Starting phenix.real_space_refine on Mon Jul 28 15:37:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sck_25037/07_2025/7sck_25037.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sck_25037/07_2025/7sck_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sck_25037/07_2025/7sck_25037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sck_25037/07_2025/7sck_25037.map" model { file = "/net/cci-nas-00/data/ceres_data/7sck_25037/07_2025/7sck_25037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sck_25037/07_2025/7sck_25037.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.02, per 1000 atoms: 0.59 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.09 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: 2.88 Time building geometry restraints manager: 3.02 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: 0.700 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 24.450 Find NCS groups from input model: 0.150 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:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.450 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (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 TRP 0.013 0.002 TRP B 556 HIS 0.003 0.001 HIS A 285 PHE 0.014 0.002 PHE B 306 TYR 0.025 0.002 TYR B 399 ARG 0.006 0.000 ARG B 562 Details of bonding type rmsd link_NAG-ASN : bond 0.00803 ( 2) link_NAG-ASN : angle 2.84728 ( 6) 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) hydrogen bonds : bond 0.17391 ( 291) hydrogen bonds : angle 6.51032 ( 810) SS BOND : bond 0.00333 ( 9) SS BOND : angle 1.21535 ( 18) covalent geometry : bond 0.00492 (10528) covalent geometry : angle 0.61464 (14312) *********************** 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 : 1.205 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: 1.1063 time to fit residues: 405.2915 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 : 1.155 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN B 669 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.155143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.137604 restraints weight = 13757.994| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.07 r_work: 0.3779 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1569 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= 0.151 Angle : 0.626 7.798 14351 Z= 0.308 Chirality : 0.045 0.236 1570 Planarity : 0.005 0.065 1806 Dihedral : 11.891 102.308 1598 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.07 % Allowed : 13.13 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1228 helix: 0.84 (0.27), residues: 390 sheet: 0.01 (0.51), residues: 110 loop : -0.53 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 396 HIS 0.004 0.001 HIS A 285 PHE 0.013 0.002 PHE B 684 TYR 0.021 0.002 TYR B 107 ARG 0.009 0.001 ARG A 243 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 2) link_NAG-ASN : angle 2.92650 ( 6) link_ALPHA1-4 : bond 0.01281 ( 1) link_ALPHA1-4 : angle 1.58267 ( 3) link_BETA1-4 : bond 0.00605 ( 4) link_BETA1-4 : angle 2.15039 ( 12) hydrogen bonds : bond 0.04357 ( 291) hydrogen bonds : angle 5.31881 ( 810) SS BOND : bond 0.00797 ( 9) SS BOND : angle 1.41826 ( 18) covalent geometry : bond 0.00341 (10528) covalent geometry : angle 0.61807 (14312) *********************** 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 298 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 275 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7733 (pm20) cc_final: 0.7477 (pm20) REVERT: A 105 ASP cc_start: 0.6532 (t70) cc_final: 0.6306 (t70) REVERT: A 147 ASP cc_start: 0.7572 (t0) cc_final: 0.7358 (t0) REVERT: A 270 ARG cc_start: 0.8122 (ptm-80) cc_final: 0.7290 (ptt90) REVERT: A 305 GLN cc_start: 0.7600 (mp10) cc_final: 0.7223 (mp10) REVERT: A 383 GLU cc_start: 0.6641 (tm-30) cc_final: 0.6361 (tm-30) REVERT: A 458 TYR cc_start: 0.7961 (t80) cc_final: 0.7758 (t80) REVERT: A 508 GLN cc_start: 0.7915 (pm20) cc_final: 0.7412 (pm20) REVERT: A 576 ASP cc_start: 0.6374 (m-30) cc_final: 0.6038 (m-30) REVERT: A 603 LYS cc_start: 0.8446 (tppp) cc_final: 0.8153 (mmmt) REVERT: A 648 GLN cc_start: 0.8189 (tm130) cc_final: 0.7873 (tm-30) REVERT: B 98 PHE cc_start: 0.8515 (t80) cc_final: 0.8314 (t80) REVERT: B 104 ILE cc_start: 0.8757 (tt) cc_final: 0.8542 (pt) REVERT: B 135 MET cc_start: 0.7238 (mmm) cc_final: 0.6984 (mmm) REVERT: B 144 THR cc_start: 0.8420 (p) cc_final: 0.8217 (m) REVERT: B 266 ARG cc_start: 0.7607 (tpp-160) cc_final: 0.7386 (tpp-160) REVERT: B 316 THR cc_start: 0.8363 (m) cc_final: 0.8013 (t) REVERT: B 348 TYR cc_start: 0.7859 (t80) cc_final: 0.7087 (t80) REVERT: B 364 VAL cc_start: 0.8315 (t) cc_final: 0.7945 (m) REVERT: B 369 LYS cc_start: 0.7877 (tttp) cc_final: 0.7650 (tttp) REVERT: B 