Starting phenix.real_space_refine on Wed Mar 4 03:24:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sck_25037/03_2026/7sck_25037.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sck_25037/03_2026/7sck_25037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sck_25037/03_2026/7sck_25037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sck_25037/03_2026/7sck_25037.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sck_25037/03_2026/7sck_25037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sck_25037/03_2026/7sck_25037.map" } resolution = 2.8 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= 0.002 sd= 0.036 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 Mn 1 7.51 5 P 4 5.49 5 S 48 5.16 5 C 6583 2.51 5 N 1720 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10250 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5239 Classifications: {'peptide': 642} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 608} Chain breaks: 1 Chain: "B" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4854 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 558} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BDP': 2, 'NDG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.43, per 1000 atoms: 0.24 Number of scatterers: 10250 At special positions: 0 Unit cell: (110.124, 88.596, 110.952, 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) Mn 1 24.99 S 48 16.00 P 4 15.00 O 1894 8.00 N 1720 7.00 C 6583 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " distance=2.03 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 Links applied ALPHA1-4 " BDP D 2 " - " NDG D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NDG D 1 " - " BDP D 2 " " NDG D 3 " - " BDP D 4 " NAG-ASN " NAG A 802 " - " ASN A 330 " " NAG C 1 " - " ASN B 637 " Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 664.6 milliseconds 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2372 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 36.1% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.660A pdb=" N LEU A 108 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 140 Processing helix chain 'A' and resid 174 through 180 Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.501A pdb=" N PHE A 226 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 4.187A pdb=" N VAL A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 4.082A pdb=" N ASP A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.630A pdb=" N HIS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 397 through 415 Processing helix chain 'A' and resid 418 through 432 Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.554A pdb=" N TRP A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 495 through 506 removed outlier: 3.847A pdb=" N LYS A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'A' and resid 545 through 551 removed outlier: 3.580A pdb=" N ARG A 549 " --> pdb=" O MET A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.796A pdb=" N TYR A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 650 Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 696 through 713 Processing helix chain 'A' and resid 740 through 744 removed outlier: 3.703A pdb=" N ILE A 743 " --> pdb=" O TYR A 740 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 744 " --> pdb=" O ARG A 741 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 744' Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 166 through 177 Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.526A pdb=" N THR B 184 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.560A pdb=" N VAL B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.802A pdb=" N LEU B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 312' Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.949A pdb=" N ASP B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.537A pdb=" N MET B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER B 371 " --> pdb=" O GLU B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 371' Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.537A pdb=" N SER B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 399 Processing helix chain 'B' and resid 402 through 419 Processing helix chain 'B' and resid 420 through 423 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 465 through 477 removed outlier: 3.925A pdb=" N ARG B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 524 removed outlier: 3.532A pdb=" N ASN B 521 " --> pdb=" O LYS B 518 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 522 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 524 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 Processing helix chain 'B' and resid 602 through 612 removed outlier: 4.104A pdb=" N MET B 612 " --> pdb=" O TYR B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 624 Processing helix chain 'B' and resid 626 through 640 removed outlier: 3.776A pdb=" N ALA B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 685 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 145 removed outlier: 5.939A pdb=" N VAL A 116 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR A 117 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE A 154 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N PHE A 193 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N HIS A 190 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA A 217 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE A 192 " --> pdb=" O ALA A 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 297 removed outlier: 8.163A pdb=" N VAL A 293 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU A 264 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU A 295 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N PHE A 266 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N THR A 297 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY A 268 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N