Starting phenix.real_space_refine on Wed Mar 4 00:44:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uqx_26701/03_2026/7uqx_26701.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uqx_26701/03_2026/7uqx_26701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uqx_26701/03_2026/7uqx_26701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uqx_26701/03_2026/7uqx_26701.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uqx_26701/03_2026/7uqx_26701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uqx_26701/03_2026/7uqx_26701.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 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 46 5.16 5 C 6100 2.51 5 N 1593 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9491 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4759 Classifications: {'peptide': 583} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 555} Chain breaks: 3 Chain: "B" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4628 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 35, 'TRANS': 535} 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: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.24, per 1000 atoms: 0.24 Number of scatterers: 9491 At special positions: 0 Unit cell: (102.672, 86.94, 110.124, 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 46 16.00 P 4 15.00 O 1747 8.00 N 1593 7.00 C 6100 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 802 " - " ASN A 330 " " NAG C 1 " - " ASN B 637 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 409.2 milliseconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 40.2% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 105 through 112 removed outlier: 4.087A pdb=" N CYS A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 141 Processing helix chain 'A' and resid 173 through 180 removed outlier: 3.786A pdb=" N GLN A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.757A pdb=" N PHE A 226 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.535A pdb=" N ALA A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 4.164A pdb=" N VAL A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.992A pdb=" N GLN A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.537A 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 382 through 386 Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 397 through 416 removed outlier: 3.501A pdb=" N PHE A 416 " --> pdb=" O TRP A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 433 Processing helix chain 'A' and resid 441 through 447 removed outlier: 3.873A pdb=" N TRP A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 496 through 506 removed outlier: 3.557A pdb=" N VAL A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 551 removed outlier: 3.724A pdb=" N PHE A 550 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 removed outlier: 3.830A pdb=" N SER A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.594A pdb=" N LYS A 643 " --> pdb=" O PRO A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 removed outlier: 3.654A pdb=" N LEU A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 713 removed outlier: 3.774A pdb=" N ARG A 701 " --> pdb=" O HIS A 697 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 166 through 176 Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.518A pdb=" N THR B 184 " --> pdb=" O ASP B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.943A 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: 3.787A 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 366 through 370 Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.532A pdb=" N SER B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 400 Processing helix chain 'B' and resid 402 through 419 Processing helix chain 'B' and resid 420 through 423 Processing helix chain 'B' and resid 425 through 431 Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 466 through 478 removed outlier: 3.631A pdb=" N ARG B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 524 removed outlier: 4.029A pdb=" N ARG B 522 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 524 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 removed outlier: 3.799A pdb=" N GLU B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 Processing helix chain 'B' and resid 615 through 624 Processing helix chain 'B' and resid 626 through 640 removed outlier: 3.675A pdb=" N ALA B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 685 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 145 removed outlier: 6.160A pdb=" N VAL A 116 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE A 154 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE A 193 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N HIS A 190 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA A 217 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE A 192 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 292 through 295 removed outlier: 6.310A pdb=" N LEU A 264 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU A 295 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE A 266 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL A 265 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 6.721A 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 510 through 517 removed outlier: 6.923A pdb=" N PHE A 480 " --> pdb=" O GLN A 512 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE A 514 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA A 482 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU A 516 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 484 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 624 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS A 671 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS B 645 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 598 " --> pdb=" O ALA B 536 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 536 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B 600 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B 461 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE B 456 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU B 486 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ALA B 458 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 488 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL B 460 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU B 485 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL B 512 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL B 487 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 594 through 595 Processing sheet with id=AA5, first strand: chain 'A' and resid 599 through 600 Processing sheet with id=AA6, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.251A pdb=" N TYR B 107 " --> pdb=" O VAL B 154 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 189 Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 283 removed outlier: 7.970A pdb=" N LEU B 281 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU B 254 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU B 283 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N SER B 256 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE B 253 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL B 319 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU B 255 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR B 316 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL B 342 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS B 318 " --> pdb=" O VAL B 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 570 through 574 removed outlier: 3.647A pdb=" N LEU B 570 " --> pdb=" O GLU B 583 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3002 1.34 - 1.46: 2265 1.46 - 1.58: 4402 1.58 - 1.70: 5 1.70 - 1.82: 72 Bond restraints: 9746 Sorted by residual: bond pdb=" O1A UDP B 801 " pdb=" PA UDP B 801 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.91e+01 bond pdb=" N ILE B 616 " pdb=" CA ILE B 616 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.38e+00 bond pdb=" N ASP B 615 " pdb=" CA ASP B 615 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.78e+00 bond pdb=" N TYR A 324 " pdb=" CA TYR A 324 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.19e-02 7.06e+03 6.91e+00 bond pdb=" O2A UDP B 801 " pdb=" PA UDP B 801 " ideal model delta sigma weight residual 1.527 1.481 0.046 1.80e-02 3.09e+03 6.52e+00 ... (remaining 9741 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 12842 1.23 - 2.46: 273 2.46 - 3.69: 106 3.69 - 4.92: 24 4.92 - 6.15: 7 Bond angle restraints: 13252 Sorted by residual: angle pdb=" O5' UDP B 801 " pdb=" PA UDP B 801 " pdb=" O1A UDP B 801 " ideal model delta sigma weight residual 106.70 111.06 -4.36 1.00e+00 1.00e+00 1.90e+01 angle pdb=" O2A UDP B 801 " pdb=" PA UDP B 801 " pdb=" O3A UDP B 801 " ideal model delta sigma weight residual 105.97 110.21 -4.24 1.00e+00 1.00e+00 1.80e+01 angle pdb=" O5' UDP B 801 " pdb=" PA UDP B 801 " pdb=" O2A UDP B 801 " ideal model delta sigma weight residual 110.83 107.01 3.82 1.00e+00 1.00e+00 1.46e+01 angle pdb=" O1A UDP B 801 " pdb=" PA UDP B 801 " pdb=" O3A UDP B 801 " ideal model delta sigma weight residual 109.95 106.28 3.67 1.00e+00 1.00e+00 1.35e+01 angle pdb=" CA GLU A 320 " pdb=" C GLU A 320 " pdb=" O GLU A 320 " ideal model delta sigma weight residual 121.28 117.36 3.92 1.07e+00 8.73e-01 1.34e+01 ... (remaining 13247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.77: 5638 21.77 - 43.53: 222 43.53 - 65.30: 29 65.30 - 87.06: 11 87.06 - 108.83: 4 Dihedral angle restraints: 5904 sinusoidal: 2493 harmonic: 3411 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 