372 ASP cc_start: 0.7783 (m-30) cc_final: 0.7464 (m-30) REVERT: B 463 TYR cc_start: 0.7089 (t80) cc_final: 0.6653 (t80) REVERT: B 518 LYS cc_start: 0.7936 (mtpp) cc_final: 0.7669 (mtmm) REVERT: B 574 ASP cc_start: 0.6757 (t0) cc_final: 0.6228 (t0) REVERT: B 577 MET cc_start: 0.7276 (mtp) cc_final: 0.6727 (mtp) REVERT: B 592 MET cc_start: 0.7687 (mtp) cc_final: 0.7251 (mtp) REVERT: B 672 GLU cc_start: 0.7690 (tp30) cc_final: 0.7140 (tp30) REVERT: B 687 MET cc_start: 0.7373 (tpp) cc_final: 0.6802 (tpt) REVERT: B 697 ASP cc_start: 0.8082 (m-30) cc_final: 0.7865 (m-30) REVERT: B 699 VAL cc_start: 0.7432 (m) cc_final: 0.6994 (t) outliers start: 23 outliers final: 7 residues processed: 286 average time/residue: 1.1311 time to fit residues: 348.8355 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 : 1.187 ------------------------------------------------------------------------------- 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 40 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 719 HIS B 273 GLN B 313 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.154342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.136741 restraints weight = 13894.905| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.08 r_work: 0.3781 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10544 Z= 0.166 Angle : 0.620 7.296 14351 Z= 0.305 Chirality : 0.045 0.241 1570 Planarity : 0.005 0.046 1806 Dihedral : 10.791 98.037 1596 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.52 % Allowed : 15.83 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1228 helix: 0.72 (0.27), residues: 390 sheet: 0.01 (0.48), residues: 126 loop : -0.64 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 396 HIS 0.003 0.001 HIS A 448 PHE 0.014 0.002 PHE B 306 TYR 0.015 0.001 TYR A 608 ARG 0.006 0.001 ARG A 243 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 2) link_NAG-ASN : angle 3.04997 ( 6) link_ALPHA1-4 : bond 0.01402 ( 1) link_ALPHA1-4 : angle 2.13357 ( 3) link_BETA1-4 : bond 0.00537 ( 4) link_BETA1-4 : angle 2.14994 ( 12) hydrogen bonds : bond 0.04123 ( 291) hydrogen bonds : angle 5.13111 ( 810) SS BOND : bond 0.00747 ( 9) SS BOND : angle 0.99565 ( 18) covalent geometry : bond 0.00376 (10528) covalent geometry : angle 0.61240 (14312) *********************** 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 299 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 271 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7785 (pm20) cc_final: 0.7493 (pm20) REVERT: A 147 ASP cc_start: 0.7597 (t0) cc_final: 0.7356 (t0) REVERT: A 160 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7805 (m) REVERT: A 270 ARG cc_start: 0.8147 (ptm160) cc_final: 0.7381 (ptt90) REVERT: A 305 GLN cc_start: 0.7658 (mp10) cc_final: 0.7275 (mp10) REVERT: A 383 GLU cc_start: 0.6691 (tm-30) cc_final: 0.6432 (tm-30) REVERT: A 458 TYR cc_start: 0.7979 (t80) cc_final: 0.7743 (t80) REVERT: A 508 GLN cc_start: 0.8022 (pm20) cc_final: 0.7464 (pm20) REVERT: A 576 ASP cc_start: 0.6442 (m-30) cc_final: 0.6045 (m-30) REVERT: A 603 LYS cc_start: 0.8449 (tppp) cc_final: 0.8195 (mmmt) REVERT: A 648 GLN cc_start: 0.8161 (tm130) cc_final: 0.7895 (tm-30) REVERT: B 108 ILE cc_start: 0.8359 (mp) cc_final: 0.8120 (mt) REVERT: B 133 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.7004 (tp) REVERT: B 135 MET cc_start: 0.7240 (mmm) cc_final: 0.6976 (mmm) REVERT: B 250 ARG cc_start: 0.7615 (mmt-90) cc_final: 0.7390 (mmm-85) REVERT: B 266 ARG cc_start: 0.7645 (tpp-160) cc_final: 0.7311 (ttm110) REVERT: B 316 THR cc_start: 0.8356 (m) cc_final: 0.7977 (t) REVERT: B 348 TYR cc_start: 0.7874 (t80) cc_final: 0.7235 (t80) REVERT: B 364 VAL cc_start: 0.8304 (t) cc_final: 0.7924 (m) REVERT: B 428 GLU cc_start: 0.7751 (tp30) cc_final: 0.7272 (tp30) REVERT: B 463 TYR cc_start: 0.7043 (t80) cc_final: 0.6508 (t80) REVERT: B 574 ASP cc_start: 0.6774 (t0) cc_final: 0.6218 (t0) REVERT: B 577 MET cc_start: 0.7424 (mtp) cc_final: 0.6790 (mtp) REVERT: B 672 GLU cc_start: 0.7468 (tp30) cc_final: 0.7256 (tp30) REVERT: B 699 VAL cc_start: 0.7544 (m) cc_final: 0.7116 (t) outliers start: 28 outliers final: 13 residues processed: 285 average time/residue: 1.6788 time to fit residues: 520.3300 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 : 1.239 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 628 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 42 optimal weight: 0.0270 chunk 7 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.152408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.134604 restraints weight = 13833.738| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.10 r_work: 0.3753 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10544 Z= 0.234 Angle : 0.662 9.829 14351 