Starting phenix.real_space_refine on Wed Feb 4 07:36:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oci_70316/02_2026/9oci_70316.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oci_70316/02_2026/9oci_70316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oci_70316/02_2026/9oci_70316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oci_70316/02_2026/9oci_70316.map" model { file = "/net/cci-nas-00/data/ceres_data/9oci_70316/02_2026/9oci_70316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oci_70316/02_2026/9oci_70316.cif" } resolution = 3.3 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= 0.000 sd= 0.014 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 5 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 5843 2.51 5 N 1581 2.21 5 O 1697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 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: 9174 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 4279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4279 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 20, 'TRANS': 526} Chain breaks: 1 Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 557 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "A" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4278 Classifications: {'peptide': 552} Link IDs: {'PTRANS': 21, 'TRANS': 530} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.75, per 1000 atoms: 0.19 Number of scatterers: 9174 At special positions: 0 Unit cell: (71.604, 89.505, 139.893, 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 46 16.00 P 5 15.00 Mg 2 11.99 O 1697 8.00 N 1581 7.00 C 5843 6.00 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: 0.80 Conformation dependent library (CDL) restraints added in 366.2 milliseconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 69.4% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 134 through 146 Processing helix chain 'B' and resid 148 through 167 removed outlier: 3.630A pdb=" N THR B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 removed outlier: 3.856A pdb=" N TYR B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 234 Processing helix chain 'B' and resid 239 through 244 removed outlier: 3.651A pdb=" N GLU B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 244 " --> pdb=" O PHE B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 239 through 244' Processing helix chain 'B' and resid 245 through 260 removed outlier: 4.325A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 286 removed outlier: 4.360A pdb=" N ASN B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 338 removed outlier: 3.743A pdb=" N LEU B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N MET B 300 " --> pdb=" O SER B 296 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 4.317A pdb=" N LYS B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TYR B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 Processing helix chain 'B' and resid 347 through 401 removed outlier: 3.592A pdb=" N LEU B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 440 removed outlier: 3.602A pdb=" N SER B 411 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 448 removed outlier: 3.704A pdb=" N PHE B 444 " --> pdb=" O ALA B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 517 Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 545 removed outlier: 3.576A pdb=" N HIS B 543 " --> pdb=" O HIS B 539 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 590 Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 608 through 622 Processing helix chain 'B' and resid 638 through 645 removed outlier: 3.537A pdb=" N GLN B 643 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 129 through 158 removed outlier: 3.726A pdb=" N THR D 133 " --> pdb=" O TYR D 129 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 134 " --> pdb=" O GLY D 130 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET D 135 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 removed outlier: 4.502A pdb=" N CYS A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 208 removed outlier: 3.722A pdb=" N LEU A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 205 - end of helix Processing helix chain 'A' and resid 225 through 269 removed outlier: 3.662A pdb=" N LEU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 271 No H-bonds generated for 'chain 'A' and resid 270 through 271' Processing helix chain 'A' and resid 272 through 273 No H-bonds generated for 'chain 'A' and resid 272 through 273' Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 290 Processing helix chain 'A' and resid 290 through 324 removed outlier: 3.983A pdb=" N SER A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 339 through 372 removed outlier: 4.046A pdb=" N LYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 382 through 433 