288.71 179.88 108.83 1 3.00e+01 1.11e-03 1.41e+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 -59.25 106.87 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C6 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O4 BMA C 3 " ideal model delta sinusoidal sigma weight residual -163.34 -60.34 -103.00 1 3.00e+01 1.11e-03 1.31e+01 ... (remaining 5901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1205 0.054 - 0.108: 200 0.108 - 0.162: 36 0.162 - 0.216: 4 0.216 - 0.270: 3 Chirality restraints: 1448 Sorted by residual: 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 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ILE B 542 " pdb=" N ILE B 542 " pdb=" C ILE B 542 " pdb=" CB ILE B 542 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE B 537 " pdb=" N ILE B 537 " pdb=" C ILE B 537 " pdb=" CB ILE B 537 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1445 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 399 " -0.019 2.00e-02 2.50e+03 1.01e-02 2.05e+00 pdb=" CG TYR B 399 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 399 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 399 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 399 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 399 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 399 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 399 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 479 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO B 480 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 480 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 480 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 448 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO A 449 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 449 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 449 " -0.016 5.00e-02 4.00e+02 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 24 2.38 - 3.01: 5195 3.01 - 3.64: 14368 3.64 - 4.27: 22110 4.27 - 4.90: 36577 Nonbonded interactions: 78274 Sorted by model distance: nonbonded pdb=" O1A UDP B 801 " pdb="MN MN B 802 " model vdw 1.752 2.320 nonbonded pdb=" O ALA A 377 " pdb=" OG1 THR A 408 " model vdw 2.205 3.040 nonbonded pdb=" OG SER A 547 " pdb=" OD1 ASP A 647 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR B 130 " pdb=" O PRO B 155 " model vdw 2.217 3.040 nonbonded pdb=" O GLU A 587 " pdb=" OH TYR A 630 " model vdw 2.237 3.040 ... (remaining 78269 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: 1.480 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.480 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9759 Z= 0.164 Angle : 0.526 6.152 13282 Z= 0.298 Chirality : 0.045 0.270 1448 Planarity : 0.003 0.035 1675 Dihedral : 11.926 108.829 3673 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.19 % Allowed : 5.24 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.26), residues: 1138 helix: 1.40 (0.28), residues: 358 sheet: -1.03 (0.44), residues: 142 loop : -0.17 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 280 TYR 0.019 0.001 TYR B 399 PHE 0.009 0.001 PHE B 400 TRP 0.008 0.001 TRP B 396 HIS 0.002 0.001 HIS B 623 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9746) covalent geometry : angle 0.52391 (13252) SS BOND : bond 0.00204 ( 9) SS BOND : angle 0.97724 ( 18) hydrogen bonds : bond 0.19900 ( 297) hydrogen bonds : angle 6.92454 ( 816) link_BETA1-4 : bond 0.00462 ( 2) link_BETA1-4 : angle 1.09955 ( 6) link_NAG-ASN : bond 0.00260 ( 2) link_NAG-ASN : angle 0.99549 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7296 (mmtt) cc_final: 0.6898 (mmtt) REVERT: A 142 ARG cc_start: 0.8324 (ptt90) cc_final: 0.7889 (ptt90) REVERT: A 210 ASP cc_start: 0.7744 (t70) cc_final: 0.7176 (t70) REVERT: A 394 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7750 (ptp-170) REVERT: A 546 MET cc_start: 0.4384 (ppp) cc_final: 0.3916 (ppp) REVERT: A 600 ASP cc_start: 0.7023 (t0) cc_final: 0.6633 (t0) REVERT: A 603 LYS cc_start: 0.7372 (ttpt) cc_final: 0.7049 (tttt) REVERT: A 615 ASP cc_start: 0.7169 (m-30) cc_final: 0.6816 (p0) REVERT: A 645 MET cc_start: 0.6936 (tpp) cc_final: 0.6621 (tpp) REVERT: A 706 ASN cc_start: 0.7586 (m-40) cc_final: 0.7096 (m-40) REVERT: B 131 ASN cc_start: 0.7903 (t0) cc_final: 0.7389 (t0) REVERT: B 268 ASP cc_start: 0.7180 (t0) cc_final: 0.6926 (t0) REVERT: B 275 LYS cc_start: 0.8500 (tmtt) cc_final: 0.8002 (tmtt) REVERT: B 310 GLN cc_start: 0.7566 (mp10) cc_final: 0.7079 (mp10) REVERT: B 370 MET cc_start: 0.7554 (tpt) cc_final: 0.7156 (tpp) REVERT: B 372 ASP cc_start: 0.7385 (t0) cc_final: 0.6721 (t0) REVERT: B 427 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6578 (mm-30) REVERT: B 431 ASP cc_start: 0.6963 (m-30) cc_final: 0.6503 (m-30) REVERT: B 435 VAL cc_start: 0.7715 (m) cc_final: 0.7509 (p) REVERT: B 566 TYR cc_start: 0.7004 (m-80) cc_final: 0.6513 (m-80) REVERT: B 583 GLU cc_start: 0.5957 (tm-30) cc_final: 0.5459 (tm-30) REVERT: B 589 GLU cc_start: 0.6544 (pm20) cc_final: 0.6222 (pm20) REVERT: B 646 VAL cc_start: 0.7834 (t) cc_final: 0.7181 (m) outliers start: 2 outliers final: 1 residues processed: 286 average time/residue: 0.1188 time to fit residues: 44.9455 Evaluate side-chains 254 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.0050 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS A 406 GLN A 431 GLN A 658 ASN B 412 GLN B 430 ASN B 517 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129448 restraints weight = 14350.297| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.58 r_work: 0.3527 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9759 Z= 0.150 Angle : 0.560 8.159 13282 Z= 0.285 Chirality : 0.044 0.165 1448 Planarity : 0.004 0.035 1675 Dihedral : 9.207 88.765 1414 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.04 % Allowed : 9.21 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1138 helix: 1.11 (0.27), residues: 373 sheet: -0.98 (0.43), residues: 141 loop : -0.14 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 595 TYR 0.020 0.002 TYR A 319 PHE 0.020 0.002 PHE A 579 TRP 0.014 0.001 TRP A 374 HIS 0.004 0.001 HIS A 448 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9746) covalent geometry : angle 0.55753 (13252) SS BOND : bond 0.00225 ( 9) SS BOND : angle 0.87893 ( 18) hydrogen bonds : bond 0.04496 ( 297) hydrogen bonds : angle 5.30801 ( 816) link_BETA1-4 : bond 0.00379 ( 2) link_BETA1-4 : angle 2.00950 ( 6) link_NAG-ASN : bond 0.00312 ( 2) link_NAG-ASN : angle 0.97543 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 268 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7585 (mmtt) cc_final: 0.7116 (mmtt) REVERT: A 132 GLN cc_start: 0.8137 (tp40) cc_final: 0.7905 (tp40) REVERT: A 142 ARG cc_start: 0.8410 (ptt90) cc_final: 0.8098 (ptt90) REVERT: A 210 ASP cc_start: 0.7888 (t70) cc_final: 0.7308 (t70) REVERT: A 211 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8008 (tt) REVERT: A 216 LEU cc_start: 0.6786 (pt) cc_final: 0.6446 (mt) REVERT: A 365 GLU cc_start: 0.6981 (tp30) cc_final: 0.6656 (tp30) REVERT: A 433 ARG cc_start: 0.8123 (ttm170) cc_final: 0.7916 (ttm170) REVERT: A 436 LYS cc_start: 0.8499 (mmmm) cc_final: 0.7991 (mmtm) REVERT: A 480 PHE cc_start: 0.8214 (p90) cc_final: 0.7895 (p90) REVERT: A 546 MET cc_start: 0.4937 (ppp) cc_final: 0.4294 (ppp) REVERT: A 595 ARG cc_start: 0.7465 (mmt-90) cc_final: 0.7081 (mmt-90) REVERT: A 603 LYS cc_start: 0.7631 (ttpt) cc_final: 0.7356 (ttpt) REVERT: A 645 MET cc_start: 0.7869 (tpp) cc_final: 0.7261 (tpp) REVERT: A 706 ASN cc_start: 0.7965 (m-40) cc_final: 0.7464 (m110) REVERT: A 721 GLN cc_start: 0.6587 (pm20) cc_final: 0.6384 (pm20) REVERT: B 131 ASN cc_start: 0.7983 (t0) cc_final: 0.6908 (t0) REVERT: B 135 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.6805 (mpp) REVERT: B 182 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.8002 (mtp85) REVERT: B 268 ASP cc_start: 0.7457 (t0) cc_final: 0.7197 (t0) REVERT: B 275 LYS cc_start: 0.8607 (tmtt) cc_final: 0.8057 (tmtt) REVERT: B 310 GLN cc_start: 0.7935 (mp10) cc_final: 0.7436 (mp10) REVERT: B 344 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.7119 (mm) REVERT: B 370 MET cc_start: 0.8161 (tpt) cc_final: 0.7714 (tpp) REVERT: B 372 ASP cc_start: 0.7719 (t0) cc_final: 0.7216 (t0) REVERT: B 427 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7015 (mm-30) REVERT: B 428 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7565 (tm-30) REVERT: B 431 ASP cc_start: 0.6984 (m-30) cc_final: 0.6723 (m-30) REVERT: B 466 VAL cc_start: 0.8095 (p) cc_final: 0.7894 (t) REVERT: B 583 GLU cc_start: 0.6643 (tm-30) cc_final: 0.5941 (tm-30) REVERT: B 589 GLU cc_start: 0.7275 (pm20) cc_final: 0.6818 (pm20) REVERT: B 693 GLU cc_start: 0.7720 (mp0) cc_final: 0.7347 (mp0) outliers start: 21 outliers final: 12 residues processed: 278 average time/residue: 0.1089 time to fit residues: 40.5892 Evaluate side-chains 265 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 250 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 501 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 74 optimal weight: 0.1980 chunk 99 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.148242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.126557 restraints weight = 14320.666| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.58 r_work: 0.3479 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9759 Z= 0.218 Angle : 0.596 8.106 13282 Z= 0.306 Chirality : 0.046 0.159 1448 Planarity : 0.004 0.036 1675 Dihedral : 8.592 89.035 1414 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.10 % Allowed : 11.35 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.25), residues: 