Z= 0.324 Chirality : 0.048 0.254 1570 Planarity : 0.005 0.050 1806 Dihedral : 10.412 97.003 1596 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.79 % Rotamer: Outliers : 3.15 % Allowed : 17.27 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1228 helix: 0.52 (0.27), residues: 389 sheet: -0.19 (0.48), residues: 127 loop : -0.75 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 396 HIS 0.004 0.001 HIS B 571 PHE 0.018 0.002 PHE A 226 TYR 0.020 0.002 TYR B 610 ARG 0.004 0.001 ARG A 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00892 ( 2) link_NAG-ASN : angle 3.22441 ( 6) link_ALPHA1-4 : bond 0.01298 ( 1) link_ALPHA1-4 : angle 2.46047 ( 3) link_BETA1-4 : bond 0.00496 ( 4) link_BETA1-4 : angle 2.24417 ( 12) hydrogen bonds : bond 0.04261 ( 291) hydrogen bonds : angle 5.10511 ( 810) SS BOND : bond 0.00512 ( 9) SS BOND : angle 1.39986 ( 18) covalent geometry : bond 0.00539 (10528) covalent geometry : angle 0.65391 (14312) *********************** 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 313 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 278 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7781 (pm20) cc_final: 0.7517 (pm20) REVERT: A 105 ASP cc_start: 0.6575 (t70) cc_final: 0.6365 (p0) REVERT: A 108 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8276 (mm) REVERT: A 147 ASP cc_start: 0.7596 (t0) cc_final: 0.7324 (t0) REVERT: A 160 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7802 (m) REVERT: A 270 ARG cc_start: 0.8115 (ptm160) cc_final: 0.7730 (ptt90) REVERT: A 305 GLN cc_start: 0.7733 (mp10) cc_final: 0.7366 (mp10) REVERT: A 318 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7446 (mm-30) REVERT: A 458 TYR cc_start: 0.8026 (t80) cc_final: 0.7821 (t80) REVERT: A 508 GLN cc_start: 0.8061 (pm20) cc_final: 0.7520 (pm20) REVERT: A 576 ASP cc_start: 0.6522 (m-30) cc_final: 0.6140 (m-30) REVERT: A 603 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8196 (mmmt) REVERT: B 108 ILE cc_start: 0.8354 (mp) cc_final: 0.8132 (mt) REVERT: B 133 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.7026 (tt) REVERT: B 135 MET cc_start: 0.7295 (mmm) cc_final: 0.6889 (mmm) REVERT: B 139 ASP cc_start: 0.7919 (m-30) cc_final: 0.7628 (m-30) REVERT: B 266 ARG cc_start: 0.7649 (tpp-160) cc_final: 0.7318 (ttm110) REVERT: B 298 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8311 (mtmt) REVERT: B 348 TYR cc_start: 0.7935 (t80) cc_final: 0.7655 (t80) REVERT: B 364 VAL cc_start: 0.8344 (t) cc_final: 0.7963 (m) REVERT: B 369 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7680 (ttmm) REVERT: B 428 GLU cc_start: 0.7788 (tp30) cc_final: 0.7202 (tp30) REVERT: B 463 TYR cc_start: 0.7198 (t80) cc_final: 0.6606 (t80) REVERT: B 510 LYS cc_start: 0.8194 (ptmt) cc_final: 0.7862 (ptpt) REVERT: B 574 ASP cc_start: 0.6795 (t0) cc_final: 0.6213 (t0) REVERT: B 577 MET cc_start: 0.7434 (mtp) cc_final: 0.6728 (mtp) REVERT: B 600 TYR cc_start: 0.7863 (p90) cc_final: 0.7385 (p90) REVERT: B 672 GLU cc_start: 0.7649 (tp30) cc_final: 0.7285 (tp30) REVERT: B 699 VAL cc_start: 0.7654 (m) cc_final: 0.7252 (t) outliers start: 35 outliers final: 16 residues processed: 293 average time/residue: 1.1477 time to fit residues: 362.4108 Evaluate side-chains 285 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 264 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 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 603 LYS 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 298 LYS Chi-restraints excluded: chain B residue 305 VAL 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 Chi-restraints excluded: chain B residue 548 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 550 GLN ** 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 = 0.4112 r_free = 0.4112 target = 0.153998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.136510 restraints weight = 13880.876| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.07 r_work: 0.3777 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10544 Z= 0.159 Angle : 0.631 8.568 14351 Z= 0.308 Chirality : 0.046 0.237 1570 Planarity : 0.005 0.048 1806 Dihedral : 9.814 97.469 1596 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.72 % Favored : 95.20 % Rotamer: Outliers : 3.33 % Allowed : 17.99 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.24), residues: 1228 helix: 0.60 (0.27), residues: 390 sheet: -0.29 (0.50), residues: 117 loop : -0.67 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 396 HIS 0.003 0.001 HIS A 285 PHE 0.013 0.002 PHE A 577 TYR 0.021 0.002 TYR B 610 ARG 0.008 0.001 ARG A 741 Details of bonding type rmsd link_NAG-ASN : bond 0.00694 ( 2) link_NAG-ASN : angle 3.00084 ( 6) link_ALPHA1-4 : bond 0.01492 ( 1) link_ALPHA1-4 : angle 