Starting phenix.real_space_refine on Fri Feb 14 17:42:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sck_25037/02_2025/7sck_25037.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sck_25037/02_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_25037/02_2025/7sck_25037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sck_25037/02_2025/7sck_25037.map" model { file = "/net/cci-nas-00/data/ceres_data/7sck_25037/02_2025/7sck_25037.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sck_25037/02_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-5592/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: 6.60, per 1000 atoms: 0.64 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: 2.92 Conformation dependent library (CDL) restraints added in 1.4 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: 1.30 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: 3.32 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2584 1.33 - 1.45: 2239 1.45 - 1.58: 5626 1.58 - 1.70: 5 1.70 - 1.82: 74 Bond restraints: 10528 Sorted by residual: bond pdb=" C3 BDP D 2 " pdb=" O3 BDP D 2 " ideal model delta sigma weight residual 1.411 1.515 -0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C3 BDP D 4 " pdb=" O3 BDP D 4 " ideal model delta sigma weight residual 1.411 1.515 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C1 BDP D 2 " pdb=" O5 BDP D 2 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C1 BDP D 4 " pdb=" O5 BDP D 4 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O1B UDP B 901 " pdb=" PB UDP B 901 " ideal model delta sigma weight residual 1.530 1.492 0.038 1.00e-02 1.00e+04 1.48e+01 ... (remaining 10523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 14012 1.82 - 3.65: 240 3.65 - 5.47: 47 5.47 - 7.30: 11 7.30 - 9.12: 2 Bond angle restraints: 14312 Sorted by residual: angle pdb=" O1B UDP B 901 " pdb=" PB UDP B 901 " pdb=" O3A UDP B 901 " ideal model delta sigma weight residual 102.95 112.07 -9.12 1.00e+00 1.00e+00 8.33e+01 angle pdb=" O3A UDP B 901 " pdb=" PB UDP B 901 " pdb=" O3B UDP B 901 " ideal model delta sigma weight residual 112.01 103.15 8.86 1.00e+00 1.00e+00 7.86e+01 angle pdb=" CA ASP B 561 " pdb=" CB ASP B 561 " pdb=" CG ASP B 561 " ideal model delta sigma weight residual 112.60 116.16 -3.56 1.00e+00 1.00e+00 1.26e+01 angle pdb=" N ARG B 562 " pdb=" CA ARG B 562 " pdb=" CB ARG B 562 " ideal model delta sigma weight residual 110.49 104.68 5.81 1.69e+00 3.50e-01 1.18e+01 angle pdb=" C PRO B 560 " pdb=" N ASP B 561 " pdb=" CA ASP B 561 " ideal model delta sigma weight residual 122.49 117.30 5.19 1.57e+00 4.06e-01 1.09e+01 ... (remaining 14307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.95: 6182 21.95 - 43.91: 206 43.91 - 65.86: 33 65.86 - 87.81: 23 87.81 - 109.76: 12 Dihedral angle restraints: 6456 sinusoidal: 2786 harmonic: 3670 Sorted by residual: dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 288.71 178.95 109.76 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" C3 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 47.62 -60.39 108.01 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C3 NDG D 1 " pdb=" C4 NDG D 1 " pdb=" C5 NDG D 1 " pdb=" O5 NDG D 1 " ideal model delta sinusoidal sigma weight residual 53.31 -52.51 105.82 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 6453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1373 0.067 - 0.135: 187 0.135 - 0.202: 3 0.202 - 0.269: 5 0.269 - 0.336: 2 Chirality restraints: 1570 Sorted by residual: chirality pdb=" C4 NDG D 1 " pdb=" C3 NDG D 1 " pdb=" C5 NDG D 1 " pdb=" O4 NDG D 1 " both_signs ideal model delta sigma weight residual False -2.30 -2.64 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C4 NDG D 3 " pdb=" C3 NDG D 3 " pdb=" C5 NDG D 3 " pdb=" O4 NDG D 3 " both_signs ideal model delta sigma weight residual False -2.30 -2.61 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1567 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 561 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ASP B 561 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP B 561 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG B 562 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 399 " -0.025 2.00e-02 2.50e+03 1.31e-02 3.41e+00 pdb=" CG TYR B 399 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 399 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 399 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 399 