MET A 263 " --> pdb=" O PHE A 333 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A 335 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A 265 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N THR A 332 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL A 358 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N CYS A 334 " --> pdb=" O VAL A 358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 536 through 540 removed outlier: 8.539A pdb=" N VAL A 537 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE A 513 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ILE A 539 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 515 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N PHE A 480 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE A 514 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA A 482 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU A 516 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE A 484 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR A 481 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU A 564 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL A 483 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 605 through 609 Processing sheet with id=AA5, first strand: chain 'A' and resid 722 through 725 removed outlier: 6.960A pdb=" N LYS B 645 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU B 563 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL B 646 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 565 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR B 457 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE B 537 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE B 459 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE B 456 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU B 486 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA B 458 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL B 488 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL B 460 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N LYS B 510 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 485 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL B 512 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 487 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.479A pdb=" N LEU B 188 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU B 212 " --> pdb=" O VAL B 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 283 removed outlier: 7.679A pdb=" N LEU B 281 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 254 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LEU B 283 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER B 256 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE B 253 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL B 319 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU B 255 " --> pdb=" O VAL B 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 300 Processing sheet with id=AB1, first strand: chain 'B' and resid 570 through 574 291 hydrogen bonds defined for protein. 810 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: 1.84 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2584 1.33 - 1.45: 2239 1.45 - 1.58: 5626 1.58 - 1.70: 5 1.70 - 1.82: 74 Bond restraints: 10528 Sorted by residual: bond pdb=" C3 BDP D 2 " pdb=" O3 BDP D 2 " ideal model delta sigma weight residual 1.411 1.515 -0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C3 BDP D 4 " pdb=" O3 BDP D 4 " ideal model delta sigma weight residual 1.411 1.515 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C1 BDP D 2 " pdb=" O5 BDP D 2 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C1 BDP D 4 " pdb=" O5 BDP D 4 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O1B UDP B 901 " pdb=" PB UDP B 901 " ideal model delta sigma weight residual 1.530 1.492 0.038 1.00e-02 1.00e+04 1.48e+01 ... (remaining 10523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 14012 1.82 - 3.65: 240 3.65 - 5.47: 47 5.47 - 7.30: 11 7.30 - 9.12: 2 Bond angle restraints: 14312 Sorted by residual: angle pdb=" O1B UDP B 901 " pdb=" PB UDP B 901 " pdb=" O3A UDP B 901 " ideal model delta sigma weight residual 102.95 112.07 -9.12 1.00e+00 1.00e+00 8.33e+01 angle pdb=" O3A UDP B 901 " pdb=" PB UDP B 901 " pdb=" O3B UDP B 901 " ideal model delta sigma weight residual 112.01 103.15 8.86 1.00e+00 1.00e+00 7.86e+01 angle pdb=" CA ASP B 561 " pdb=" CB ASP B 561 " pdb=" CG ASP B 561 " ideal model delta sigma weight residual 112.60 116.16 -3.56 1.00e+00 1.00e+00 1.26e+01 angle pdb=" N ARG B 562 " pdb=" CA ARG B 562 " pdb=" CB ARG B 562 " ideal model delta sigma weight residual 110.49 104.68 5.81 1.69e+00 3.50e-01 1.18e+01 angle pdb=" C PRO B 560 " pdb=" N ASP B 561 " pdb=" CA ASP B 561 " ideal model delta sigma weight residual 122.49 117.30 5.19 1.57e+00 4.06e-01 1.09e+01 ... (remaining 14307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.95: 6182 21.95 - 43.91: 206 43.91 - 65.86: 33 65.86 - 87.81: 23 87.81 - 109.76: 12 Dihedral angle restraints: 6456 sinusoidal: 2786 harmonic: 3670 Sorted by residual: dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.95 109.76 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C3 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 47.62 -60.39 108.01 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C3 NDG D 1 " pdb=" C4 NDG D 1 " pdb=" C5 NDG D 1 " pdb=" O5 NDG D 1 " ideal model delta sinusoidal sigma weight residual 53.31 -52.51 105.82 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 6453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1373 0.067 - 0.135: 187 0.135 - 0.202: 3 0.202 - 0.269: 5 0.269 - 0.336: 2 Chirality restraints: 1570 Sorted by residual: chirality pdb=" C4 NDG D 1 " pdb=" C3 NDG D 1 " pdb=" C5 NDG D 1 " pdb=" O4 NDG D 1 " both_signs ideal model delta sigma weight residual False -2.30 -2.64 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C4 