2.23353 ( 3) link_BETA1-4 : bond 0.00539 ( 4) link_BETA1-4 : angle 2.08862 ( 12) hydrogen bonds : bond 0.03920 ( 291) hydrogen bonds : angle 5.00715 ( 810) SS BOND : bond 0.00838 ( 9) SS BOND : angle 1.27632 ( 18) covalent geometry : bond 0.00366 (10528) covalent geometry : angle 0.62373 (14312) *********************** 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 300 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 263 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7786 (pm20) cc_final: 0.7526 (pm20) REVERT: A 105 ASP cc_start: 0.6491 (t70) cc_final: 0.5912 (p0) REVERT: A 108 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7973 (mm) REVERT: A 147 ASP cc_start: 0.7597 (t0) cc_final: 0.7309 (t0) REVERT: A 160 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7833 (m) REVERT: A 270 ARG cc_start: 0.8103 (ptm160) cc_final: 0.7706 (ptt90) REVERT: A 305 GLN cc_start: 0.7687 (mp10) cc_final: 0.7299 (mp10) REVERT: A 318 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7416 (mm-30) REVERT: A 388 GLN cc_start: 0.6992 (mp10) cc_final: 0.6627 (mp10) REVERT: A 458 TYR cc_start: 0.7962 (t80) cc_final: 0.7758 (t80) REVERT: A 508 GLN cc_start: 0.7967 (pm20) cc_final: 0.7429 (pm20) REVERT: A 576 ASP cc_start: 0.6499 (m-30) cc_final: 0.6068 (m-30) REVERT: A 579 PHE cc_start: 0.8190 (t80) cc_final: 0.7887 (t80) REVERT: A 603 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8207 (mmmt) REVERT: B 103 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7925 (mmtt) REVERT: B 108 ILE cc_start: 0.8324 (mp) cc_final: 0.8109 (mt) REVERT: B 133 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.7028 (tp) REVERT: B 135 MET cc_start: 0.7231 (mmm) cc_final: 0.6983 (mmm) REVERT: B 266 ARG cc_start: 0.7596 (tpp-160) cc_final: 0.7258 (ttm110) REVERT: B 298 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8293 (mmmt) REVERT: B 348 TYR cc_start: 0.7912 (t80) cc_final: 0.7569 (t80) REVERT: B 364 VAL cc_start: 0.8328 (t) cc_final: 0.7953 (m) REVERT: B 369 LYS cc_start: 0.7930 (ttmm) cc_final: 0.7615 (ttmm) REVERT: B 428 GLU cc_start: 0.7753 (tp30) cc_final: 0.7128 (tp30) REVERT: B 463 TYR cc_start: 0.7138 (t80) cc_final: 0.6581 (t80) REVERT: B 574 ASP cc_start: 0.6789 (t0) cc_final: 0.6267 (t0) REVERT: B 577 MET cc_start: 0.7412 (mtp) cc_final: 0.6718 (mtp) REVERT: B 600 TYR cc_start: 0.7829 (p90) cc_final: 0.7360 (p90) REVERT: B 672 GLU cc_start: 0.7704 (tp30) cc_final: 0.7323 (tp30) REVERT: B 699 VAL cc_start: 0.7576 (m) cc_final: 0.7151 (t) outliers start: 37 outliers final: 20 residues processed: 281 average time/residue: 1.1548 time to fit residues: 349.8271 Evaluate side-chains 281 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 256 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 603 LYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 298 LYS 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 446 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 548 GLU 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 20 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS A 702 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN B 384 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.153549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.135848 restraints weight = 13962.848| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.09 r_work: 0.3772 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10544 Z= 0.182 Angle : 0.648 9.847 14351 Z= 0.318 Chirality : 0.047 0.244 1570 Planarity : 0.005 0.049 1806 Dihedral : 9.620 96.733 1596 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.72 % Favored : 95.20 % Rotamer: Outliers : 2.97 % Allowed : 17.99 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1228 helix: 0.57 (0.27), residues: 389 sheet: -0.43 (0.48), residues: 132 loop : -0.70 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 502 HIS 0.004 0.001 HIS A 448 PHE 0.014 0.002 PHE B 306 TYR 0.019 0.002 TYR B 610 ARG 0.007 0.001 ARG A 741 Details of bonding type rmsd link_NAG-ASN : bond 0.00740 ( 2) link_NAG-ASN : angle 3.04899 ( 6) link_ALPHA1-4 : bond 0.01473 ( 1) link_ALPHA1-4 : angle 2.39601 ( 3) link_BETA1-4 : bond 0.00510 ( 4) link_BETA1-4 : angle 2.16501 ( 12) hydrogen bonds : bond 0.03994 ( 291) hydrogen bonds : angle 5.03769 ( 810) SS BOND : bond 0.00482 ( 9) SS BOND : angle 1.64009 ( 18) covalent geometry : bond 0.00424 (10528) covalent geometry : angle 0.63919 (14312) *********************** 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 295 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 262 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7807 (pm20) cc_final: 0.7548 (pm20) REVERT: A 160 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7820 (m) REVERT: A 270 