removed outlier: 4.038A pdb=" N LYS A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 474 removed outlier: 4.368A pdb=" N PHE A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN A 456 " --> pdb=" O MET A 452 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Proline residue: A 466 - end of helix Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.543A pdb=" N SER A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 646 through 658 removed outlier: 3.908A pdb=" N ALA A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 687 Processing helix chain 'A' and resid 688 through 694 removed outlier: 3.938A pdb=" N TYR A 692 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 733 removed outlier: 3.834A pdb=" N LYS A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 492 through 493 removed outlier: 5.765A pdb=" N PHE B 470 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 528 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ASP B 472 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLN B 526 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 546 through 549 removed outlier: 4.835A pdb=" N VAL B 674 " --> pdb=" O GLN B 681 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AA4, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'A' and resid 521 through 524 removed outlier: 5.828A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 521 through 524 removed outlier: 5.828A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 508 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY A 559 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 581 through 584 removed outlier: 6.630A pdb=" N LEU A 664 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE A 699 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 666 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 533 " --> pdb=" O HIS A 711 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N LEU A 713 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA A 535 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU A 715 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL A 537 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 722 " --> pdb=" O PHE A 714 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU A 716 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ILE A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) 595 hydrogen bonds defined for protein. 1719 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: 1.66 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3018 1.35 - 1.46: 2051 1.46 - 1.58: 4190 1.58 - 1.70: 8 1.70 - 1.82: 76 Bond restraints: 9343 Sorted by residual: bond pdb=" CA ARG B 668 " pdb=" C ARG B 668 " ideal model delta sigma weight residual 1.524 1.608 -0.084 1.48e-02 4.57e+03 3.22e+01 bond pdb=" N PRO A 466 " pdb=" CD PRO A 466 " ideal model delta sigma weight residual 1.473 1.519 -0.046 1.40e-02 5.10e+03 1.10e+01 bond pdb=" N LEU A 211 " pdb=" CA LEU A 211 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.16e-02 7.43e+03 7.26e+00 bond pdb=" N VAL B 560 " pdb=" CA VAL B 560 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.19e-02 7.06e+03 6.77e+00 bond pdb=" N THR A 208 " pdb=" CA THR A 208 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.23e-02 6.61e+03 6.46e+00 ... (remaining 9338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 12476 2.30 - 4.59: 147 4.59 - 6.89: 36 6.89 - 9.18: 7 9.18 - 11.48: 6 Bond angle restraints: 12672 Sorted by residual: angle pdb=" N MET B 391 " pdb=" CA MET B 391 " pdb=" C MET B 391 " ideal model delta sigma weight residual 111.71 121.24 -9.53 1.15e+00 7.56e-01 6.87e+01 angle pdb=" N ALA B 669 " pdb=" CA ALA B 669 " pdb=" C ALA B 669 " ideal model delta sigma weight residual 110.28 98.80 11.48 1.48e+00 4.57e-01 6.01e+01 angle pdb=" N GLN B 667 " pdb=" CA GLN B 667 " pdb=" C GLN B 667 " ideal model delta sigma weight residual 111.75 121.21 -9.46 1.28e+00 6.10e-01 5.47e+01 angle pdb=" N VAL B 382 " pdb=" CA VAL B 382 " pdb=" C VAL B 382 " ideal model delta sigma weight residual 110.53 104.24 6.29 9.40e-01 1.13e+00 4.47e+01 angle pdb=" N CYS B 209 " pdb=" CA CYS B 209 " pdb=" C CYS B 209 " ideal model delta sigma weight residual 112.54 120.12 -7.58 1.22e+00 6.72e-01 3.86e+01 ... (remaining 12667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5060 17.90 - 35.81: 419 35.81 - 53.71: 107 53.71 - 71.61: 22 71.61 - 89.51: 12 Dihedral angle restraints: 5620 sinusoidal: 2264 harmonic: 3356 Sorted by residual: dihedral pdb=" C LEU B 390 " pdb=" N LEU B 390 " pdb=" CA LEU B 390 " pdb=" CB LEU B 390 " ideal model delta harmonic sigma weight residual -122.60 -132.45 9.85 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" CA ARG A 659 " pdb=" C ARG A 659 " pdb=" N LYS A 660 " pdb=" CA LYS A 660 " ideal model delta harmonic sigma weight residual 180.00 -161.28 -18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ARG A 694 " pdb=" C ARG A 694 " pdb=" N SER A 695 " pdb=" CA SER A 695 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1351 0.069 - 0.138: 108 0.138 - 0.207: 8 0.207 - 0.276: 3 0.276 - 0.345: 2 Chirality restraints: 1472 Sorted by residual: chirality pdb=" CA LEU B 390 " pdb=" N LEU B 390 " pdb=" C LEU B 390 " pdb=" CB LEU B 390 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA GLN B 667 " pdb=" N GLN B 667 " pdb=" C GLN B 667 " pdb=" CB GLN B 667 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA CYS B 209 " pdb=" N CYS B 209 " pdb=" C CYS B 209 " pdb=" CB CYS B 209 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 1469 not shown) Planarity restraints: 1609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 428 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C TYR A 428 " 0.070 2.00e-02 2.50e+03 pdb=" O TYR A 428 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE A 429 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 210 " -0.235 9.50e-02 1.11e+02 1.05e-01 6.81e+00 pdb=" NE ARG A 210 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 210 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 210 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 210 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 380 " 0.130 9.50e-02 1.11e+02 5.85e-02 2.10e+00 pdb=" NE ARG B 380 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B 380 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 380 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 380 " 0.004 2.00e-02 2.50e+03 ... (remaining 1606 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 43 2.59 - 3.16: 7606 3.16 - 3.74: 13827 3.74 - 4.32: 18709 4.32 - 4.90: 31871 Nonbonded interactions: 72056 Sorted by model distance: nonbonded pdb=" O1G ATP A 901 " pdb="MG MG A 902 " model vdw 2.006 2.170 nonbonded pdb=" O1B ADP B 701 " pdb="MG MG B 702 " model vdw 2.049 2.170 nonbonded pdb=" OG SER A 545 " pdb="MG MG A 902 " model vdw 2.059 2.170 nonbonded pdb=" OE1 GLN A 586 " pdb="MG MG A 902 " model vdw 2.134 2.170 nonbonded pdb=" O2B ATP A 901 " pdb="MG MG A 902 " model vdw 2.215 2.170 ... (remaining 72051 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: 5.970 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.750 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 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 : 0.003 0.084 9343 Z= 0.168 Angle : 0.679 11.476 12672 Z= 0.407 Chirality : 0.043 0.345 1472 Planarity : 0.005 0.105 1609 Dihedral : 14.821 89.514 3466 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.10 % Allowed : 8.34 % Favored : 91.56 % 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: 0.61 (0.24), residues: 1158 helix: 0.37 (0.18), residues: 716 sheet: 1.53 (0.62), residues: 78 loop : 0.57 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 373 TYR 0.016 0.001 TYR D 129 PHE 0.009 0.001 PHE D 112 TRP 0.005 0.000 TRP A 322 HIS 0.003 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9343) covalent geometry : angle 0.67892 (12672) hydrogen bonds : bond 0.25153 ( 593) hydrogen bonds : angle 6.56603 ( 1719) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.364 Fit side-chains REVERT: D 127 GLU cc_start: 0.7993 (tp30) cc_final: 0.7751 (tp30) REVERT: A 408 TYR cc_start: 0.8956 (t80) cc_final: 0.8734 (t80) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.1193 time to fit residues: 21.3160 Evaluate side-chains 111 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.0570 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN A 574 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.101500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.080859 restraints weight = 16202.643| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.54 r_work: 0.2823 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9343 Z= 0.150 Angle : 0.593 8.116 12672 Z= 0.301 Chirality : 0.040 0.127 1472 Planarity : 0.004 0.033 1609 Dihedral : 6.590 76.196 1313 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.51 % Allowed : 10.25 % Favored : 88.24 % 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: 2.01 (0.25), residues: 1158 helix: 1.87 (0.19), residues: 724 sheet: 1.29 (0.62), residues: 78 loop : 0.34 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 210 TYR 0.011 0.001 TYR B 376 PHE 0.020 0.001 PHE A 276 TRP 0.007 0.001 TRP A 308 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9343) covalent geometry : angle 0.59282 (12672) hydrogen bonds : bond 0.06988 ( 593) hydrogen bonds : angle 4.27127 ( 1719) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.390 Fit side-chains REVERT: A 408 TYR cc_start: 0.9097 (t80) cc_final: 0.8788 (t80) outliers start: 15 outliers final: 9 residues processed: 132 average time/residue: 0.1127 time to fit residues: 