1138 helix: 0.79 (0.27), residues: 371 sheet: -1.05 (0.45), residues: 129 loop : -0.38 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 383 TYR 0.023 0.002 TYR A 319 PHE 0.027 0.002 PHE A 577 TRP 0.017 0.001 TRP A 374 HIS 0.007 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 9746) covalent geometry : angle 0.59422 (13252) SS BOND : bond 0.00333 ( 9) SS BOND : angle 0.89668 ( 18) hydrogen bonds : bond 0.04717 ( 297) hydrogen bonds : angle 5.19957 ( 816) link_BETA1-4 : bond 0.00269 ( 2) link_BETA1-4 : angle 2.06931 ( 6) link_NAG-ASN : bond 0.00313 ( 2) link_NAG-ASN : angle 1.03484 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8284 (m-80) cc_final: 0.7860 (m-80) REVERT: A 115 LYS cc_start: 0.7619 (mmtt) cc_final: 0.7173 (mmtt) REVERT: A 142 ARG cc_start: 0.8519 (ptt90) cc_final: 0.8128 (ptt90) REVERT: A 181 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8385 (mm) REVERT: A 210 ASP cc_start: 0.7950 (t70) cc_final: 0.7337 (t70) REVERT: A 211 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8027 (tt) REVERT: A 213 GLN cc_start: 0.7252 (mt0) cc_final: 0.7031 (mt0) REVERT: A 216 LEU cc_start: 0.6706 (pt) cc_final: 0.6496 (mt) REVERT: A 223 THR cc_start: 0.8502 (p) cc_final: 0.8119 (t) REVERT: A 243 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7756 (tpp80) REVERT: A 267 LYS cc_start: 0.7116 (tttm) cc_final: 0.6827 (tttp) REVERT: A 436 LYS cc_start: 0.8520 (mmmm) cc_final: 0.7999 (mmtt) REVERT: A 454 VAL cc_start: 0.7694 (t) cc_final: 0.7388 (m) REVERT: A 546 MET cc_start: 0.5020 (ppp) cc_final: 0.4319 (ppp) REVERT: A 603 LYS cc_start: 0.7665 (ttpt) cc_final: 0.7347 (ttpt) REVERT: A 614 ASN cc_start: 0.7945 (t0) cc_final: 0.7705 (t0) REVERT: A 615 ASP cc_start: 0.7372 (m-30) cc_final: 0.6886 (p0) REVERT: A 645 MET cc_start: 0.7881 (tpp) cc_final: 0.7254 (tpp) REVERT: A 706 ASN cc_start: 0.8034 (m-40) cc_final: 0.7539 (m110) REVERT: B 131 ASN cc_start: 0.8000 (t0) cc_final: 0.7013 (t0) REVERT: B 135 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.6851 (mpp) REVERT: B 182 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.8014 (mtp85) REVERT: B 275 LYS cc_start: 0.8611 (tmtt) cc_final: 0.8149 (tmtt) REVERT: B 310 GLN cc_start: 0.8044 (mp10) cc_final: 0.7525 (mp10) REVERT: B 372 ASP cc_start: 0.7831 (t0) cc_final: 0.7346 (t0) REVERT: B 416 ASP cc_start: 0.7713 (m-30) cc_final: 0.7194 (m-30) REVERT: B 428 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7381 (tm-30) REVERT: B 466 VAL cc_start: 0.8229 (p) cc_final: 0.8019 (t) REVERT: B 541 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7353 (mm) REVERT: B 554 GLU cc_start: 0.6650 (mm-30) cc_final: 0.6435 (mm-30) REVERT: B 583 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6289 (tm-30) REVERT: B 589 GLU cc_start: 0.7280 (pm20) cc_final: 0.6820 (pm20) outliers start: 32 outliers final: 22 residues processed: 278 average time/residue: 0.1124 time to fit residues: 41.5628 Evaluate side-chains 278 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 252 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 151 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 646 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS A 719 HIS B 162 GLN B 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.148371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126518 restraints weight = 14407.626| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.60 r_work: 0.3480 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9759 Z= 0.189 Angle : 0.584 8.357 13282 Z= 0.300 Chirality : 0.045 0.248 1448 Planarity : 0.004 0.036 1675 Dihedral : 8.187 87.332 1414 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.59 % Allowed : 13.00 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.25), residues: 1138 helix: 0.68 (0.27), residues: 370 sheet: -1.08 (0.45), residues: 129 loop : -0.44 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 383 TYR 0.026 0.002 TYR A 319 PHE 0.038 0.002 PHE A 577 TRP 0.014 0.001 TRP A 374 HIS 0.004 0.001 HIS A 448 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 9746) covalent geometry : angle 0.58142 (13252) SS BOND : bond 0.00303 ( 9) SS BOND : angle 0.98244 ( 18) hydrogen bonds : bond 0.04363 ( 297) hydrogen bonds : angle 5.07348 ( 816) link_BETA1-4 : bond 0.00301 ( 2) link_BETA1-4 : angle 2.10252 ( 6) link_NAG-ASN : bond 0.00343 ( 2) link_NAG-ASN : angle 1.01505 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 262 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7623 (mmtt) cc_final: 0.7180 (mmtt) REVERT: A 131 TYR cc_start: 0.7492 (t80) cc_final: 0.7181 (t80) REVERT: A 142 ARG cc_start: 0.8517 (ptt90) cc_final: 0.8188 (ptt90) REVERT: A 147 ASP cc_start: 0.7863 (t0) cc_final: 0.7422 (t0) REVERT: A 181 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8378 (mm) REVERT: A 210 ASP