ARG cc_start: 0.8109 (ptm160) cc_final: 0.7707 (ptt90) REVERT: A 305 GLN cc_start: 0.7691 (mp10) cc_final: 0.7306 (mp10) REVERT: A 311 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6994 (mtt90) REVERT: A 318 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7365 (mm-30) REVERT: A 388 GLN cc_start: 0.6979 (mp10) cc_final: 0.6595 (mp10) REVERT: A 508 GLN cc_start: 0.7973 (pm20) cc_final: 0.7427 (pm20) REVERT: A 576 ASP cc_start: 0.6502 (m-30) cc_final: 0.6042 (m-30) REVERT: A 579 PHE cc_start: 0.8188 (t80) cc_final: 0.7883 (t80) REVERT: A 603 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8213 (mmmt) REVERT: A 701 ARG cc_start: 0.8029 (mtt-85) cc_final: 0.7720 (mtp180) REVERT: B 103 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7853 (mmtt) REVERT: B 108 ILE cc_start: 0.8316 (mp) cc_final: 0.8099 (mt) REVERT: B 133 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.7022 (tt) REVERT: B 135 MET cc_start: 0.7243 (mmm) cc_final: 0.6975 (mmm) REVERT: B 266 ARG cc_start: 0.7617 (tpp-160) cc_final: 0.7298 (ttm110) REVERT: B 364 VAL cc_start: 0.8318 (t) cc_final: 0.7944 (m) REVERT: B 428 GLU cc_start: 0.7691 (tp30) cc_final: 0.7050 (tp30) REVERT: B 463 TYR cc_start: 0.7074 (t80) cc_final: 0.6487 (t80) REVERT: B 574 ASP cc_start: 0.6725 (t0) cc_final: 0.6207 (t0) REVERT: B 577 MET cc_start: 0.7381 (mtp) cc_final: 0.6663 (mtp) REVERT: B 600 TYR cc_start: 0.7821 (p90) cc_final: 0.7374 (p90) REVERT: B 672 GLU cc_start: 0.7714 (tp30) cc_final: 0.7335 (tp30) REVERT: B 699 VAL cc_start: 0.7620 (m) cc_final: 0.7204 (t) outliers start: 33 outliers final: 20 residues processed: 277 average time/residue: 1.2461 time to fit residues: 373.0391 Evaluate side-chains 277 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 254 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 320 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 603 LYS 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 A residue 744 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 133 LEU 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 305 VAL 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 548 GLU 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 53 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 397 HIS ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 430 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.154760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.136984 restraints weight = 14003.757| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.10 r_work: 0.3786 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10544 Z= 0.147 Angle : 0.637 9.812 14351 Z= 0.312 Chirality : 0.046 0.236 1570 Planarity : 0.004 0.047 1806 Dihedral : 9.237 96.394 1596 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 2.88 % Allowed : 18.79 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1228 helix: 0.60 (0.27), residues: 390 sheet: -0.42 (0.48), residues: 132 loop : -0.68 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 180 HIS 0.003 0.001 HIS A 241 PHE 0.012 0.001 PHE A 577 TYR 0.019 0.002 TYR A 608 ARG 0.007 0.001 ARG A 243 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 2) link_NAG-ASN : angle 2.87155 ( 6) link_ALPHA1-4 : bond 0.01517 ( 1) link_ALPHA1-4 : angle 2.33905 ( 3) link_BETA1-4 : bond 0.00531 ( 4) link_BETA1-4 : angle 2.03762 ( 12) hydrogen bonds : bond 0.03743 ( 291) hydrogen bonds : angle 4.97188 ( 810) SS BOND : bond 0.00420 ( 9) SS BOND : angle 1.54562 ( 18) covalent geometry : bond 0.00341 (10528) covalent geometry : angle 0.62905 (14312) *********************** 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 295 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ARG cc_start: 0.8124 (ptm160) cc_final: 0.7720 (ptt90) REVERT: A 305 GLN cc_start: 0.7679 (mp10) cc_final: 0.7301 (mp10) REVERT: A 311 ARG cc_start: 0.7176 (mtm-85) cc_final: 0.6941 (mtt90) REVERT: A 318 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7376 (mm-30) REVERT: A 388 GLN cc_start: 0.7001 (mp10) cc_final: 0.6630 (mp10) REVERT: A 508 GLN cc_start: 0.7979 (pm20) cc_final: 0.7438 (pm20) REVERT: A 576 ASP cc_start: 0.6514 (m-30) cc_final: 0.6057 (m-30) REVERT: A 579 PHE cc_start: 0.8173 (t80) cc_final: 0.7859 (t80) REVERT: A 603 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8215 (mmmt) REVERT: B 103 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7837 (mmtt) REVERT: B 133 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.7010 (tp) REVERT: B 135 MET cc_start: 0.7264 (mmm) cc_final: 0.6989 (mmm) REVERT: B 266 ARG cc_start: 0.7633 (tpp-160) cc_final: 0.7304 (ttm110) REVERT: B 364 VAL cc_start: 0.8297 (t) cc_final: 0.7917 (m) REVERT: B 369 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7675 (ttmm) REVERT: B 428 GLU cc_start: 0.7660 (tp30) cc_final: 0.7020 (tp30) REVERT: B 574 ASP cc_start: 0.6706 (t0) cc_final: 0.6181 (t0) REVERT: B 577 MET cc_start: 0.7430 (mtp) cc_final: 0.6693 (mtp) REVERT: B 600 TYR cc_start: 0.7793 (p90) cc_final: 0.7480 (p90) REVERT: B 672 GLU cc_start: 0.7750 (tp30) cc_final: 0.7387 (tp30) REVERT: B 699 VAL cc_start: 0.7541 (m) cc_final: 0.7086 (t) outliers start: 32 outliers final: 20 residues processed: 278 average time/residue: 1.6932 time to fit residues: 505.9163 Evaluate side-chains 278 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 256 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 241 HIS 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 603 LYS 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 93 VAL Chi-restraints excluded: chain B residue 133 LEU 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 305 VAL 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 548 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0970 chunk 69 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 120 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 397 HIS ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 GLN B 430 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.155227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.137498 restraints weight = 13951.981| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.10 r_work: 0.3791 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2571 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= 0.143 Angle : 0.648 10.716 14351 Z= 0.318 Chirality : 0.046 0.233 1570 Planarity : 0.005 0.046 1806 Dihedral : 9.031 95.902 1596 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 2.79 % Allowed : 20.05 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1228 helix: 0.56 (0.27), residues: 391 sheet: -0.49 (0.48), residues: 132 loop : -0.67 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP B 180 HIS 0.003 0.001 HIS A 448 PHE 0.014 0.001 PHE A 577 TYR 0.017 0.001 TYR A 608 ARG 0.009 0.001 ARG A 243 Details of bonding type rmsd link_NAG-ASN : bond 0.00677 ( 2) link_NAG-ASN : angle 2.80053 ( 6) link_ALPHA1-4 : bond 0.01550 ( 1) link_ALPHA1-4 : angle 2.39366 ( 3) link_BETA1-4 : bond 0.00555 ( 4) link_BETA1-4 : angle 2.04363 ( 12) hydrogen bonds : bond 0.03637 ( 291) hydrogen bonds : angle 5.01977 ( 810) SS BOND : bond 0.00375 ( 9) SS BOND : angle 1.35724 ( 18) covalent geometry : bond 0.00332 (10528) covalent geometry : angle 0.64138 (14312) *********************** 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 295 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 264 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7573 (t0) cc_final: 0.7297 (t0) REVERT: A 270 ARG cc_start: 0.8144 (ptm160) cc_final: 0.7745 (ptt90) REVERT: A 305 GLN cc_start: 0.7663 (mp10) cc_final: 0.7283 (mp10) REVERT: A 311 ARG cc_start: 0.7211 (mtm-85) cc_final: 0.6968 (mtt90) REVERT: A 318 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7374 (mm-30) REVERT: A 388 GLN cc_start: 0.7116 (mp10) cc_final: 0.6690 (mp10) REVERT: A 508 GLN cc_start: 0.7989 (pm20) cc_final: 0.7449 (pm20) REVERT: A 576 ASP cc_start: 0.6512 (m-30) cc_final: 0.6048 (m-30) REVERT: A 579 PHE cc_start: 0.8150 (t80) cc_final: 0.7913 (t80) REVERT: A 603 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8206 (mmmt) REVERT: A 710 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8147 (m) REVERT: B 103 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7811 (mmtt) REVERT: B 133 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.7009 (tp) REVERT: B 135 MET cc_start: 0.7286 (mmm) cc_final: 0.7006 (mmm) REVERT: B 266 ARG cc_start: 0.7616 (tpp-160) cc_final: 0.7278 (ttm110) REVERT: B 364 VAL cc_start: 0.8287 (t) cc_final: 0.7916 (m) REVERT: B 369 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7621 (ttmm) REVERT: B 428 GLU cc_start: 0.7600 (tp30) cc_final: 0.7061 (tp30) REVERT: B 574 ASP cc_start: 0.6739 (t0) cc_final: 0.6204 (t0) REVERT: B 577 MET cc_start: 0.7408 (mtp) cc_final: 0.6671 (mtp) REVERT: B 600 TYR cc_start: 0.7689 (p90) cc_final: 0.7331 (p90) REVERT: B 610 TYR cc_start: 0.7876 (m-80) cc_final: 0.7647 (m-80) REVERT: B 672 GLU cc_start: 0.7729 (tp30) cc_final: 0.7386 (tp30) REVERT: B 699 VAL cc_start: 0.7530 (m) cc_final: 0.7067 (t) outliers start: 31 outliers final: 20 residues processed: 278 average time/residue: 1.5454 time to fit residues: 464.7872 Evaluate side-chains 281 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 258 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 132 GLN 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 603 LYS 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 133 LEU 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 