732 (14902) hydrogen bonds : bond 0.04336 ( 616) hydrogen bonds : angle 4.42499 ( 1821) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 321 ASP cc_start: 0.6664 (p0) cc_final: 0.6377 (p0) outliers start: 27 outliers final: 27 residues processed: 136 average time/residue: 0.2012 time to fit residues: 39.9652 Evaluate side-chains 138 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 596 HIS Chi-restraints excluded: chain D residue 648 HIS Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 559 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 55 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 119 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.118992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.091603 restraints weight = 55448.730| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.20 r_work: 0.3409 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11130 Z= 0.136 Angle : 0.495 5.584 14902 Z= 0.266 Chirality : 0.038 0.166 1575 Planarity : 0.004 0.053 1800 Dihedral : 17.180 122.201 2179 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.65 % Allowed : 23.35 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.24), residues: 1241 helix: 1.71 (0.19), residues: 789 sheet: -1.29 (0.63), residues: 66 loop : -2.75 (0.27), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 518 TYR 0.012 0.001 TYR D 200 PHE 0.012 0.001 PHE D 323 TRP 0.013 0.001 TRP C 78 HIS 0.009 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00307 (11130) covalent geometry : angle 0.49535 (14902) hydrogen bonds : bond 0.04364 ( 616) hydrogen bonds : angle 4.42917 ( 1821) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 321 ASP cc_start: 0.6676 (p0) cc_final: 0.6391 (p0) outliers start: 28 outliers final: 26 residues processed: 136 average time/residue: 0.2319 time to fit residues: 46.0445 Evaluate side-chains 142 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 648 HIS Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 559 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 80 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.117848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.090304 restraints weight = 55674.276| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.20 r_work: 0.3385 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11130 Z= 0.183 Angle : 0.532 6.238 14902 Z= 0.284 Chirality : 0.039 0.152 1575 Planarity : 0.004 0.052 1800 Dihedral : 17.410 118.594 2179 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.93 % Allowed : 23.06 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.24), residues: 1241 helix: 1.54 (0.18), residues: 792 sheet: -1.35 (0.64), residues: 66 loop : -2.79 (0.27), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 518 TYR 0.016 0.001 TYR D 200 PHE 0.015 0.001 PHE D 323 TRP 0.014 0.001 TRP C 78 HIS 0.009 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00423 (11130) covalent geometry : angle 0.53218 (14902) hydrogen bonds : bond 0.04648 ( 616) hydrogen bonds : angle 4.56010 ( 1821) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 321 ASP cc_start: 0.6728 (p0) cc_final: 0.6429 (p0) outliers start: 31 outliers final: 29 residues processed: 140 average time/residue: 0.1992 time to fit residues: 41.0081 Evaluate side-chains 142 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 596 HIS Chi-restraints excluded: chain D residue 648 HIS Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 559 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 8 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.118390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.090865 restraints weight = 55734.563| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.21 r_work: 0.3398 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11130 Z= 0.150 Angle : 0.508 6.118 14902 Z= 0.273 Chirality : 0.038 0.151 1575 Planarity : 0.004 0.053 1800 Dihedral : 17.186 116.906 2179 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.55 % Allowed : 23.35 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.24), residues: 1241 helix: 1.60 (0.19), residues: 792 sheet: -1.35 (0.63), residues: 66 loop : -2.76 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 518 TYR 0.014 0.001 TYR D 200 PHE 0.012 0.001 PHE D 323 TRP 0.012 0.001 TRP C 78 HIS 0.007 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00342 (11130) covalent geometry : angle 0.50816 (14902) hydrogen bonds : bond 0.04521 ( 616) hydrogen bonds : angle 4.48841 ( 1821) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 321 ASP cc_start: 0.6651 (p0) cc_final: 0.6351 (p0) outliers start: 27 outliers final: 27 residues processed: 136 average time/residue: 0.2295 time to fit residues: 45.3785 Evaluate side-chains 142 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 408 GLU Chi-restraints excluded: chain D residue 435 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 648 HIS Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 434 TYR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 559 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.118670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.091189 restraints weight = 55499.705| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.21 r_work: 0.3404 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11130 Z= 0.137 Angle : 0.500 5.927 14902 Z= 0.268 Chirality : 0.038 0.151 1575 Planarity : 0.004 0.053 1800 Dihedral : 16.881 113.231 2179 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.46 % Allowed : 23.63 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1241 helix: 1.66 (0.19), residues: 792 sheet: -1.33 (0.63), residues: 66 loop : -2.75 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 518 TYR 0.013 0.001 TYR D 200 PHE 0.012 0.001 PHE D 323 TRP 0.012 0.001 TRP C 78 HIS 0.007 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00311 (11130) covalent geometry : angle 0.49984 (14902) hydrogen bonds : bond 0.04441 ( 616) hydrogen bonds : angle 4.44158 ( 1821) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5706.75 seconds wall clock time: 97 minutes 25.80 seconds (5845.80 seconds total)