cc_start: 0.7949 (t70) cc_final: 0.7285 (t70) REVERT: A 223 THR cc_start: 0.8468 (p) cc_final: 0.8094 (t) REVERT: A 436 LYS cc_start: 0.8508 (mmmm) cc_final: 0.8096 (mmtt) REVERT: A 464 ASP cc_start: 0.7188 (m-30) cc_final: 0.6902 (m-30) REVERT: A 546 MET cc_start: 0.5110 (ppp) cc_final: 0.4402 (ppp) REVERT: A 603 LYS cc_start: 0.7683 (ttpt) cc_final: 0.7371 (ttpt) REVERT: A 645 MET cc_start: 0.7852 (tpp) cc_final: 0.7195 (tpp) REVERT: A 705 MET cc_start: 0.8368 (mtp) cc_final: 0.8142 (mtp) REVERT: A 706 ASN cc_start: 0.8026 (m-40) cc_final: 0.7682 (m-40) REVERT: A 715 MET cc_start: 0.7118 (tpp) cc_final: 0.6650 (tpp) REVERT: B 105 LYS cc_start: 0.8159 (mttp) cc_final: 0.7833 (mttp) REVERT: B 109 TYR cc_start: 0.7790 (m-80) cc_final: 0.7501 (m-80) REVERT: B 135 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7180 (mpp) REVERT: B 182 ARG cc_start: 0.8314 (mmm-85) cc_final: 0.8024 (mtp85) REVERT: B 212 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8125 (mt) REVERT: B 275 LYS cc_start: 0.8639 (tmtt) cc_final: 0.8126 (tmtt) REVERT: B 310 GLN cc_start: 0.8029 (mp10) cc_final: 0.7524 (mp10) REVERT: B 344 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7495 (mm) REVERT: B 370 MET cc_start: 0.8126 (tpt) cc_final: 0.7712 (tpp) REVERT: B 372 ASP cc_start: 0.7870 (t0) cc_final: 0.7339 (t0) REVERT: B 428 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7459 (tm-30) REVERT: B 435 VAL cc_start: 0.8093 (p) cc_final: 0.7892 (m) REVERT: B 466 VAL cc_start: 0.8238 (p) cc_final: 0.8026 (t) REVERT: B 516 GLU cc_start: 0.7288 (mp0) cc_final: 0.6995 (mp0) REVERT: B 541 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7380 (mm) REVERT: B 554 GLU cc_start: 0.6625 (mm-30) cc_final: 0.6415 (mm-30) REVERT: B 583 GLU cc_start: 0.6798 (tm-30) cc_final: 0.6077 (tm-30) REVERT: B 589 GLU cc_start: 0.7267 (pm20) cc_final: 0.6785 (pm20) REVERT: B 678 ASN cc_start: 0.7847 (m-40) cc_final: 0.7577 (m-40) outliers start: 37 outliers final: 24 residues processed: 285 average time/residue: 0.1070 time to fit residues: 41.1475 Evaluate side-chains 277 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 646 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS A 398 GLN A 597 HIS ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.147426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125945 restraints weight = 14350.555| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.56 r_work: 0.3469 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9759 Z= 0.212 Angle : 0.606 8.396 13282 Z= 0.311 Chirality : 0.046 0.238 1448 Planarity : 0.005 0.045 1675 Dihedral : 8.027 89.666 1413 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.88 % Allowed : 14.65 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.25), residues: 1138 helix: 0.59 (0.27), residues: 370 sheet: -1.06 (0.46), residues: 128 loop : -0.52 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 383 TYR 0.021 0.002 TYR A 319 PHE 0.043 0.002 PHE A 577 TRP 0.015 0.001 TRP A 374 HIS 0.005 0.001 HIS A 448 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 9746) covalent geometry : angle 0.60402 (13252) SS BOND : bond 0.00315 ( 9) SS BOND : angle 0.80958 ( 18) hydrogen bonds : bond 0.04511 ( 297) hydrogen bonds : angle 5.09638 ( 816) link_BETA1-4 : bond 0.00225 ( 2) link_BETA1-4 : angle 2.12518 ( 6) link_NAG-ASN : bond 0.00291 ( 2) link_NAG-ASN : angle 1.01679 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7632 (mmtt) cc_final: 0.7218 (mmtt) REVERT: A 131 TYR cc_start: 0.7574 (t80) cc_final: 0.7093 (t80) REVERT: A 142 ARG cc_start: 0.8544 (ptt90) cc_final: 0.8175 (ptt90) REVERT: A 147 ASP cc_start: 0.7881 (t0) cc_final: 0.7470 (t0) REVERT: A 181 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8365 (mm) REVERT: A 202 ASP cc_start: 0.7060 (t0) cc_final: 0.6590 (m-30) REVERT: A 210 ASP cc_start: 0.8134 (t70) cc_final: 0.7423 (t70) REVERT: A 223 THR cc_start: 0.8472 (p) cc_final: 0.8010 (t) REVERT: A 248 ARG cc_start: 0.7060 (tpt90) cc_final: 0.6836 (tpp80) REVERT: A 365 GLU cc_start: 0.7114 (tp30) cc_final: 0.6673 (tp30) REVERT: A 436 LYS cc_start: 0.8475 (mmmm) cc_final: 0.8112 (mmtt) REVERT: A 464 ASP cc_start: 0.7223 (m-30) cc_final: 0.6934 (m-30) REVERT: A 603 LYS cc_start: 0.7698 (ttpt) cc_final: 0.7215 (tttt) REVERT: A 645 MET cc_start: 0.7825 (tpp) cc_final: 0.7219 (tpp) REVERT: A 706 ASN cc_start: 0.8044 (m-40) cc_final: 0.7662 (m-40) REVERT: A 715 MET cc_start: 0.7171 (tpp) cc_final: 0.6815 (tpp) REVERT: B 109 TYR cc_start: 0.7825 (m-80) cc_final: 0.7538 (m-80) REVERT: B 212 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8131 (mt) REVERT: B 275 LYS cc_start: 0.8645 (tmtt) cc_final: 0.8165 (tmtt) REVERT: B 310 GLN cc_start: 0.8060 (mp10) cc_final: 0.7543 (mp10) REVERT: B 344 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7622 (mm) REVERT: B 