305 VAL 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 548 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 10 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN 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 = 0.4126 r_free = 0.4126 target = 0.155327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.137435 restraints weight = 14031.387| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.13 r_work: 0.3791 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10544 Z= 0.150 Angle : 0.659 10.130 14351 Z= 0.325 Chirality : 0.046 0.236 1570 Planarity : 0.005 0.057 1806 Dihedral : 8.909 95.259 1596 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 2.70 % Allowed : 20.41 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1228 helix: 0.52 (0.27), residues: 391 sheet: -0.54 (0.48), residues: 132 loop : -0.67 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP B 180 HIS 0.004 0.001 HIS A 241 PHE 0.014 0.001 PHE A 577 TYR 0.020 0.001 TYR A 608 ARG 0.011 0.001 ARG B 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 2) link_NAG-ASN : angle 2.76317 ( 6) link_ALPHA1-4 : bond 0.01565 ( 1) link_ALPHA1-4 : angle 2.53089 ( 3) link_BETA1-4 : bond 0.00542 ( 4) link_BETA1-4 : angle 2.06661 ( 12) hydrogen bonds : bond 0.03707 ( 291) hydrogen bonds : angle 5.04421 ( 810) SS BOND : bond 0.00390 ( 9) SS BOND : angle 1.29656 ( 18) covalent geometry : bond 0.00352 (10528) covalent geometry : angle 0.65235 (14312) *********************** 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 281 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 251 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7570 (t0) cc_final: 0.7308 (t0) REVERT: A 256 ILE cc_start: 0.8588 (pt) cc_final: 0.8195 (mm) REVERT: A 270 ARG cc_start: 0.8180 (ptm160) cc_final: 0.7770 (ptt90) REVERT: A 277 SER cc_start: 0.7792 (p) cc_final: 0.7426 (t) REVERT: A 305 GLN cc_start: 0.7685 (mp10) cc_final: 0.7296 (mp10) REVERT: A 311 ARG cc_start: 0.7190 (mtm-85) cc_final: 0.6931 (mtt90) REVERT: A 318 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7363 (mm-30) REVERT: A 388 GLN cc_start: 0.7137 (mp10) cc_final: 0.6718 (mp10) REVERT: A 508 GLN cc_start: 0.8010 (pm20) cc_final: 0.7469 (pm20) REVERT: A 546 MET cc_start: 0.7457 (mmm) cc_final: 0.7214 (mmm) REVERT: A 576 ASP cc_start: 0.6516 (m-30) cc_final: 0.6052 (m-30) REVERT: A 579 PHE cc_start: 0.8132 (t80) cc_final: 0.7876 (t80) REVERT: A 603 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8205 (mmmt) REVERT: A 710 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8158 (m) REVERT: B 133 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.7019 (tp) REVERT: B 135 MET cc_start: 0.7315 (mmm) cc_final: 0.7026 (mmm) REVERT: B 250 ARG cc_start: 0.7379 (mmt-90) cc_final: 0.7160 (mmm-85) REVERT: B 266 ARG cc_start: 0.7621 (tpp-160) cc_final: 0.7274 (ttm110) REVERT: B 364 VAL cc_start: 0.8288 (t) cc_final: 0.7902 (m) REVERT: B 369 LYS cc_start: 0.7953 (ttmm) cc_final: 0.7679 (ttmm) REVERT: B 428 GLU cc_start: 0.7601 (tp30) cc_final: 0.7090 (tp30) REVERT: B 558 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7707 (mt-10) REVERT: B 574 ASP cc_start: 0.6797 (t0) cc_final: 0.6252 (t0) REVERT: B 577 MET cc_start: 0.7322 (mtp) cc_final: 0.6534 (mtp) REVERT: B 672 GLU cc_start: 0.7699 (tp30) cc_final: 0.7334 (tp30) REVERT: B 699 VAL cc_start: 0.7519 (m) cc_final: 0.7063 (t) outliers start: 30 outliers final: 22 residues processed: 261 average time/residue: 1.4424 time to fit residues: 404.0960 Evaluate side-chains 274 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 132 GLN 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 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 603 LYS 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 93 VAL Chi-restraints excluded: chain B residue 133 LEU 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 305 VAL 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 548 GLU Chi-restraints excluded: chain B residue 650 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 98 optimal weight: 0.4980 chunk 70 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 678 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 = 0.4130 r_free = 0.4130 target = 0.155580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.137840 restraints weight = 13931.680| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.09 r_work: 0.3795 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10544 Z= 0.150 Angle : 0.667 12.750 14351 Z= 0.328 Chirality : 0.046 0.236 1570 Planarity : 0.005 0.057 1806 Dihedral : 8.783 94.696 1596 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.72 % Favored : 95.20 % Rotamer: Outliers : 2.25 % Allowed : 21.13 