20.2422 Evaluate side-chains 119 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain D residue 155 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 493 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 113 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 overall best weight: 0.5070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.082144 restraints weight = 16042.706| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.53 r_work: 0.2851 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9343 Z= 0.125 Angle : 0.530 6.638 12672 Z= 0.265 Chirality : 0.039 0.151 1472 Planarity : 0.003 0.031 1609 Dihedral : 6.276 71.653 1313 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.11 % Allowed : 11.06 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.51 (0.25), residues: 1158 helix: 2.39 (0.19), residues: 723 sheet: 1.08 (0.61), residues: 78 loop : 0.35 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 128 TYR 0.010 0.001 TYR B 376 PHE 0.012 0.001 PHE A 276 TRP 0.008 0.001 TRP A 322 HIS 0.002 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9343) covalent geometry : angle 0.53011 (12672) hydrogen bonds : bond 0.06172 ( 593) hydrogen bonds : angle 3.90467 ( 1719) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.294 Fit side-chains REVERT: B 300 MET cc_start: 0.6552 (mmp) cc_final: 0.5347 (mtp) outliers start: 21 outliers final: 14 residues processed: 141 average time/residue: 0.0909 time to fit residues: 17.8379 Evaluate side-chains 126 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 684 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 108 optimal weight: 0.0060 chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 111 optimal weight: 0.3980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.083878 restraints weight = 16164.506| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.56 r_work: 0.2875 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9343 Z= 0.115 Angle : 0.513 6.972 12672 Z= 0.258 Chirality : 0.038 0.132 1472 Planarity : 0.003 0.028 1609 Dihedral : 6.088 69.589 1313 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.61 % Allowed : 11.46 % Favored : 85.93 % 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: 2.74 (0.25), residues: 1158 helix: 2.63 (0.19), residues: 723 sheet: 1.02 (0.62), residues: 78 loop : 0.34 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 109 TYR 0.030 0.001 TYR A 736 PHE 0.009 0.001 PHE B 241 TRP 0.007 0.001 TRP A 322 HIS 0.002 0.000 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 9343) covalent geometry : angle 0.51317 (12672) hydrogen bonds : bond 0.05456 ( 593) hydrogen bonds : angle 3.74221 ( 1719) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.238 Fit side-chains REVERT: B 300 MET cc_start: 0.6456 (mmp) cc_final: 0.5328 (mtp) REVERT: B 316 GLU cc_start: 0.8586 (tp30) cc_final: 0.8319 (tp30) REVERT: B 569 GLN cc_start: 0.8339 (pm20) cc_final: 0.7676 (mp10) REVERT: B 587 ASP cc_start: 0.9147 (t0) cc_final: 0.8897 (m-30) outliers start: 26 outliers final: 19 residues processed: 139 average time/residue: 0.1011 time to fit residues: 19.1723 Evaluate side-chains 140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 668 ASP Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 739 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN A 388 GLN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.080327 restraints weight = 16237.593| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.51 r_work: 0.2815 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9343 Z= 0.168 Angle : 0.554 8.915 12672 Z= 0.276 Chirality : 0.040 0.187 1472 Planarity : 0.003 0.030 1609 Dihedral : 6.203 78.801 1313 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.12 % Allowed : 11.66 % Favored : 85.23 % 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: 2.67 (0.25), residues: 1158 helix: 2.62 (0.19), residues: 723 sheet: 0.88 (0.60), residues: 78 loop : 0.24 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 561 TYR 0.023 0.001 TYR A 736 PHE 0.016 0.001 PHE D 124 TRP 0.007 0.001 TRP A 322 HIS 0.002 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9343) covalent geometry : angle 0.55384 (12672) hydrogen bonds : bond 0.05981 ( 593) hydrogen bonds : angle 3.80615 ( 1719) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: B 569 GLN cc_start: 0.8357 (pm20) cc_final: 0.8150 (pm20) REVERT: A 358 GLU cc_start: 0.8606 (tt0) cc_final: 0.8261 (tp30) outliers start: 31 outliers final: 23 residues processed: 137 average time/residue: 0.1010 time to fit residues: 18.9379 Evaluate side-chains 134 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 659 ARG Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 739 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN B 681 GLN A 451 GLN A 574 HIS A 676 