370 MET cc_start: 0.8112 (tpt) cc_final: 0.7726 (tpp) REVERT: B 372 ASP cc_start: 0.7881 (t0) cc_final: 0.7414 (t0) REVERT: B 428 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7547 (tm-30) REVERT: B 435 VAL cc_start: 0.8138 (p) cc_final: 0.7929 (m) REVERT: B 466 VAL cc_start: 0.8276 (p) cc_final: 0.8070 (t) REVERT: B 516 GLU cc_start: 0.7284 (mp0) cc_final: 0.6981 (mp0) REVERT: B 541 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7341 (mm) REVERT: B 554 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6361 (mm-30) REVERT: B 583 GLU cc_start: 0.6879 (tm-30) cc_final: 0.6174 (tm-30) REVERT: B 612 MET cc_start: 0.7460 (tpt) cc_final: 0.6897 (tpt) outliers start: 40 outliers final: 30 residues processed: 277 average time/residue: 0.1170 time to fit residues: 43.0102 Evaluate side-chains 282 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 646 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.147813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126201 restraints weight = 14439.907| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.58 r_work: 0.3476 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9759 Z= 0.177 Angle : 0.593 8.858 13282 Z= 0.302 Chirality : 0.045 0.225 1448 Planarity : 0.005 0.040 1675 Dihedral : 7.790 89.783 1413 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.59 % Allowed : 14.94 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1138 helix: 0.63 (0.27), residues: 365 sheet: -1.18 (0.44), residues: 140 loop : -0.43 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 383 TYR 0.021 0.002 TYR A 714 PHE 0.041 0.002 PHE A 577 TRP 0.012 0.001 TRP A 374 HIS 0.004 0.001 HIS A 448 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9746) covalent geometry : angle 0.59073 (13252) SS BOND : bond 0.00266 ( 9) SS BOND : angle 0.69555 ( 18) hydrogen bonds : bond 0.04310 ( 297) hydrogen bonds : angle 5.05717 ( 816) link_BETA1-4 : bond 0.00285 ( 2) link_BETA1-4 : angle 2.13501 ( 6) link_NAG-ASN : bond 0.00293 ( 2) link_NAG-ASN : angle 0.98642 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 252 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7631 (mmtt) cc_final: 0.7212 (mmtt) REVERT: A 131 TYR cc_start: 0.7505 (t80) cc_final: 0.7096 (t80) REVERT: A 142 ARG cc_start: 0.8541 (ptt90) cc_final: 0.8170 (ptt90) REVERT: A 147 ASP cc_start: 0.7879 (t0) cc_final: 0.7470 (t0) REVERT: A 181 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8355 (mm) REVERT: A 210 ASP cc_start: 0.8135 (t70) cc_final: 0.7402 (t70) REVERT: A 223 THR cc_start: 0.8453 (p) cc_final: 0.7999 (t) REVERT: A 365 GLU cc_start: 0.7083 (tp30) cc_final: 0.6657 (tp30) REVERT: A 436 LYS cc_start: 0.8431 (mmmm) cc_final: 0.8093 (mmtt) REVERT: A 464 ASP cc_start: 0.7223 (m-30) cc_final: 0.6937 (m-30) REVERT: A 580 THR cc_start: 0.8264 (t) cc_final: 0.8064 (p) REVERT: A 600 ASP cc_start: 0.7057 (t0) cc_final: 0.6608 (t0) REVERT: A 603 LYS cc_start: 0.7720 (ttpt) cc_final: 0.7182 (tttt) REVERT: A 645 MET cc_start: 0.7794 (tpp) cc_final: 0.7175 (tpp) REVERT: A 705 MET cc_start: 0.8359 (mtp) cc_final: 0.8126 (mtp) REVERT: A 706 ASN cc_start: 0.8049 (m-40) cc_final: 0.7641 (m-40) REVERT: A 715 MET cc_start: 0.7150 (tpp) cc_final: 0.6776 (tpp) REVERT: B 105 LYS cc_start: 0.8190 (mttm) cc_final: 0.7903 (mttp) REVERT: B 109 TYR cc_start: 0.7834 (m-80) cc_final: 0.7549 (m-80) REVERT: B 212 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8117 (mt) REVERT: B 275 LYS cc_start: 0.8645 (tmtt) cc_final: 0.8171 (tmtt) REVERT: B 310 GLN cc_start: 0.8015 (mp10) cc_final: 0.7481 (mp10) REVERT: B 344 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7674 (mm) REVERT: B 370 MET cc_start: 0.8124 (tpt) cc_final: 0.7739 (tpp) REVERT: B 372 ASP cc_start: 0.7906 (t0) cc_final: 0.7396 (t0) REVERT: B 466 VAL cc_start: 0.8270 (p) cc_final: 0.8069 (t) REVERT: B 516 GLU cc_start: 0.7264 (mp0) cc_final: 0.6968 (mp0) REVERT: B 541 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7302 (mm) REVERT: B 554 GLU cc_start: 0.6527 (mm-30) cc_final: 0.6264 (mm-30) REVERT: B 583 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6117 (tm-30) REVERT: B 612 MET cc_start: 0.7475 (tpt) cc_final: 0.6887 (tpt) outliers start: 37 outliers final: 29 residues processed: 275 average time/residue: 0.1029 time to fit residues: 38.1237 Evaluate side-chains 280 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 646 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 74 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS A 631 HIS B 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.149364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.127912 restraints weight = 14364.250| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.58 r_work: 0.3504 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9759 Z= 0.127 Angle : 0.569 7.203 13282 