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 399 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 399 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 399 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 479 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO B 480 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 480 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 480 " -0.023 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 25 2.38 - 3.01: 5720 3.01 - 3.64: 15432 3.64 - 4.27: 24009 4.27 - 4.90: 40214 Nonbonded interactions: 85400 Sorted by model distance: nonbonded pdb=" O2A UDP B 901 " pdb="MN MN B 902 " model vdw 1.744 2.320 nonbonded pdb=" OH TYR B 130 " pdb=" O PRO B 155 " model vdw 2.229 3.040 nonbonded pdb=" NZ LYS B 484 " pdb=" O GLU B 528 " model vdw 2.241 3.120 nonbonded pdb=" O ARG B 209 " pdb=" OH TYR B 226 " model vdw 2.241 3.040 nonbonded pdb=" N ASP B 539 " pdb=" OD1 ASP B 539 " model vdw 2.252 3.120 ... (remaining 85395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.310 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.750 ------------------------------------------------------------------------------- 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 10528 Z= 0.322 Angle : 0.615 9.125 14312 Z= 0.328 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 *********************** 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 : 1.084 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: 1.1399 time to fit residues: 417.5434 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 : 1.349 ------------------------------------------------------------------------------- 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): 0.3895 rms_B_bonded: 2.07 r_work: 0.3782 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 10528 Z= 0.223 Angle : 0.618 7.798 14312 Z= 0.306 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 *********************** 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 : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7721 (pm20) cc_final: 0.7465 (pm20) REVERT: A 105 ASP cc_start: 0.6519 (t70) cc_final: 0.6292 (t70) REVERT: A 147 ASP cc_start: 0.7567 (t0) cc_final: 0.7355 (t0) REVERT: A 270 ARG cc_start: 0.8113 (ptm-80) cc_final: 0.7278 (ptt90) REVERT: A 305 GLN cc_start: 0.7595 (mp10) cc_final: 0.7223 (mp10) REVERT: A 383 GLU cc_start: 0.6625 (tm-30) cc_final: 0.6343 (tm-30) REVERT: A 458 TYR cc_start: 0.7956 (t80) cc_final: 0.7754 (t80) REVERT: A 508 GLN cc_start: 0.7915 (pm20) cc_final: 0.7410 (pm20) REVERT: A 576 ASP cc_start: 0.6372 (m-30) cc_final: 0.6035 (m-30) REVERT: A 603 LYS cc_start: 0.8441 (tppp) cc_final: 0.8150 (mmmt) REVERT: A 648 GLN cc_start: 0.8163 (tm130) cc_final: 0.7846 (tm-30) REVERT: B 104 ILE cc_start: 0.8759 (tt) cc_final: 0.8540 (pt) REVERT: B 135 MET cc_start: 0.7239 (mmm) cc_final: 0.6983 (mmm) REVERT: B 144 THR cc_start: 0.8417 (p) cc_final: 0.8213 (m) REVERT: B 266 ARG cc_start: 0.7612 (tpp-160) cc_final: 0.7392 (tpp-160) REVERT: B 316 THR cc_start: 0.8357 (m) cc_final: 0.8011 (t) REVERT: B 348 TYR cc_start: 0.7856 (t80) cc_final: 0.7086 (t80) REVERT: B 364 VAL cc_start: 0.8310 (t) cc_final: 0.7939 (m) REVERT: B 369 LYS cc_start: 0.7878 (tttp) cc_final: 0.7650 (tttp) REVERT: B 372 ASP cc_start: 0.7770 (m-30) cc_final: 0.7452 (m-30) REVERT: B 463 TYR cc_start: 0.7076 (t80) cc_final: 0.6644 (t80) REVERT: B 518 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7664 (mtmm) REVERT: B 574 ASP cc_start: 0.6736 (t0) cc_final: 0.6213 (t0) REVERT: B 577 MET cc_start: 0.7295 (mtp) cc_final: 0.6745 (mtp) REVERT: B 592 MET cc_start: 0.7686 (mtp) cc_final: 0.7247 (mtp) REVERT: B 672 GLU cc_start: 0.7678 (tp30) cc_final: 0.7131 (tp30) REVERT: B 687 MET cc_start: 0.7378 (tpp) cc_final: 0.6809 (tpt) REVERT: B 697 ASP cc_start: 0.8083 (m-30) cc_final: 0.7866 (m-30) REVERT: B 699 VAL cc_start: 0.7427 (m) cc_final: 0.6989 (t) outliers start: 23 outliers final: 7 residues processed: 286 average time/residue: 1.1634 time to fit residues: 359.5849 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 : 1.196 ------------------------------------------------------------------------------- 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: 0.0570 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: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.155469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.137762 restraints weight = 