NDG D 3 " pdb=" C3 NDG D 3 " pdb=" C5 NDG D 3 " pdb=" O4 NDG D 3 " both_signs ideal model delta sigma weight residual False -2.30 -2.61 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1567 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 561 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ASP B 561 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP B 561 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG B 562 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 399 " -0.025 2.00e-02 2.50e+03 1.31e-02 3.41e+00 pdb=" CG TYR B 399 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 399 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 399 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 399 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 399 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 399 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 399 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 479 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO B 480 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 480 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 480 " -0.023 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 25 2.38 - 3.01: 5720 3.01 - 3.64: 15432 3.64 - 4.27: 24009 4.27 - 4.90: 40214 Nonbonded interactions: 85400 Sorted by model distance: nonbonded pdb=" O2A UDP B 901 " pdb="MN MN B 902 " model vdw 1.744 2.320 nonbonded pdb=" OH TYR B 130 " pdb=" O PRO B 155 " model vdw 2.229 3.040 nonbonded pdb=" NZ LYS B 484 " pdb=" O GLU B 528 " model vdw 2.241 3.120 nonbonded pdb=" O ARG B 209 " pdb=" OH TYR B 226 " model vdw 2.241 3.040 nonbonded pdb=" N ASP B 539 " pdb=" OD1 ASP B 539 " model vdw 2.252 3.120 ... (remaining 85395 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.560 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:9.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 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 : 0.005 0.104 10544 Z= 0.245 Angle : 0.621 9.125 14351 Z= 0.330 Chirality : 0.047 0.336 1570 Planarity : 0.004 0.042 1806 Dihedral : 13.394 109.764 4057 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.36 % Allowed : 5.49 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.14 (0.24), residues: 1228 helix: 0.91 (0.28), residues: 382 sheet: -0.17 (0.48), residues: 122 loop : -0.60 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 562 TYR 0.025 0.002 TYR B 399 PHE 0.014 0.002 PHE B 306 TRP 0.013 0.002 TRP B 556 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00492 (10528) covalent geometry : angle 0.61464 (14312) SS BOND : bond 0.00333 ( 9) SS BOND : angle 1.21535 ( 18) hydrogen bonds : bond 0.17391 ( 291) hydrogen bonds : angle 6.51032 ( 810) link_ALPHA1-4 : bond 0.00855 ( 1) link_ALPHA1-4 : angle 1.45113 ( 3) link_BETA1-4 : bond 0.00289 ( 4) link_BETA1-4 : angle 2.04802 ( 12) link_NAG-ASN : bond 0.00803 ( 2) link_NAG-ASN : angle 2.84728 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 335 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7327 (pm20) cc_final: 0.7094 (pm20) REVERT: A 269 LYS cc_start: 0.7811 (ptpp) cc_final: 0.7398 (ptpp) REVERT: A 305 GLN cc_start: 0.7284 (mp10) cc_final: 0.7018 (mp10) REVERT: A 321 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7733 (mmtm) REVERT: A 447 LYS cc_start: 0.8047 (ttmm) cc_final: 0.7831 (ttmm) REVERT: A 458 TYR cc_start: 0.7805 (t80) cc_final: 0.7587 (t80) REVERT: A 547 SER cc_start: 0.7504 (p) cc_final: 0.7243 (m) REVERT: A 576 ASP cc_start: 0.5474 (m-30) cc_final: 0.5149 (m-30) REVERT: A 739 LYS cc_start: 0.7048 (ttpt) cc_final: 0.6727 (ttpt) REVERT: B 104 ILE cc_start: 0.8449 (tt) cc_final: 0.8217 (pt) REVERT: B 108 ILE cc_start: 0.8351 (mp) cc_final: 0.7949 (mt) REVERT: B 135 MET cc_start: 0.6573 (mmm) cc_final: 0.6252 (mmm) REVERT: B 144 THR cc_start: 0.8380 (p) cc_final: 0.8157 (m) REVERT: B 266 ARG cc_start: 0.7461 (tpp-160) cc_final: 0.7217 (ttm110) REVERT: B 268 ASP cc_start: 0.7218 (m-30) cc_final: 0.6991 (m-30) REVERT: B 281 LEU cc_start: 0.8276 (tp) cc_final: 0.8055 (tt) REVERT: B 348 TYR cc_start: 0.7755 (t80) cc_final: 0.7008 (t80) REVERT: B 359 LYS cc_start: 0.7259 (mmtm) cc_final: 0.6983 (tppp) REVERT: B 369 LYS cc_start: 0.7608 (tttp) cc_final: 0.7383 (tttp) REVERT: B 372 ASP cc_start: 0.7208 (m-30) cc_final: 0.6783 (m-30) REVERT: B 574 ASP cc_start: 0.6238 (t0) cc_final: 0.5805 (t0) REVERT: B 699 VAL cc_start: 0.7262 (m) cc_final: 0.6213 (p) outliers start: 4 outliers final: 1 residues processed: 339 average time/residue: 0.5265 time to fit residues: 192.3112 Evaluate side-chains 266 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 719 HIS B 273 GLN B 313 GLN B 378 GLN B 430 ASN B 490 ASN B 550 GLN ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 669 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.155374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.137600 restraints weight = 13731.936| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.09 r_work: 0.3782 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10544 Z= 0.146 Angle : 0.625 7.858 14351 Z= 0.307 Chirality : 0.045 0.230 1570 Planarity : 0.005 0.063 1806 Dihedral : 11.921 101.971 1598 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.07 % Allowed : 13.04 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.06 (0.24), residues: 1228 helix: 0.87 (0.27), residues: 390 sheet: -0.02 (0.50), residues: 111 loop : -0.52 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 243 TYR 0.021 0.001 TYR B 107 PHE 0.012 0.002 PHE A 577 TRP 0.014 0.001 TRP B 396 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00327 (10528) covalent geometry : angle 0.61761 (14312) SS BOND : bond 0.00497 ( 9) SS BOND : angle 1.31325 ( 18) hydrogen bonds : bond 0.04264 ( 291) hydrogen bonds : angle 5.32125 ( 810) link_ALPHA1-4 : bond 0.01040 ( 1) link_ALPHA1-4 : angle 1.47083 ( 3) link_BETA1-4 : bond 0.00494 ( 4) link_BETA1-4 : angle 