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1228 helix: 0.52 (0.27), residues: 391 sheet: -0.54 (0.49), residues: 122 loop : -0.63 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 180 HIS 0.005 0.001 HIS B 571 PHE 0.014 0.001 PHE A 577 TYR 0.019 0.002 TYR A 608 ARG 0.013 0.001 ARG B 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00655 ( 2) link_NAG-ASN : angle 2.74289 ( 6) link_ALPHA1-4 : bond 0.01597 ( 1) link_ALPHA1-4 : angle 2.66081 ( 3) link_BETA1-4 : bond 0.00549 ( 4) link_BETA1-4 : angle 2.05860 ( 12) hydrogen bonds : bond 0.03741 ( 291) hydrogen bonds : angle 5.02733 ( 810) SS BOND : bond 0.00379 ( 9) SS BOND : angle 1.15537 ( 18) covalent geometry : bond 0.00355 (10528) covalent geometry : angle 0.66089 (14312) ********************** 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 278 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ASP cc_start: 0.7552 (t0) cc_final: 0.7286 (t0) REVERT: A 256 ILE cc_start: 0.8573 (pt) cc_final: 0.8209 (mm) REVERT: A 270 ARG cc_start: 0.8169 (ptm160) cc_final: 0.7747 (ptt90) REVERT: A 277 SER cc_start: 0.7795 (p) cc_final: 0.7435 (t) REVERT: A 305 GLN cc_start: 0.7693 (mp10) cc_final: 0.7303 (mp10) REVERT: A 311 ARG cc_start: 0.7200 (mtm-85) cc_final: 0.6552 (mtt90) REVERT: A 314 ARG cc_start: 0.7269 (ttp-170) cc_final: 0.6971 (ttp-170) REVERT: A 318 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7340 (mm-30) REVERT: A 388 GLN cc_start: 0.7116 (mp10) cc_final: 0.6702 (mp10) REVERT: A 508 GLN cc_start: 0.7997 (pm20) cc_final: 0.7453 (pm20) REVERT: A 546 MET cc_start: 0.7445 (mmm) cc_final: 0.7204 (mmm) REVERT: A 576 ASP cc_start: 0.6496 (m-30) cc_final: 0.6034 (m-30) REVERT: A 579 PHE cc_start: 0.8114 (t80) cc_final: 0.7809 (t80) REVERT: A 603 LYS cc_start: 0.8417 (tppp) cc_final: 0.8211 (mmmt) REVERT: A 710 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.8148 (m) REVERT: B 135 MET cc_start: 0.7284 (mmm) cc_final: 0.6992 (mmm) REVERT: B 266 ARG cc_start: 0.7634 (tpp-160) cc_final: 0.7281 (ttm110) REVERT: B 364 VAL cc_start: 0.8263 (t) cc_final: 0.7884 (m) REVERT: B 369 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7686 (ttmm) REVERT: B 428 GLU cc_start: 0.7595 (tp30) cc_final: 0.7075 (tp30) REVERT: B 558 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7753 (mt-10) REVERT: B 574 ASP cc_start: 0.6758 (t0) cc_final: 0.6192 (t0) REVERT: B 577 MET cc_start: 0.7316 (mtp) cc_final: 0.6535 (mtp) REVERT: B 672 GLU cc_start: 0.7713 (tp30) cc_final: 0.7336 (tp30) REVERT: B 699 VAL cc_start: 0.7520 (m) cc_final: 0.7069 (t) outliers start: 25 outliers final: 20 residues processed: 262 average time/residue: 1.3920 time to fit residues: 394.7033 Evaluate side-chains 270 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 224 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 93 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 305 VAL 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 548 GLU Chi-restraints excluded: chain B residue 650 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 82 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 118 optimal weight: 0.0030 chunk 42 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 5 optimal weight: 0.0170 chunk 88 optimal weight: 0.8980 overall best weight: 0.5230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 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 = 0.4143 r_free = 0.4143 target = 0.156437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.138428 restraints weight = 13899.559| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.14 r_work: 0.3808 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10544 Z= 0.136 Angle : 0.669 12.899 14351 Z= 0.327 Chirality : 0.046 0.233 1570 Planarity : 0.005 0.053 1806 Dihedral : 8.596 94.429 1596 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 2.16 % Allowed : 21.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1228 helix: 0.68 (0.27), residues: 379 sheet: -0.54 (0.49), residues: 122 loop : -0.63 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP B 180 HIS 0.004 0.001 HIS A 241 PHE 0.014 0.001 PHE A 577 TYR 0.018 0.002 TYR A 608 ARG 0.010 0.001 ARG B 297 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 2) link_NAG-ASN : angle 2.70234 ( 6) link_ALPHA1-4 : bond 0.01633 ( 1) link_ALPHA1-4 : angle 2.68857 ( 3) link_BETA1-4 : bond 0.00533 ( 4) link_BETA1-4 : angle 2.01458 ( 12) hydrogen bonds : bond 0.03635 ( 291) hydrogen bonds : angle 5.03411 ( 810) SS BOND : bond 0.00369 ( 9) SS BOND : angle 1.04615 ( 18) covalent geometry : bond 0.00319 (10528) covalent geometry : angle 0.66303 (14312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10173.39 seconds wall clock time: 183 minutes 29.24 seconds (11009.24 seconds total)