13896.309| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.09 r_work: 0.3785 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10528 Z= 0.195 Angle : 0.595 7.232 14312 Z= 0.293 Chirality : 0.044 0.233 1570 Planarity : 0.004 0.044 1806 Dihedral : 10.662 99.122 1596 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 2.61 % Allowed : 15.47 % Favored : 81.92 % 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: -0.12 (0.24), residues: 1228 helix: 0.84 (0.27), residues: 390 sheet: 0.02 (0.49), residues: 127 loop : -0.59 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 396 HIS 0.004 0.001 HIS B 88 PHE 0.012 0.001 PHE A 577 TYR 0.014 0.001 TYR B 399 ARG 0.006 0.001 ARG A 243 *********************** 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 300 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 271 time to evaluate : 1.069 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: 0.7751 (pm20) cc_final: 0.7451 (pm20) REVERT: A 147 ASP cc_start: 0.7597 (t0) cc_final: 0.7356 (t0) REVERT: A 160 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7792 (m) REVERT: A 270 ARG cc_start: 0.8099 (ptm160) cc_final: 0.7254 (ptt90) REVERT: A 305 GLN cc_start: 0.7643 (mp10) cc_final: 0.7254 (mp10) REVERT: A 383 GLU cc_start: 0.6582 (tm-30) cc_final: 0.6322 (tm-30) REVERT: A 508 GLN cc_start: 0.7996 (pm20) cc_final: 0.7477 (pm20) REVERT: A 576 ASP cc_start: 0.6420 (m-30) cc_final: 0.6052 (m-30) REVERT: A 603 LYS cc_start: 0.8453 (tppp) cc_final: 0.8189 (mmmt) REVERT: A 648 GLN cc_start: 0.8144 (tm130) cc_final: 0.7887 (tm-30) REVERT: B 108 ILE cc_start: 0.8302 (mp) cc_final: 0.8071 (mt) REVERT: B 135 MET cc_start: 0.7223 (mmm) cc_final: 0.6965 (mmm) REVERT: B 266 ARG cc_start: 0.7626 (tpp-160) cc_final: 0.7286 (ttm110) REVERT: B 316 THR cc_start: 0.8363 (m) cc_final: 0.8107 (m) REVERT: B 348 TYR cc_start: 0.7858 (t80) cc_final: 0.7568 (t80) REVERT: B 364 VAL cc_start: 0.8267 (t) cc_final: 0.7874 (m) REVERT: B 428 GLU cc_start: 0.7726 (tp30) cc_final: 0.7220 (tp30) REVERT: B 463 TYR cc_start: 0.6976 (t80) cc_final: 0.6440 (t80) REVERT: B 574 ASP cc_start: 0.6722 (t0) cc_final: 0.6189 (t0) REVERT: B 577 MET cc_start: 0.7383 (mtp) cc_final: 0.6765 (mtp) REVERT: B 672 GLU cc_start: 0.7490 (tp30) cc_final: 0.7263 (tp30) REVERT: B 697 ASP cc_start: 0.8046 (m-30) cc_final: 0.7832 (m-30) REVERT: B 699 VAL cc_start: 0.7400 (m) cc_final: 0.6953 (t) outliers start: 29 outliers final: 10 residues processed: 285 average time/residue: 1.1552 time to fit residues: 355.8642 Evaluate side-chains 269 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 258 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 106 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS ** 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 605 ASN ** 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 = 0.4077 r_free = 0.4077 target = 0.151097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.133575 restraints weight = 13835.886| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.05 r_work: 0.3741 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 10528 Z= 0.467 Angle : 0.706 10.542 14312 Z= 0.350 Chirality : 0.051 0.264 1570 Planarity : 0.005 0.059 1806 Dihedral : 10.705 95.367 1596 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.81 % Rotamer: Outliers : 2.97 % Allowed : 17.27 % Favored : 79.77 % 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: -0.57 (0.24), residues: 1228 helix: 0.41 (0.26), residues: 384 sheet: -0.28 (0.48), residues: 127 loop : -0.82 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 556 HIS 0.006 0.001 HIS B 571 PHE 0.024 0.003 PHE A 226 TYR 0.019 0.002 TYR A 608 ARG 0.006 0.001 ARG A 346 *********************** 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 312 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7827 (pm20) cc_final: 0.7574 (pm20) REVERT: A 105 ASP cc_start: 0.6544 (t70) cc_final: 0.6325 (p0) REVERT: A 108 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8278 (mm) REVERT: A 147 ASP cc_start: 0.7603 (t0) cc_final: 0.7351 (t0) REVERT: A 160 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7861 (m) REVERT: A 210 ASP cc_start: 0.7206 (t0) cc_final: 0.6999 (t0) REVERT: A 270 ARG cc_start: 0.8116 (ptm160) cc_final: 0.7656 (ptt90) REVERT: A 305 GLN cc_start: 0.7749 (mp10) cc_final: 0.7382 (mp10) REVERT: A 311 ARG cc_start: 0.7269 (mtm-85) cc_final: 0.7046 (mtt90) REVERT: A 508 GLN cc_start: 0.8090 (pm20) cc_final: 0.7552 (pm20) REVERT: A 576 ASP cc_start: 0.6504 (m-30) cc_final: 0.6135 (m-30) REVERT: A 603 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8230 (mmmt) REVERT: B 103 LYS cc_start: 0.8233 (mmtt) cc_final: 0.8025 (mmtt) REVERT: B 108 ILE cc_start: 0.8367 (mp) cc_final: 0.8145 (mt) REVERT: B 135 MET cc_start: 0.7297 (mmm) cc_final: 0.6897 (mmm) REVERT: B 139 ASP cc_start: 0.7940 (m-30) cc_final: 0.7636 (m-30) REVERT: B 255 LEU cc_start: 0.8277 (tt) cc_final: 0.8072 (tp) REVERT: B 266 ARG cc_start: 0.7659 (tpp-160) cc_final: 0.7334 (ttm110) REVERT: B 348 TYR cc_start: 0.7981 (t80) cc_final: 0.7694 (t80) REVERT: B 364 VAL cc_start: 0.8358 (t) cc_final: 0.7994 (m) REVERT: B 369 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7686 (ttmm) REVERT: B 428 GLU cc_start: 0.7784 (tp30) cc_final: 0.7179 (tp30) REVERT: B 463 TYR cc_start: 0.7216 (t80) cc_final: 0.6633 (t80) REVERT: B 510 LYS cc_start: 0.8222 (ptmt) cc_final: 0.7903 (ptpt) REVERT: B 574 ASP cc_start: 0.6777 (t0) cc_final: 0.6245 (t0) REVERT: B 577 MET cc_start: 0.7497 (mtp) cc_final: 0.6792 (mtp) REVERT: B 600 TYR cc_start: 0.7840 (p90) cc_final: 0.7403 (p90) REVERT: B 672 GLU cc_start: 0.7661 (tp30) cc_final: 0.7306 (tp30) REVERT: B 699 VAL cc_start: 0.7780 (m) cc_final: 0.7345 (t) outliers start: 33 outliers final: 15 residues processed: 295 average time/residue: 1.2694 time to fit residues: 403.0889 Evaluate side-chains 283 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 265 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 657 MET Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 472 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 0.0050 chunk 16 optimal weight: 0.9990 chunk 102 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.4952 ------------------------------------------------------------------------------- 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 550 GLN ** 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 = 0.4123 r_free = 0.4123 target = 0.154936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.137637 restraints weight = 13914.267| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.08 r_work: 0.3790 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10528 Z= 0.191 Angle : 0.612 9.408 14312 Z= 0.299 Chirality : 0.045 0.228 1570 Planarity : 0.004 0.046 1806 Dihedral : 9.530 97.888 1596 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.58 % Favored : 96.34 % Rotamer: Outliers : 2.52 % Allowed : 18.44 % Favored : 79.05 % 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: 0.62 (0.27), residues: 390 sheet: -0.44 (0.49), residues: 122 loop : -0.63 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 396 HIS 0.004 0.001 HIS B 88 PHE 0.013 0.001 PHE A 577 TYR 0.016 0.001 TYR A 608 ARG 0.009 0.001 ARG A 741 *********************** 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 293 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8209 (mm) REVERT: A 160 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7804 (m) REVERT: A 210 ASP cc_start: 0.7171 (t0) cc_final: 0.6963 (t0) REVERT: A 270 ARG cc_start: 0.8144 (ptm160) cc_final: 0.7796 (ptt90) REVERT: A 305 GLN cc_start: 0.7700 (mp10) cc_final: 0.7322 (mp10) REVERT: A 318 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7388 (mm-30) REVERT: A 388 GLN cc_start: 0.6994 (mp10) cc_final: 0.6638 (mp10) REVERT: A 508 GLN cc_start: 0.7950 (pm20) cc_final: 0.7393 (pm20) REVERT: A 576 ASP cc_start: 0.6493 (m-30) cc_final: 0.6028 (m-30) REVERT: A 579 PHE cc_start: 0.8209 (t80) cc_final: 0.7889 (t80) REVERT: A 603 LYS cc_start: 0.8455 (tppp) cc_final: 0.8229 (mmmt) REVERT: B 103 LYS cc_start: 0.8216 (mmtt) cc_final: 0.8008 (mmtt) REVERT: B 135 MET cc_start: 0.7203 (mmm) cc_final: 0.6951 (mmm) REVERT: B 266 ARG cc_start: 0.7607 (tpp-160) cc_final: 0.7270 (ttm110) REVERT: B 348 TYR cc_start: 0.7897 (t80) cc_final: 0.7593 (t80) REVERT: B 364 VAL cc_start: 0.8317 (t) cc_final: 0.7950 (m) REVERT: B 369 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7627 (ttmm) REVERT: B 428 GLU cc_start: 0.7689 (tp30) cc_final: 0.7057 (tp30) REVERT: B 463 TYR cc_start: 0.7109 (t80) cc_final: 0.6530 (t80) REVERT: B 510 LYS cc_start: 0.8124 (ptmt) cc_final: 0.7789 (ptpt) REVERT: B 518 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7727 (mtmm) REVERT: B 574 ASP cc_start: 0.6779 (t0) cc_final: 0.6267 (t0) REVERT: B 577 MET cc_start: 0.7429 (mtp) cc_final: 0.6710 (mtp) REVERT: B 583 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 