2.09859 ( 12) link_NAG-ASN : bond 0.00627 ( 2) link_NAG-ASN : angle 2.90555 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 276 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7720 (pm20) cc_final: 0.7467 (pm20) REVERT: A 147 ASP cc_start: 0.7558 (t0) cc_final: 0.7339 (t0) REVERT: A 270 ARG cc_start: 0.8109 (ptm-80) cc_final: 0.7276 (ptt90) REVERT: A 305 GLN cc_start: 0.7590 (mp10) cc_final: 0.7221 (mp10) REVERT: A 383 GLU cc_start: 0.6614 (tm-30) cc_final: 0.6336 (tm-30) REVERT: A 458 TYR cc_start: 0.7960 (t80) cc_final: 0.7756 (t80) REVERT: A 508 GLN cc_start: 0.7916 (pm20) cc_final: 0.7414 (pm20) REVERT: A 576 ASP cc_start: 0.6365 (m-30) cc_final: 0.6027 (m-30) REVERT: A 603 LYS cc_start: 0.8443 (tppp) cc_final: 0.8143 (mmmt) REVERT: A 648 GLN cc_start: 0.8168 (tm130) cc_final: 0.7849 (tm-30) REVERT: B 104 ILE cc_start: 0.8764 (tt) cc_final: 0.8534 (pt) REVERT: B 135 MET cc_start: 0.7240 (mmm) cc_final: 0.6809 (mmm) REVERT: B 139 ASP cc_start: 0.7925 (m-30) cc_final: 0.7616 (m-30) REVERT: B 266 ARG cc_start: 0.7613 (tpp-160) cc_final: 0.7390 (tpp-160) REVERT: B 298 LYS cc_start: 0.8391 (mppt) cc_final: 0.8146 (mppt) REVERT: B 316 THR cc_start: 0.8360 (m) cc_final: 0.8011 (t) REVERT: B 348 TYR cc_start: 0.7851 (t80) cc_final: 0.7087 (t80) REVERT: B 364 VAL cc_start: 0.8306 (t) cc_final: 0.7934 (m) REVERT: B 369 LYS cc_start: 0.7887 (tttp) cc_final: 0.7654 (tttp) REVERT: B 372 ASP cc_start: 0.7776 (m-30) cc_final: 0.7433 (m-30) REVERT: B 463 TYR cc_start: 0.7065 (t80) cc_final: 0.6641 (t80) REVERT: B 518 LYS cc_start: 0.7917 (mtpp) cc_final: 0.7566 (mtmm) REVERT: B 574 ASP cc_start: 0.6743 (t0) cc_final: 0.6218 (t0) REVERT: B 577 MET cc_start: 0.7291 (mtp) cc_final: 0.6738 (mtp) REVERT: B 592 MET cc_start: 0.7692 (mtp) cc_final: 0.7250 (mtp) REVERT: B 672 GLU cc_start: 0.7677 (tp30) cc_final: 0.7125 (tp30) REVERT: B 687 MET cc_start: 0.7370 (tpp) cc_final: 0.6737 (tpt) REVERT: B 697 ASP cc_start: 0.8080 (m-30) cc_final: 0.7878 (m-30) REVERT: B 699 VAL cc_start: 0.7411 (m) cc_final: 0.6983 (t) outliers start: 23 outliers final: 7 residues processed: 287 average time/residue: 0.5338 time to fit residues: 165.3076 Evaluate side-chains 266 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 259 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 625 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN A 397 HIS A 702 GLN A 719 HIS ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.153290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.135735 restraints weight = 13889.553| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.07 r_work: 0.3768 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10544 Z= 0.210 Angle : 0.646 9.161 14351 Z= 0.318 Chirality : 0.047 0.248 1570 Planarity : 0.005 0.047 1806 Dihedral : 11.045 97.537 1596 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.79 % Rotamer: Outliers : 2.52 % Allowed : 15.92 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 1228 helix: 0.61 (0.27), residues: 391 sheet: -0.11 (0.48), residues: 127 loop : -0.68 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 243 TYR 0.019 0.002 TYR A 608 PHE 0.017 0.002 PHE B 306 TRP 0.015 0.002 TRP B 396 HIS 0.004 0.001 HIS A 448 Details of bonding type rmsd covalent geometry : bond 0.00481 (10528) covalent geometry : angle 0.63763 (14312) SS BOND : bond 0.00839 ( 9) SS BOND : angle 1.22329 ( 18) hydrogen bonds : bond 0.04355 ( 291) hydrogen bonds : angle 5.20015 ( 810) link_ALPHA1-4 : bond 0.01323 ( 1) link_ALPHA1-4 : angle 2.38343 ( 3) link_BETA1-4 : bond 0.00471 ( 4) link_BETA1-4 : angle 2.24106 ( 12) link_NAG-ASN : bond 0.00832 ( 2) link_NAG-ASN : angle 3.14556 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7778 (pm20) cc_final: 0.7496 (pm20) REVERT: A 147 ASP cc_start: 0.7599 (t0) cc_final: 0.7358 (t0) REVERT: A 160 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7816 (m) REVERT: A 270 ARG cc_start: 0.8129 (ptm160) cc_final: 0.7370 (ptt90) REVERT: A 305 GLN cc_start: 0.7656 (mp10) cc_final: 0.7264 (mp10) REVERT: A 383 GLU cc_start: 0.6711 (tm-30) cc_final: 0.6457 (tm-30) REVERT: A 458 TYR cc_start: 0.8008 (t80) cc_final: 0.7794 (t80) REVERT: A 508 GLN cc_start: 0.8041 (pm20) cc_final: 0.7479 (pm20) REVERT: A 576 ASP cc_start: 0.6457 (m-30) cc_final: 0.6063 (m-30) REVERT: A 603 LYS cc_start: 0.8448 (tppp) cc_final: 0.8176 (mmmt) REVERT: A 648 GLN cc_start: 0.8173 (tm130) cc_final: 0.7901 (tm-30) REVERT: A 702 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7681 (mm110) REVERT: B 103 LYS cc_start: 0.8252 (mmtt) cc_final: 0.8035 (mmtt) REVERT: B 108 ILE cc_start: 0.8372 (mp) cc_final: 0.8132 (mt) REVERT: B 133 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6989 (tt) REVERT: B 135 MET cc_start: 0.7240 (mmm) cc_final: 0.6828 (mmm) REVERT: B 139 ASP cc_start: 0.7943 (m-30) cc_final: 0.7632 (m-30) REVERT: B 250 ARG cc_start: 0.7643 (mmt-90) cc_final: 0.7403 (mmm-85) REVERT: B 266 ARG cc_start: 0.7623 (tpp-160) cc_final: 0.7295 (ttm110) REVERT: B 298 LYS cc_start: 0.8359 (mppt) cc_final: 0.8156 (mmmt) REVERT: B 316 THR cc_start: 0.8370 (m) cc_final: 0.7984 (t) REVERT: B 348 TYR cc_start: 0.7897 (t80) cc_final: 0.7245 (t80) REVERT: B 364 VAL cc_start: 0.8331 (t) cc_final: 0.7952 (m) REVERT: B 428 GLU cc_start: 0.7747 (tp30) cc_final: 0.7268 (tp30) REVERT: B 463 TYR cc_start: 0.7108 (t80) cc_final: 0.6610 (t80) REVERT: B 574 ASP cc_start: 0.6788 (t0) cc_final: 0.6243 (t0) REVERT: B 577 MET cc_start: 0.7384 (mtp) cc_final: 0.6726 (mtp) REVERT: B 672 GLU cc_start: 0.7510 (tp30) cc_final: 0.7248 (tp30) REVERT: B 699 VAL cc_start: 0.7602 (m) cc_final: 0.7185 (t) outliers start: 28 outliers final: 12 residues processed: 284 average time/residue: 0.5159 time to fit residues: 158.4399 Evaluate side-chains 279 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 264 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 0.0770 chunk 115 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 