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.079747 restraints weight = 16311.744| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.53 r_work: 0.2805 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9343 Z= 0.167 Angle : 0.554 8.868 12672 Z= 0.276 Chirality : 0.040 0.187 1472 Planarity : 0.003 0.031 1609 Dihedral : 6.239 82.797 1313 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.22 % Allowed : 12.16 % Favored : 84.62 % 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: 2.67 (0.25), residues: 1158 helix: 2.64 (0.19), residues: 724 sheet: 0.75 (0.60), residues: 78 loop : 0.18 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 561 TYR 0.020 0.001 TYR A 736 PHE 0.013 0.001 PHE A 390 TRP 0.006 0.001 TRP A 322 HIS 0.002 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9343) covalent geometry : angle 0.55407 (12672) hydrogen bonds : bond 0.05988 ( 593) hydrogen bonds : angle 3.81612 ( 1719) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: B 391 MET cc_start: 0.8443 (tpt) cc_final: 0.8145 (tpt) REVERT: B 569 GLN cc_start: 0.8340 (pm20) cc_final: 0.8111 (pm20) REVERT: A 358 GLU cc_start: 0.8599 (tt0) cc_final: 0.8321 (tp30) outliers start: 32 outliers final: 25 residues processed: 135 average time/residue: 0.1150 time to fit residues: 21.0721 Evaluate side-chains 141 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 659 ARG Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 739 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 76 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN A 451 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.100902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.080507 restraints weight = 16181.142| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.51 r_work: 0.2817 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9343 Z= 0.137 Angle : 0.539 8.021 12672 Z= 0.268 Chirality : 0.039 0.178 1472 Planarity : 0.003 0.031 1609 Dihedral : 6.164 82.501 1313 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.12 % Allowed : 12.76 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.75 (0.25), residues: 1158 helix: 2.72 (0.19), residues: 724 sheet: 0.74 (0.60), residues: 78 loop : 0.19 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 140 TYR 0.018 0.001 TYR A 736 PHE 0.019 0.001 PHE D 124 TRP 0.006 0.001 TRP A 322 HIS 0.002 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9343) covalent geometry : angle 0.53867 (12672) hydrogen bonds : bond 0.05725 ( 593) hydrogen bonds : angle 3.76276 ( 1719) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: B 316 GLU cc_start: 0.8640 (tp30) cc_final: 0.8367 (tp30) REVERT: B 391 MET cc_start: 0.8499 (tpt) cc_final: 0.8202 (tpt) REVERT: B 569 GLN cc_start: 0.8323 (pm20) cc_final: 0.8067 (pm20) REVERT: A 358 GLU cc_start: 0.8581 (tt0) cc_final: 0.8340 (tp30) outliers start: 31 outliers final: 28 residues processed: 141 average time/residue: 0.1080 time to fit residues: 20.7509 Evaluate side-chains 142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 659 ARG Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 739 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN A 676 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.080967 restraints weight = 16049.356| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.51 r_work: 0.2826 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9343 Z= 0.131 Angle : 0.548 7.621 12672 Z= 0.272 Chirality : 0.039 0.172 1472 Planarity : 0.003 0.031 1609 Dihedral : 6.099 81.985 1313 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.02 % Allowed : 12.96 % Favored : 84.02 % 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: 2.84 (0.25), residues: 1158 helix: 2.80 (0.19), residues: 724 sheet: 0.74 (0.60), residues: 78 loop : 0.22 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 484 TYR 0.010 0.001 TYR B 376 PHE 0.010 0.001 PHE A 505 TRP 0.006 0.001 TRP A 322 HIS 0.003 0.001 HIS B 384 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9343) covalent geometry : angle 0.54836 (12672) hydrogen bonds : bond 0.05554 ( 593) hydrogen bonds : angle 3.72074 ( 1719) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.379 Fit side-chains REVERT: B 316 GLU cc_start: 0.8633 (tp30) cc_final: 0.8362 (tp30) REVERT: B 569 GLN cc_start: 0.8323 (pm20) cc_final: 0.8075 (pm20) REVERT: A 358 GLU cc_start: 0.8570 (tt0) cc_final: 0.8367 (tp30) outliers start: 30 outliers final: 25 residues processed: 134 average time/residue: 0.1078 time to fit residues: 19.7259 Evaluate side-chains 146 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 739 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 41 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 0.0370 chunk 84 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.101474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.081134 restraints