672 GLU cc_start: 0.7695 (tp30) cc_final: 0.7307 (tp30) REVERT: B 699 VAL cc_start: 0.7449 (m) cc_final: 0.7028 (t) outliers start: 28 outliers final: 16 residues processed: 280 average time/residue: 1.1826 time to fit residues: 357.0986 Evaluate side-chains 274 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 256 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 332 THR 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 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 20 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS ** 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 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 = 0.4111 r_free = 0.4111 target = 0.153762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.136111 restraints weight = 13966.457| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.09 r_work: 0.3766 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10528 Z= 0.267 Angle : 0.646 9.767 14312 Z= 0.316 Chirality : 0.047 0.244 1570 Planarity : 0.005 0.049 1806 Dihedral : 9.478 96.871 1596 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.72 % Favored : 95.20 % Rotamer: Outliers : 3.24 % Allowed : 18.79 % Favored : 77.97 % 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: 0.57 (0.27), residues: 389 sheet: -0.48 (0.49), residues: 122 loop : -0.65 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 180 HIS 0.004 0.001 HIS A 448 PHE 0.013 0.002 PHE B 306 TYR 0.020 0.002 TYR A 608 ARG 0.007 0.001 ARG A 741 *********************** 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 296 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 260 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7858 (m) REVERT: A 210 ASP cc_start: 0.7201 (t0) cc_final: 0.6979 (t0) REVERT: A 270 ARG cc_start: 0.8109 (ptm160) cc_final: 0.7716 (ptt90) REVERT: A 305 GLN cc_start: 0.7702 (mp10) cc_final: 0.7320 (mp10) REVERT: A 318 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7394 (mm-30) REVERT: A 388 GLN cc_start: 0.7008 (mp10) cc_final: 0.6617 (mp10) REVERT: A 508 GLN cc_start: 0.7939 (pm20) cc_final: 0.7387 (pm20) REVERT: A 576 ASP cc_start: 0.6433 (m-30) cc_final: 0.5976 (m-30) REVERT: A 579 PHE cc_start: 0.8200 (t80) cc_final: 0.7873 (t80) REVERT: A 603 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8227 (mmmt) REVERT: A 649 LEU cc_start: 0.8376 (tp) cc_final: 0.8173 (tp) REVERT: B 103 LYS cc_start: 0.8240 (mmtt) cc_final: 0.8032 (mmtt) REVERT: B 108 ILE cc_start: 0.8295 (mp) cc_final: 0.8049 (mt) REVERT: B 135 MET cc_start: 0.7242 (mmm) cc_final: 0.6965 (mmm) REVERT: B 266 ARG cc_start: 0.7621 (tpp-160) cc_final: 0.7299 (ttm110) REVERT: B 348 TYR cc_start: 0.7897 (t80) cc_final: 0.7611 (t80) REVERT: B 364 VAL cc_start: 0.8314 (t) cc_final: 0.7935 (m) REVERT: B 428 GLU cc_start: 0.7682 (tp30) cc_final: 0.7099 (tp30) REVERT: B 463 TYR cc_start: 0.7077 (t80) cc_final: 0.6508 (t80) REVERT: B 574 ASP cc_start: 0.6699 (t0) cc_final: 0.6174 (t0) REVERT: B 577 MET cc_start: 0.7399 (mtp) cc_final: 0.6678 (mtp) REVERT: B 600 TYR cc_start: 0.7828 (p90) cc_final: 0.7477 (p90) REVERT: B 672 GLU cc_start: 0.7721 (tp30) cc_final: 0.7329 (tp30) REVERT: B 699 VAL cc_start: 0.7531 (m) cc_final: 0.7114 (t) outliers start: 36 outliers final: 19 residues processed: 278 average time/residue: 1.2109 time to fit residues: 363.0630 Evaluate side-chains 271 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 320 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 499 LYS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 657 MET Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN ** 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 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 = 0.4078 r_free = 0.4078 target = 0.151180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.133219 restraints weight = 14006.671| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.13 r_work: 0.3725 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 10528 Z= 0.464 Angle : 0.731 9.967 14312 Z= 0.365 Chirality : 0.051 0.268 1570 Planarity : 0.005 0.056 1806 Dihedral : 9.803 93.414 1596 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.03 % Favored : 93.89 % Rotamer: Outliers : 2.43 % Allowed : 20.41 % Favored : 77.16 % 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: -0.78 (0.24), residues: 1228 helix: 0.24 (0.26), residues: 384 sheet: -0.62 (0.47), residues: 132 loop : -0.90 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP B 180 HIS 0.007 0.001 HIS B 571 PHE 0.022 0.003 PHE B 306 TYR 0.024 0.002 TYR A 608 ARG 0.009 0.001 ARG B 182 *********************** 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 296 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 269 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 210 ASP cc_start: 0.7239 (t0) cc_final: 0.7008 (t0) REVERT: A 256 ILE cc_start: 0.8733 (pt) cc_final: 0.8343 (mm) REVERT: A 270 ARG cc_start: 0.8154 (ptm160) cc_final: 0.7772 (ptt90) REVERT: A 277 SER cc_start: 0.7811 (p) cc_final: 0.7410 (t) REVERT: A 305 GLN cc_start: 0.7698 (mp10) cc_final: 0.7301 (mp10) REVERT: A 318 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7407 (mm-30) REVERT: A 508 GLN cc_start: 0.8031 (pm20) cc_final: 0.7467 (pm20) REVERT: A 576 ASP cc_start: 0.6445 (m-30) cc_final: 0.6024 (m-30) REVERT: A 579 PHE cc_start: 0.8228 (t80) cc_final: 0.7879 (t80) REVERT: A 603 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8188 (mmmt) REVERT: A 612 TRP cc_start: 0.7022 (m-10) cc_final: 0.6730 (m-10) REVERT: B 108 ILE cc_start: 0.8346 (mp) cc_final: 0.8102 (mt) REVERT: B 135 MET cc_start: 0.7279 (mmm) cc_final: 0.7014 (mmm) REVERT: B 266 ARG cc_start: 0.7614 (tpp-160) cc_final: 0.7289 (ttm110) REVERT: B 348 TYR cc_start: 0.7931 (t80) cc_final: 0.7617 (t80) REVERT: B 364 VAL cc_start: 0.8374 (t) cc_final: 0.8030 (m) REVERT: B 428 GLU cc_start: 0.7749 (tp30) cc_final: 0.7133 (tp30) REVERT: B 463 TYR cc_start: 0.7163 (t80) cc_final: 0.6586 (t80) REVERT: B 510 LYS cc_start: 0.8201 (ptmt) cc_final: 0.7851 (ptpt) REVERT: B 518 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7779 (mtpp) REVERT: B 574 ASP cc_start: 0.6725 (t0) cc_final: 0.6196 (t0) REVERT: B 576 GLU cc_start: 0.7246 (mp0) cc_final: 0.7027 (mp0) REVERT: B 577 MET cc_start: 0.7460 (mtp) cc_final: 0.6739 (mtp) REVERT: B 672 GLU cc_start: 0.7717 (tp30) cc_final: 0.7305 (tp30) outliers start: 27 outliers final: 20 residues processed: 278 average time/residue: 1.1603 time to fit residues: 348.5338 Evaluate side-chains 278 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 257 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 224 GLU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 332 THR 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 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.0870 chunk 69 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 316 ASN A 397 HIS ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 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 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 = 0.4122 r_free = 0.4122 target = 0.154970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.137054 restraints weight = 13859.483| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.09 r_work: 0.3774 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10528 Z= 0.226 Angle : 0.662 10.387 14312 Z= 0.327 Chirality : 0.046 0.236 1570 Planarity : 0.005 0.051 1806 Dihedral : 9.202 95.527 1596 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.72 % Favored : 95.20 % Rotamer: Outliers : 2.88 % Allowed : 20.95 % Favored : 76.17 % 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: -0.56 (0.24), residues: 1228 helix: 0.43 (0.27), residues: 384 sheet: -0.61 (0.49), residues: 122 loop : -0.74 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP B 180 HIS 0.003 0.001 HIS A 448 PHE 0.015 0.002 PHE A 333 TYR 0.020 0.002 TYR B 426 ARG 0.007 0.001 ARG A 243 *********************** 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: 32 poor density : 263 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.6283 (p0) cc_final: 0.5933 (p0) REVERT: A 108 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7799 (mm) REVERT: A 210 ASP cc_start: 0.7241 (t0) cc_final: 0.7016 (t0) REVERT: A 256 ILE cc_start: 0.8679 (pt) cc_final: 0.8298 (mm) REVERT: A 270 ARG cc_start: 0.8224 (ptm160) cc_final: 0.7862 (ptt90) REVERT: A 277 SER cc_start: 0.7834 (p) cc_final: 0.7455 (t) REVERT: A 305 GLN cc_start: 0.7641 (mp10) cc_final: 0.7252 (mp10) REVERT: A 318 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7420 (mm-30) REVERT: A 508 GLN cc_start: 0.7981 (pm20) cc_final: 0.7423 (pm20) REVERT: A 576 ASP cc_start: 0.6438 (m-30) cc_final: 0.5969 (m-30) REVERT: A 579 PHE cc_start: 0.8155 (t80) cc_final: 0.7843 (t80) REVERT: A 603 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8224 (mmmt) REVERT: A 700 GLN cc_start: 0.8255 (mt0) cc_final: 