0.1980 chunk 77 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 0.0470 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS B 273 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 550 GLN B 605 ASN B 625 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.156214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.138623 restraints weight = 13965.298| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.08 r_work: 0.3807 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10544 Z= 0.115 Angle : 0.596 8.381 14351 Z= 0.291 Chirality : 0.044 0.224 1570 Planarity : 0.004 0.042 1806 Dihedral : 9.759 98.834 1596 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 2.61 % Allowed : 17.09 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.20 (0.24), residues: 1228 helix: 0.75 (0.27), residues: 390 sheet: -0.24 (0.48), residues: 132 loop : -0.58 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 701 TYR 0.015 0.001 TYR A 468 PHE 0.015 0.001 PHE A 577 TRP 0.013 0.001 TRP B 396 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00258 (10528) covalent geometry : angle 0.59002 (14312) SS BOND : bond 0.00382 ( 9) SS BOND : angle 1.03047 ( 18) hydrogen bonds : bond 0.03478 ( 291) hydrogen bonds : angle 4.95038 ( 810) link_ALPHA1-4 : bond 0.01669 ( 1) link_ALPHA1-4 : angle 1.82625 ( 3) link_BETA1-4 : bond 0.00551 ( 4) link_BETA1-4 : angle 1.88139 ( 12) link_NAG-ASN : bond 0.00666 ( 2) link_NAG-ASN : angle 2.87243 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7727 (pm20) cc_final: 0.7415 (pm20) REVERT: A 147 ASP cc_start: 0.7580 (t0) cc_final: 0.7301 (t0) REVERT: A 160 THR cc_start: 0.8127 (OUTLIER) cc_final: 0.7813 (m) REVERT: A 270 ARG cc_start: 0.8073 (ptm160) cc_final: 0.7701 (ptt90) REVERT: A 305 GLN cc_start: 0.7684 (mp10) cc_final: 0.7296 (mp10) REVERT: A 318 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7383 (mm-30) REVERT: A 458 TYR cc_start: 0.7912 (t80) cc_final: 0.7641 (t80) REVERT: A 508 GLN cc_start: 0.7973 (pm20) cc_final: 0.7416 (pm20) REVERT: A 576 ASP cc_start: 0.6503 (m-30) cc_final: 0.6057 (m-30) REVERT: A 603 LYS cc_start: 0.8446 (tppp) cc_final: 0.8212 (mmmt) REVERT: A 648 GLN cc_start: 0.8158 (tm130) cc_final: 0.7945 (tm-30) REVERT: B 103 LYS cc_start: 0.8254 (mmtt) cc_final: 0.8033 (mmtt) REVERT: B 135 MET cc_start: 0.7215 (mmm) cc_final: 0.6986 (mmm) REVERT: B 266 ARG cc_start: 0.7586 (tpp-160) cc_final: 0.7243 (ttm110) REVERT: B 298 LYS cc_start: 0.8357 (mppt) cc_final: 0.8128 (mppt) REVERT: B 348 TYR cc_start: 0.7857 (t80) cc_final: 0.7536 (t80) REVERT: B 364 VAL cc_start: 0.8250 (t) cc_final: 0.7856 (m) REVERT: B 369 LYS cc_start: 0.7939 (ttmm) cc_final: 0.7666 (ttmm) REVERT: B 428 GLU cc_start: 0.7683 (tp30) cc_final: 0.7127 (tp30) REVERT: B 463 TYR cc_start: 0.6989 (t80) cc_final: 0.6397 (t80) REVERT: B 512 VAL cc_start: 0.8060 (t) cc_final: 0.7758 (p) REVERT: B 574 ASP cc_start: 0.6816 (t0) cc_final: 0.6274 (t0) REVERT: B 577 MET cc_start: 0.7436 (mtp) cc_final: 0.6750 (mtp) REVERT: B 625 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7116 (p0) REVERT: B 672 GLU cc_start: 0.7640 (tp30) cc_final: 0.7334 (tp30) REVERT: B 699 VAL cc_start: 0.7346 (m) cc_final: 0.6075 (p) outliers start: 29 outliers final: 13 residues processed: 279 average time/residue: 0.5392 time to fit residues: 162.1481 Evaluate side-chains 280 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 265 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 625 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 78 optimal weight: 0.0020 chunk 24 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 21 optimal weight: 0.0670 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.3526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS A 702 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN B 625 ASN ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.156666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.138961 restraints weight = 13848.335| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.10 r_work: 0.3811 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10544 Z= 0.117 Angle : 0.613 9.376 14351 Z= 0.299 Chirality : 0.044 0.224 1570 Planarity : 0.004 0.042 1806 Dihedral : 9.421 99.477 1596 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 2.79 % Allowed : 18.08 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.19 (0.24), residues: 1228 helix: 0.83 (0.27), residues: 384 sheet: -0.27 (0.48), residues: 132 loop : -0.59 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 741 TYR 0.016 0.001 TYR A 468 PHE 0.013 0.001 PHE A 577 TRP 0.017 0.001 TRP B 394 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00264 (10528) covalent geometry : angle 0.60447 (14312) SS BOND : bond 0.00378 ( 9) SS BOND : angle 1.87449 ( 18) hydrogen bonds : bond 0.03455 ( 291) hydrogen bonds : angle 4.84540 ( 810) link_ALPHA1-4 : bond 0.01525 ( 1) link_ALPHA1-4 : angle 1.55824 ( 3) link_BETA1-4 : bond 0.00594 ( 4) link_BETA1-4 : angle 1.98140 ( 12) link_NAG-ASN : bond 0.00647 ( 2) link_NAG-ASN : angle 2.89159 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7521 (t0) cc_final: 0.7249 (t0) REVERT: A 160 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7749 (m) REVERT: A 209 PHE cc_start: 0.8077 (p90) cc_final: 0.7673 (p90) REVERT: A 270 ARG cc_start: 0.8065 (ptm160) cc_final: 0.7713 (ptt90) REVERT: A 305 GLN cc_start: 0.7630 (mp10) cc_final: 0.7236 (mp10) REVERT: A 314 ARG cc_start: 0.7153 (ttp-170) cc_final: 0.6882 (ttp-170) REVERT: A 318 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7366 (mm-30) REVERT: A 458 TYR cc_start: 0.7929 (t80) cc_final: 0.7706 (t80) REVERT: A 508 GLN cc_start: 0.7977 (pm20) cc_final: 0.7442 (pm20) REVERT: A 576 ASP cc_start: 0.6458 (m-30) cc_final: 0.6007 (m-30) REVERT: A 579 PHE cc_start: 0.8213 (t80) cc_final: 0.7912 (t80) REVERT: A 603 LYS cc_start: 0.8424 (tppp) cc_final: 0.8219 (mmmt) REVERT: B 135 MET cc_start: 0.7188 (mmm) cc_final: 0.6932 (mmm) REVERT: B 250 ARG cc_start: 0.7551 (mmt-90) cc_final: 0.7339 (mmm-85) REVERT: B 348 TYR cc_start: 0.7818 (t80) cc_final: 0.7552 (t80) REVERT: B 364 VAL cc_start: 0.8187 (t) cc_final: 0.7801 (m) REVERT: B 428 GLU cc_start: 0.7713 (tp30) cc_final: 0.7160 (tp30) REVERT: B 463 TYR cc_start: 0.7011 (t80) cc_final: 0.6401 (t80) REVERT: B 512 VAL cc_start: 0.8001 (t) cc_final: 0.7716 (p) REVERT: B 574 ASP cc_start: 0.6775 (t0) cc_final: 0.6142 (t0) REVERT: B 577 MET cc_start: 0.7231 (mtp) cc_final: 0.6539 (mtp) REVERT: B 600 TYR cc_start: 0.7799 (p90) cc_final: 0.7329 (p90) REVERT: B 699 VAL cc_start: 0.7318 (m) cc_final: 0.6052 (p) outliers start: 31 outliers final: 17 residues processed: 286 average time/residue: 0.5374 time to fit residues: 165.7029 Evaluate side-chains 275 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 257 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.0370 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 96 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS A 702 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.157028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.139285 restraints weight = 14034.673| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.12 r_work: 0.3816 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10544 Z= 0.119 Angle : 0.613 9.570 14351 Z= 0.296 Chirality : 0.044 0.224 1570 Planarity : 0.004 0.041 1806 Dihedral : 9.071 98.279 1596 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Rotamer: Outliers : 2.34 % Allowed : 19.24 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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 (0.25), residues: 1228 helix: 0.84 (0.27), residues: 385 sheet: -0.31 (0.48), residues: 132 loop : -0.55 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 243 TYR 0.017 0.001 TYR B 610 PHE 0.013 0.001 PHE A 577 TRP 0.041 0.001 TRP B 180 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00274 (10528) covalent geometry : angle 0.60664 (14312) SS BOND : bond 0.00464 ( 9) SS BOND : angle 1.27131 ( 18) hydrogen bonds : bond 0.03372 ( 291) hydrogen bonds : angle 4.80863 ( 810) link_ALPHA1-4 : bond 0.01521 ( 1) link_ALPHA1-4 : angle 1.79753 ( 3) link_BETA1-4 : bond 0.00549 ( 4) link_BETA1-4 : angle 1.98250 ( 12) link_NAG-ASN : bond 0.00642 ( 2) link_NAG-ASN : angle 2.81258 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 274 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7519 (t0) cc_final: 0.7245 (t0) REVERT: A 160 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7720 (m) REVERT: A 270 ARG cc_start: 0.8091 (ptm160) cc_final: 0.7728 (ptt90) REVERT: A 305 GLN cc_start: 0.7636 (mp10) cc_final: 0.7243 (mp10) REVERT: A 314 ARG cc_start: 0.7187 (ttp-170) cc_final: 0.6892 (ttp-170) REVERT: A 318 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7417 (mm-30) REVERT: A 458 TYR cc_start: 0.7936 (t80) cc_final: 0.7685 (t80) REVERT: A 508 GLN cc_start: 0.7991 (pm20) cc_final: 0.7444 (pm20) REVERT: A 576 ASP cc_start: 0.6463 (m-30) cc_final: 0.6008 (m-30) REVERT: A 710 SER cc_start: 0.8396 (p) cc_final: 0.8102 (m) REVERT: B 135 MET cc_start: 0.7141 (mmm) cc_final: 0.6870 (mmm) REVERT: B 250 ARG cc_start: 0.7513 (mmt-90) cc_final: 0.7308 (mmm-85) REVERT: B 364 VAL cc_start: 0.8178 (t) cc_final: 0.7769 (m) REVERT: B 428 GLU cc_start: 0.7666 (tp30) cc_final: 0.7096 (tp30) REVERT: B 512 VAL cc_start: 0.7984 (t) cc_final: 0.7710 (p) REVERT: B 574 ASP cc_start: 0.6751 (t0) cc_final: 0.6081 (t0) REVERT: B 577 MET cc_start: 0.7272 (mtp) cc_final: 0.6541 (mtp) REVERT: B 600 TYR cc_start: 0.7772 (p90) cc_final: 0.7488 (p90) REVERT: B 687 MET cc_start: 0.7348 (tpp) cc_final: 0.6977 (tpt) REVERT: B 699 VAL cc_start: 0.7318 (m) cc_final: 0.6026 (p) outliers start: 26 outliers final: 18 residues processed: 288 average time/residue: 0.5408 time to fit residues: 167.7746 Evaluate side-chains 279 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 260 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS A 702 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.155810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.138405 restraints weight = 14015.991| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.10 r_work: 0.3804 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10544 Z= 0.154 Angle : 0.638 8.748 14351 Z= 0.313 Chirality : 0.046 0.237 1570 Planarity : 0.005 0.077 1806 Dihedral : 9.022 96.795 1596 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.72 % Favored : 95.20 % Rotamer: Outliers : 2.43 % Allowed : 19.96 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 1228 helix: 0.72 (0.27), residues: 384 sheet: -0.41 (0.48), residues: 132 loop : -0.57 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 243 TYR 0.018 0.002 TYR B 610 PHE 0.015 0.002 PHE A 209 TRP 0.064 0.002 TRP B 180 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00362 (10528) covalent geometry : angle 0.63084 (14312) SS BOND : bond 0.00496 ( 9) SS BOND : angle 1.16469 ( 18) hydrogen bonds : bond 0.03530 ( 291) hydrogen bonds : angle 4.87446 ( 810) link_ALPHA1-4 : bond 0.01393 ( 1) link_ALPHA1-4 : angle 2.13058 ( 3) link_BETA1-4 : bond 0.00469 ( 4) link_BETA1-4 : angle 2.07022 ( 12) link_NAG-ASN : bond 0.00681 ( 2) link_NAG-ASN : angle 2.89038 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 264 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7481 (t0) cc_final: 0.7216 (t0) REVERT: A 270 ARG cc_start: 0.8112 (ptm160) cc_final: 0.7743 (ptt90) REVERT: A 305 GLN cc_start: 0.7662 (mp10) cc_final: 0.7284 (mp10) REVERT: A 314 ARG cc_start: 0.7161 (ttp-170) cc_final: 0.6891 (ttp-170) REVERT: A 318 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7363 (mm-30) REVERT: A 388 GLN cc_start: 0.7064 (mp10) cc_final: 0.6793 (mp10) REVERT: A 458 TYR cc_start: 0.7951 (t80) cc_final: 0.7703 (t80) REVERT: A 508 GLN cc_start: 0.8004 (pm20) cc_final: 0.7477 (pm20) REVERT: A 546 MET cc_start: 0.7422 (mmm) cc_final: 0.7179 (mmm) REVERT: A 576 ASP cc_start: 0.6414 (m-30) cc_final: 0.5950 (m-30) REVERT: A 603 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8145 (mmmt) REVERT: A 710 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.8075 (m) REVERT: B 135 MET cc_start: 0.7156 (mmm) cc_final: 0.6876 (mmm) REVERT: B 250 ARG cc_start: 0.7552 (mmt-90) cc_final: 0.7342 (mmm-85) REVERT: B 364 VAL cc_start: 0.8217 (t) cc_final: 0.7839 (m) REVERT: B 428 GLU cc_start: 0.7621 (tp30) cc_final: 0.7085 (tp30) REVERT: B 574 ASP cc_start: 0.6736 (t0) cc_final: 0.6033 (t0) REVERT: B 577 MET cc_start: 0.7294 (mtp) cc_final: 0.6553 (mtp) REVERT: B 600 TYR cc_start: 0.7669 (p90) cc_final: 0.7269 (p90) REVERT: B 687 MET cc_start: 0.7351 (tpp) cc_final: 0.7036 (tpt) REVERT: B 699 VAL cc_start: 0.7453 (m) cc_final: 0.6092 (p) outliers start: 27 outliers final: 18 residues processed: 277 average time/residue: 0.5428 time to fit residues: 161.8994 Evaluate side-chains 271 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 252 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 78 optimal weight: 0.0570 chunk 73 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 86 optimal weight: 0.0020 chunk 113 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.4308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS A 702 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.156783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.139212 restraints weight = 13871.249| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.10 r_work: 0.3820 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10544 Z= 0.127 Angle : 0.635 9.712 14351 Z= 0.312 Chirality : 0.045 0.231 1570 Planarity : 0.004 0.046 1806 Dihedral : 8.806 96.829 1596 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 2.34 % Allowed : 19.87 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.29 (0.25), residues: 1228 helix: 0.69 (0.27), residues: 385 sheet: -0.47 (0.48), residues: 134 loop : -0.59 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 182 TYR 0.015 0.001 TYR A 468 PHE 0.013 0.001 PHE A 577 TRP 0.070 0.002 TRP B 180 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00294 (10528) covalent geometry : angle 0.62917 (14312) SS BOND : bond 0.00446 ( 9) SS BOND : angle 0.93342 ( 18) hydrogen bonds : bond 0.03419 ( 291) hydrogen bonds : angle 4.92458 ( 810) link_ALPHA1-4 : bond 0.01576 ( 1) link_ALPHA1-4 : angle 2.06140 ( 3) link_BETA1-4 : bond 0.00572 ( 4) link_BETA1-4 : angle 1.95004 ( 12) link_NAG-ASN : bond 0.00663 ( 2) link_NAG-ASN : angle 2.73661 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7485 (t0) cc_final: 0.7211 (t0) REVERT: A 270 ARG cc_start: 0.8120 (ptm160) cc_final: 0.7724 (ptt90) REVERT: A 305 GLN cc_start: 0.7652 (mp10) cc_final: 0.7266 (mp10) REVERT: A 314 ARG cc_start: 0.7206 (ttp-170) cc_final: 0.6918 (ttp-170) REVERT: A 318 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7347 (mm-30) REVERT: A 458 TYR cc_start: 0.7946 (t80) cc_final: 0.7670 (t80) REVERT: A 508 GLN cc_start: 0.8013 (pm20) cc_final: 0.7467 (pm20) REVERT: A 546 MET cc_start: 0.7394 (mmm) cc_final: 0.7149 (mmm) REVERT: A 547 SER cc_start: 0.7512 (p) cc_final: 0.7250 (m) REVERT: A 576 ASP cc_start: 0.6436 (m-30) cc_final: 0.5961 (m-30) REVERT: A 603 LYS cc_start: 0.8388 (mmmt) cc_final: 0.8129 (mmmt) REVERT: A 710 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8080 (m) REVERT: B 135 MET cc_start: 0.7136 (mmm) cc_final: 0.6861 (mmm) REVERT: B 250 ARG cc_start: 0.7514 (mmt-90) cc_final: 0.7314 (mmm-85) REVERT: B 364 VAL cc_start: 0.8180 (t) cc_final: 0.7773 (m) REVERT: B 428 GLU cc_start: 0.7594 (tp30) cc_final: 0.7058 (tp30) REVERT: B 512 VAL cc_start: 0.7997 (t) cc_final: 0.7722 (p) REVERT: B 574 ASP cc_start: 0.6766 (t0) cc_final: 0.5998 (t0) REVERT: B 577 MET cc_start: 0.7259 (mtp) cc_final: 0.6522 (mtp) REVERT: B 600 TYR cc_start: 0.7700 (p90) cc_final: 0.7344 (p90) REVERT: B 699 VAL cc_start: 0.7307 (m) cc_final: 0.5981 (p) outliers start: 26 outliers final: 19 residues processed: 270 average time/residue: 0.5318 time to fit residues: 154.5459 Evaluate side-chains 275 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 255 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 435 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 0.0060 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 59 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 HIS A 702 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.156878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.139250 restraints weight = 13992.309| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.11 r_work: 0.3820 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10544 Z= 0.134 Angle : 0.643 9.657 14351 Z= 0.316 Chirality : 0.045 0.276 1570 Planarity : 0.004 0.057 1806 Dihedral : 8.658 95.740 1596 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 2.07 % Allowed : 20.50 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 1228 helix: 0.80 (0.28), residues: 379 sheet: -0.46 (0.48), residues: 134 loop : -0.61 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 182 TYR 0.016 0.001 TYR A 468 PHE 0.012 0.001 PHE A 577 TRP 0.064 0.002 TRP B 180 HIS 0.004 0.001 HIS B 276 Details of bonding type rmsd covalent geometry : bond 0.00315 (10528) covalent geometry : angle 0.63757 (14312) SS BOND : bond 0.00438 ( 9) SS BOND : angle 0.87610 ( 18) hydrogen bonds : bond 0.03480 ( 291) hydrogen bonds : angle 4.91766 ( 810) link_ALPHA1-4 : bond 0.01552 ( 1) link_ALPHA1-4 : angle 2.28066 ( 3) link_BETA1-4 : bond 0.00542 ( 4) link_BETA1-4 : angle 2.01826 ( 12) link_NAG-ASN : bond 0.00650 ( 2) link_NAG-ASN : angle 2.74221 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 0.376 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: A 147 ASP cc_start: 0.7472 (t0) cc_final: 0.7195 (t0) REVERT: A 270 ARG cc_start: 0.8130 (ptm160) cc_final: 0.7731 (ptt90) REVERT: A 305 GLN cc_start: 0.7675 (mp10) cc_final: 0.7277 (mp10) REVERT: A 314 ARG cc_start: 0.7244 (ttp-170) cc_final: 0.6957 (ttp-170) REVERT: A 318 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7361 (mm-30) REVERT: A 458 TYR cc_start: 0.7954 (t80) cc_final: 0.7667 (t80) REVERT: A 508 GLN cc_start: 0.8022 (pm20) cc_final: 0.7478 (pm20) REVERT: A 546 MET cc_start: 0.7451 (mmm) cc_final: 0.7195 (mmm) REVERT: A 576 ASP cc_start: 0.6477 (m-30) cc_final: 0.6010 (m-30) REVERT: A 603 LYS cc_start: 0.8395 (mmmt) cc_final: 0.8117 (mmmt) REVERT: A 710 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.8078 (m) REVERT: B 103 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7891 (tppt) REVERT: B 135 MET cc_start: 0.7146 (mmm) cc_final: 0.6850 (mmm) REVERT: B 364 VAL cc_start: 0.8167 (t) cc_final: 0.7766 (m) REVERT: B 428 GLU cc_start: 0.7589 (tp30) cc_final: 0.7048 (tp30) REVERT: B 574 ASP cc_start: 0.6807 (t0) cc_final: 0.6104 (t0) REVERT: B 577 MET cc_start: 0.7299 (mtp) cc_final: 0.6534 (mtp) REVERT: B 699 VAL cc_start: 0.7321 (m) cc_final: 0.5953 (p) outliers start: 23 outliers final: 15 residues processed: 262 average time/residue: 0.5580 time to fit residues: 156.6937 Evaluate side-chains 267 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 251 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 23 optimal weight: 0.0060 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 106 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.156676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.139072 restraints weight = 13899.300| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.12 r_work: 0.3816 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10544 Z= 0.144 Angle : 0.648 11.438 14351 Z= 0.318 Chirality : 0.045 0.239 1570 Planarity : 0.005 0.064 1806 Dihedral : 8.559 94.699 1596 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 1.71 % Allowed : 21.04 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.33 (0.24), residues: 1228 helix: 0.69 (0.27), residues: 385 sheet: -0.47 (0.48), residues: 134 loop : -0.65 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 182 TYR 0.014 0.002 TYR A 608 PHE 0.011 0.002 PHE A 209 TRP 0.059 0.002 TRP B 180 HIS 0.004 0.001 HIS A 448 Details of bonding type rmsd covalent geometry : bond 0.00340 (10528) covalent geometry : angle 0.64168 (14312) SS BOND : bond 0.00439 ( 9) SS BOND : angle 0.94451 ( 18) hydrogen bonds : bond 0.03560 ( 291) hydrogen bonds : angle 4.92071 ( 810) link_ALPHA1-4 : bond 0.01576 ( 1) link_ALPHA1-4 : angle 2.55245 ( 3) link_BETA1-4 : bond 0.00522 ( 4) link_BETA1-4 : angle 2.02220 ( 12) link_NAG-ASN : bond 0.00660 ( 2) link_NAG-ASN : angle 2.77821 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 0.405 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: A 147 ASP cc_start: 0.7453 (t0) cc_final: 0.7174 (t0) REVERT: A 256 ILE cc_start: 0.8663 (pt) cc_final: 0.8211 (mm) REVERT: A 270 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7709 (ptt90) REVERT: A 305 GLN cc_start: 0.7662 (mp10) cc_final: 0.7278 (mp10) REVERT: A 314 ARG cc_start: 0.7249 (ttp-170) cc_final: 0.6963 (ttp-170) REVERT: A 318 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7347 (mm-30) REVERT: A 458 TYR cc_start: 0.7942 (t80) cc_final: 0.7644 (t80) REVERT: A 508 GLN cc_start: 0.7968 (pm20) cc_final: 0.7424 (pm20) REVERT: A 546 MET cc_start: 0.7474 (mmm) cc_final: 0.7213 (mmm) REVERT: A 547 SER cc_start: 0.7543 (p) cc_final: 0.7270 (m) REVERT: A 576 ASP cc_start: 0.6471 (m-30) cc_final: 0.6010 (m-30) REVERT: A 603 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8094 (mmmt) REVERT: A 710 SER cc_start: 0.8377 (p) cc_final: 0.8086 (m) REVERT: B 103 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7998 (tppt) REVERT: B 135 MET cc_start: 0.7124 (mmm) cc_final: 0.6822 (mmm) REVERT: B 364 VAL cc_start: 0.8222 (t) cc_final: 0.7831 (m) REVERT: B 384 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7368 (tt0) REVERT: B 428 GLU cc_start: 0.7573 (tp30) cc_final: 0.7002 (tp30) REVERT: B 574 ASP cc_start: 0.6780 (t0) cc_final: 0.6046 (t0) REVERT: B 577 MET cc_start: 0.7161 (mtp) cc_final: 0.6351 (mtp) REVERT: B 699 VAL cc_start: 0.7376 (m) cc_final: 0.5995 (p) outliers start: 19 outliers final: 17 residues processed: 265 average time/residue: 0.5651 time to fit residues: 160.6962 Evaluate side-chains 268 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 251 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.0070 chunk 4 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 78 optimal weight: 0.0870 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.157418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.139887 restraints weight = 13946.541| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.11 r_work: 0.3826 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10544 Z= 0.133 Angle : 0.660 11.833 14351 Z= 0.319 Chirality : 0.045 0.234 1570 Planarity : 0.005 0.056 1806 Dihedral : 8.422 94.647 1596 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 1.89 % Allowed : 21.58 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: -0.29 (0.24), residues: 1228 helix: 0.77 (0.27), residues: 379 sheet: -0.37 (0.47), residues: 136 loop : -0.65 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 182 TYR 0.018 0.002 TYR B 399 PHE 0.025 0.001 PHE A 143 TRP 0.054 0.002 TRP B 180 HIS 0.004 0.001 HIS A 448 Details of bonding type rmsd covalent geometry : bond 0.00315 (10528) covalent geometry : angle 0.65454 (14312) SS BOND : bond 0.00414 ( 9) SS BOND : angle 0.87268 ( 18) hydrogen bonds : bond 0.03482 ( 291) hydrogen bonds : angle 4.92951 ( 810) link_ALPHA1-4 : bond 0.01627 ( 1) link_ALPHA1-4 : angle 2.58242 ( 3) link_BETA1-4 : bond 0.00544 ( 4) link_BETA1-4 : angle 1.98130 ( 12) link_NAG-ASN : bond 0.00690 ( 2) link_NAG-ASN : angle 2.69539 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4270.83 seconds wall clock time: 73 minutes 16.07 seconds (4396.07 seconds total)