weight = 16154.727| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.52 r_work: 0.2830 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9343 Z= 0.131 Angle : 0.544 7.835 12672 Z= 0.270 Chirality : 0.039 0.170 1472 Planarity : 0.003 0.031 1609 Dihedral : 6.053 82.029 1313 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.91 % Allowed : 13.47 % Favored : 83.62 % 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: 2.87 (0.25), residues: 1158 helix: 2.84 (0.19), residues: 724 sheet: 0.71 (0.60), residues: 78 loop : 0.20 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 467 TYR 0.010 0.001 TYR B 376 PHE 0.022 0.001 PHE D 124 TRP 0.006 0.001 TRP A 322 HIS 0.002 0.001 HIS A 578 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9343) covalent geometry : angle 0.54367 (12672) hydrogen bonds : bond 0.05467 ( 593) hydrogen bonds : angle 3.69789 ( 1719) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: B 316 GLU cc_start: 0.8625 (tp30) cc_final: 0.8350 (tp30) REVERT: B 569 GLN cc_start: 0.8327 (pm20) cc_final: 0.8076 (pm20) outliers start: 29 outliers final: 25 residues processed: 140 average time/residue: 0.1066 time to fit residues: 20.2568 Evaluate side-chains 137 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 659 ARG Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 739 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 77 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.0570 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 102 optimal weight: 0.0170 chunk 23 optimal weight: 0.9990 chunk 38 optimal weight: 0.0060 chunk 12 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 overall best weight: 0.2952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN A 574 HIS A 589 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.103507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.083357 restraints weight = 16132.083| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.53 r_work: 0.2867 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9343 Z= 0.116 Angle : 0.542 8.335 12672 Z= 0.268 Chirality : 0.038 0.157 1472 Planarity : 0.003 0.030 1609 Dihedral : 5.884 78.807 1313 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.21 % Allowed : 13.87 % Favored : 83.92 % 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: 3.00 (0.25), residues: 1158 helix: 2.94 (0.19), residues: 724 sheet: 0.72 (0.60), residues: 78 loop : 0.26 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 467 TYR 0.010 0.001 TYR B 376 PHE 0.010 0.001 PHE B 444 TRP 0.007 0.001 TRP A 322 HIS 0.002 0.000 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9343) covalent geometry : angle 0.54192 (12672) hydrogen bonds : bond 0.05002 ( 593) hydrogen bonds : angle 3.60229 ( 1719) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: B 300 MET cc_start: 0.6449 (mmp) cc_final: 0.5328 (mtp) REVERT: B 316 GLU cc_start: 0.8580 (tp30) cc_final: 0.8308 (tp30) REVERT: B 569 GLN cc_start: 0.8297 (pm20) cc_final: 0.8044 (pm20) REVERT: D 120 LYS cc_start: 0.8094 (ptpp) cc_final: 0.7669 (ptpp) REVERT: A 589 GLN cc_start: 0.8899 (mt0) cc_final: 0.8659 (mt0) REVERT: A 705 LEU cc_start: 0.8962 (tp) cc_final: 0.8731 (tt) outliers start: 22 outliers final: 22 residues processed: 133 average time/residue: 0.1025 time to fit residues: 18.2836 Evaluate side-chains 140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 659 ARG Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 739 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.5980 chunk 38 optimal weight: 0.0010 chunk 77 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 108 optimal weight: 0.0670 chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.5326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.103610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.083489 restraints weight = 15963.545| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.50 r_work: 0.2867 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9343 Z= 0.118 Angle : 0.553 12.377 12672 Z= 0.271 Chirality : 0.038 0.157 1472 Planarity : 0.003 0.031 1609 Dihedral : 5.839 78.757 1313 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.51 % Allowed : 13.97 % Favored : 83.52 % 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: 3.02 (0.25), residues: 1158 helix: 2.97 (0.19), residues: 723 sheet: 0.71 (0.60), residues: 78 loop : 0.25 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 467 TYR 0.010 0.001 TYR B 376 PHE 0.024 0.001 PHE D 124 TRP 0.009 0.001 TRP A 413 HIS 0.002 0.000 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9343) covalent geometry : angle 0.55339 (12672) hydrogen bonds : bond 0.04969 ( 593) hydrogen bonds : angle 3.57064 ( 1719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1915.78 seconds wall clock time: 33 minutes 40.85 seconds (2020.85 seconds total)