0.7643 (mp10) REVERT: B 108 ILE cc_start: 0.8262 (mp) cc_final: 0.8030 (mt) REVERT: B 135 MET cc_start: 0.7307 (mmm) cc_final: 0.7033 (mmm) REVERT: B 266 ARG cc_start: 0.7559 (tpp-160) cc_final: 0.7221 (ttm110) REVERT: B 348 TYR cc_start: 0.7854 (t80) cc_final: 0.7555 (t80) REVERT: B 364 VAL cc_start: 0.8339 (t) cc_final: 0.7977 (m) REVERT: B 428 GLU cc_start: 0.7638 (tp30) cc_final: 0.7130 (tp30) REVERT: B 463 TYR cc_start: 0.7080 (t80) cc_final: 0.6489 (t80) REVERT: B 574 ASP cc_start: 0.6692 (t0) cc_final: 0.6178 (t0) REVERT: B 577 MET cc_start: 0.7431 (mtp) cc_final: 0.6697 (mtp) REVERT: B 672 GLU cc_start: 0.7685 (tp30) cc_final: 0.7316 (tp30) REVERT: B 691 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7688 (t) outliers start: 32 outliers final: 19 residues processed: 277 average time/residue: 1.1777 time to fit residues: 351.9589 Evaluate side-chains 281 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 259 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 332 THR 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 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 691 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 29 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.155994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.137848 restraints weight = 13936.051| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.13 r_work: 0.3787 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10528 Z= 0.231 Angle : 0.684 10.245 14312 Z= 0.335 Chirality : 0.046 0.233 1570 Planarity : 0.005 0.048 1806 Dihedral : 8.914 95.064 1596 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.36 % Rotamer: Outliers : 2.34 % Allowed : 22.57 % Favored : 75.09 % 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: -0.51 (0.24), residues: 1228 helix: 0.52 (0.27), residues: 383 sheet: -0.60 (0.49), residues: 122 loop : -0.74 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 180 HIS 0.004 0.001 HIS B 88 PHE 0.016 0.001 PHE A 577 TYR 0.016 0.002 TYR A 608 ARG 0.011 0.001 ARG B 297 *********************** 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 293 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.6369 (p0) cc_final: 0.6084 (p0) REVERT: A 108 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7692 (mm) REVERT: A 210 ASP cc_start: 0.7227 (t0) cc_final: 0.6997 (t0) REVERT: A 256 ILE cc_start: 0.8656 (pt) cc_final: 0.8270 (mm) REVERT: A 270 ARG cc_start: 0.8188 (ptm160) cc_final: 0.7822 (ptt90) REVERT: A 277 SER cc_start: 0.7838 (p) cc_final: 0.7491 (t) REVERT: A 305 GLN cc_start: 0.7677 (mp10) cc_final: 0.7284 (mp10) REVERT: A 318 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7364 (mm-30) REVERT: A 393 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7565 (mt) REVERT: A 508 GLN cc_start: 0.7965 (pm20) cc_final: 0.7419 (pm20) REVERT: A 547 SER cc_start: 0.7492 (p) cc_final: 0.7246 (m) REVERT: A 576 ASP cc_start: 0.6445 (m-30) cc_final: 0.5986 (m-30) REVERT: A 579 PHE cc_start: 0.8137 (t80) cc_final: 0.7859 (t80) REVERT: A 603 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8230 (mmmt) REVERT: A 710 SER cc_start: 0.8413 (p) cc_final: 0.8130 (m) REVERT: B 135 MET cc_start: 0.7299 (mmm) cc_final: 0.7024 (mmm) REVERT: B 250 ARG cc_start: 0.7426 (mmt-90) cc_final: 0.7217 (mmm-85) REVERT: B 266 ARG cc_start: 0.7586 (tpp-160) cc_final: 0.7230 (ttm110) REVERT: B 283 LEU cc_start: 0.8258 (mm) cc_final: 0.7985 (mp) REVERT: B 364 VAL cc_start: 0.8296 (t) cc_final: 0.7937 (m) REVERT: B 369 LYS cc_start: 0.7929 (ttmm) cc_final: 0.7695 (ttmm) REVERT: B 384 GLN cc_start: 0.7740 (tm-30) cc_final: 0.7504 (tt0) REVERT: B 428 GLU cc_start: 0.7613 (tp30) cc_final: 0.7007 (tp30) REVERT: B 574 ASP cc_start: 0.6725 (t0) cc_final: 0.6202 (t0) REVERT: B 577 MET cc_start: 0.7492 (mtp) cc_final: 0.6765 (mtp) REVERT: B 672 GLU cc_start: 0.7684 (tp30) cc_final: 0.7318 (tp30) outliers start: 26 outliers final: 14 residues processed: 277 average time/residue: 1.1471 time to fit residues: 342.9405 Evaluate side-chains 278 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 261 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 224 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 ILE 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 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 435 VAL 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: 2.9990 chunk 75 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.155076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.137061 restraints weight = 13854.689| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 2.10 r_work: 0.3780 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10528 Z= 0.266 Angle : 0.687 9.061 14312 Z= 0.343 Chirality : 0.047 0.241 1570 Planarity : 0.005 0.053 1806 Dihedral : 8.863 93.871 1596 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 2.16 % Allowed : 23.02 % Favored : 74.82 % 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: -0.58 (0.24), residues: 1228 helix: 0.46 (0.27), residues: 384 sheet: -0.74 (0.48), residues: 123 loop : -0.76 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 180 HIS 0.005 0.001 HIS A 241 PHE 0.014 0.002 PHE A 577 TYR 0.021 0.002 TYR B 426 ARG 0.013 0.001 ARG B 182 ********************** 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 282 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.6332 (p0) cc_final: 0.6043 (p0) REVERT: A 108 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7623 (mm) REVERT: A 147 ASP cc_start: 0.7589 (t0) cc_final: 0.7308 (t0) REVERT: A 159 ASP cc_start: 0.7314 (t0) cc_final: 0.7105 (t0) REVERT: A 210 ASP cc_start: 0.7235 (t0) cc_final: 0.7005 (t0) REVERT: A 256 ILE cc_start: 0.8667 (pt) cc_final: 0.8292 (mm) REVERT: A 270 ARG cc_start: 0.8208 (ptm160) cc_final: 0.7814 (ptt90) REVERT: A 277 SER cc_start: 0.7845 (p) cc_final: 0.7483 (t) REVERT: A 305 GLN cc_start: 0.7671 (mp10) cc_final: 0.7280 (mp10) REVERT: A 318 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7386 (mm-30) REVERT: A 393 ILE cc_start: 0.7763 (mt) cc_final: 0.7554 (mt) REVERT: A 508 GLN cc_start: 0.7997 (pm20) cc_final: 0.7449 (pm20) REVERT: A 546 MET cc_start: 0.7445 (mmm) cc_final: 0.7203 (mmm) REVERT: A 547 SER cc_start: 0.7460 (p) cc_final: 0.7210 (m) REVERT: A 576 ASP cc_start: 0.6465 (m-30) cc_final: 0.5999 (m-30) REVERT: A 579 PHE cc_start: 0.8132 (t80) cc_final: 0.7847 (t80) REVERT: A 603 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8218 (mmmt) REVERT: A 710 SER cc_start: 0.8389 (OUTLIER) cc_final: 0.8104 (m) REVERT: B 103 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7946 (tppt) REVERT: B 135 MET cc_start: 0.7260 (mmm) cc_final: 0.6981 (mmm) REVERT: B 266 ARG cc_start: 0.7615 (tpp-160) cc_final: 0.7259 (ttm110) REVERT: B 283 LEU cc_start: 0.8314 (mm) cc_final: 0.8034 (mp) REVERT: B 364 VAL cc_start: 0.8297 (t) cc_final: 0.7945 (m) REVERT: B 369 LYS cc_start: 0.7909 (ttmm) cc_final: 0.7670 (ttmm) REVERT: B 428 GLU cc_start: 0.7580 (tp30) cc_final: 0.7029 (tp30) REVERT: B 558 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: B 574 ASP cc_start: 0.6835 (t0) cc_final: 0.6293 (t0) REVERT: B 577 MET cc_start: 0.7493 (mtp) cc_final: 0.6804 (mtp) REVERT: B 600 TYR cc_start: 0.7744 (p90) cc_final: 0.7343 (p90) REVERT: B 672 GLU cc_start: 0.7668 (tp30) cc_final: 0.7346 (tp30) outliers start: 24 outliers final: 15 residues processed: 265 average time/residue: 1.1935 time to fit residues: 340.9616 Evaluate side-chains 273 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 254 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 332 THR 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 710 SER Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 558 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: 0.7980 chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.0070 chunk 5 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN ** B 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.156155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.137925 restraints weight = 13811.873| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.13 r_work: 0.3785 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10528 Z= 0.241 Angle : 0.675 8.922 14312 Z= 0.335 Chirality : 0.046 0.233 1570 Planarity : 0.005 0.052 1806 Dihedral : 8.702 93.856 1596 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.64 % Favored : 95.28 % Rotamer: Outliers : 2.07 % Allowed : 23.38 % Favored : 74.55 % 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: -0.58 (0.24), residues: 1228 helix: 0.46 (0.27), residues: 385 sheet: -0.75 (0.48), residues: 123 loop : -0.76 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 180 HIS 0.005 0.001 HIS A 241 PHE 0.015 0.001 PHE A 577 TYR 0.017 0.002 TYR B 426 ARG 0.013 0.001 ARG B 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9342.84 seconds wall clock time: 165 minutes 14.25 seconds (9914.25 seconds total)