Z= 0.290 Chirality : 0.044 0.209 1448 Planarity : 0.004 0.041 1675 Dihedral : 7.414 89.688 1413 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.78 % Allowed : 14.94 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.25), residues: 1138 helix: 0.67 (0.27), residues: 365 sheet: -1.05 (0.45), residues: 138 loop : -0.39 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 383 TYR 0.026 0.002 TYR B 582 PHE 0.035 0.001 PHE A 577 TRP 0.010 0.001 TRP B 396 HIS 0.004 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9746) covalent geometry : angle 0.56698 (13252) SS BOND : bond 0.00196 ( 9) SS BOND : angle 0.64178 ( 18) hydrogen bonds : bond 0.03963 ( 297) hydrogen bonds : angle 4.98715 ( 816) link_BETA1-4 : bond 0.00370 ( 2) link_BETA1-4 : angle 2.14972 ( 6) link_NAG-ASN : bond 0.00326 ( 2) link_NAG-ASN : angle 0.95876 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7619 (mmtt) cc_final: 0.7177 (mmtt) REVERT: A 142 ARG cc_start: 0.8513 (ptt90) cc_final: 0.8164 (ptt90) REVERT: A 147 ASP cc_start: 0.7867 (t0) cc_final: 0.7469 (t0) REVERT: A 181 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8372 (mm) REVERT: A 210 ASP cc_start: 0.8117 (t70) cc_final: 0.7359 (t70) REVERT: A 365 GLU cc_start: 0.7010 (tp30) cc_final: 0.6705 (tp30) REVERT: A 394 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7548 (mtt-85) REVERT: A 436 LYS cc_start: 0.8402 (mmmm) cc_final: 0.7984 (mmtt) REVERT: A 439 SER cc_start: 0.8046 (p) cc_final: 0.7748 (m) REVERT: A 464 ASP cc_start: 0.7222 (m-30) cc_final: 0.6937 (m-30) REVERT: A 580 THR cc_start: 0.8259 (t) cc_final: 0.8014 (p) REVERT: A 595 ARG cc_start: 0.7601 (mmt-90) cc_final: 0.7210 (mmt-90) REVERT: A 600 ASP cc_start: 0.6984 (t0) cc_final: 0.6550 (t0) REVERT: A 603 LYS cc_start: 0.7724 (ttpt) cc_final: 0.7209 (tttt) REVERT: A 645 MET cc_start: 0.7766 (tpp) cc_final: 0.7148 (tpp) REVERT: A 705 MET cc_start: 0.8359 (mtp) cc_final: 0.8100 (mtp) REVERT: A 706 ASN cc_start: 0.8022 (m-40) cc_final: 0.7616 (m-40) REVERT: A 715 MET cc_start: 0.7119 (tpp) cc_final: 0.6810 (tpp) REVERT: B 105 LYS cc_start: 0.8182 (mttm) cc_final: 0.7891 (mttp) REVERT: B 109 TYR cc_start: 0.7816 (m-80) cc_final: 0.7530 (m-80) REVERT: B 135 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7154 (mpp) REVERT: B 212 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8123 (mt) REVERT: B 275 LYS cc_start: 0.8655 (tmtt) cc_final: 0.8174 (tmtt) REVERT: B 282 VAL cc_start: 0.8841 (t) cc_final: 0.8585 (m) REVERT: B 310 GLN cc_start: 0.7975 (mp10) cc_final: 0.7426 (mp10) REVERT: B 344 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7599 (mm) REVERT: B 359 LYS cc_start: 0.8210 (mppt) cc_final: 0.7806 (mppt) REVERT: B 370 MET cc_start: 0.8060 (tpt) cc_final: 0.7712 (tpp) REVERT: B 372 ASP cc_start: 0.7894 (t0) cc_final: 0.7338 (t0) REVERT: B 466 VAL cc_start: 0.8234 (p) cc_final: 0.8026 (t) REVERT: B 475 GLU cc_start: 0.7251 (tp30) cc_final: 0.7030 (tp30) REVERT: B 516 GLU cc_start: 0.7238 (mp0) cc_final: 0.6939 (mp0) REVERT: B 541 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7313 (mm) REVERT: B 554 GLU cc_start: 0.6474 (mm-30) cc_final: 0.6238 (mm-30) REVERT: B 583 GLU cc_start: 0.6752 (tm-30) cc_final: 0.6031 (tm-30) REVERT: B 611 LYS cc_start: 0.8226 (mttm) cc_final: 0.7970 (mttp) REVERT: B 612 MET cc_start: 0.7410 (tpt) cc_final: 0.6683 (tpp) outliers start: 39 outliers final: 26 residues processed: 285 average time/residue: 0.1041 time to fit residues: 40.1106 Evaluate side-chains 286 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 319 TYR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 646 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 28 optimal weight: 0.9990 chunk 97 optimal weight: 0.0980 chunk 58 optimal weight: 0.9990 chunk 59 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS A 431 GLN A 448 HIS A 631 HIS B 412 GLN B 430 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.149795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128370 restraints weight = 14272.943| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.57 r_work: 0.3514 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9759 Z= 0.128 Angle : 0.577 9.068 13282 Z= 0.293 Chirality : 0.044 0.193 1448 Planarity : 0.004 0.043 1675 Dihedral : 7.185 88.323 1413 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.69 % Allowed : 15.13 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1138 helix: 0.74 (0.27), residues: 365 sheet: -0.99 (0.45), residues: 138 loop : -0.36 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 383 TYR 0.025 0.002 TYR B 582 PHE 0.030 0.001 PHE A 577 TRP 0.011 0.001 TRP A 711 HIS 0.004 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9746) covalent geometry : angle 0.57445 (13252) SS BOND : bond 0.00244 ( 9) SS BOND : angle 1.01094 ( 18) hydrogen bonds : bond 0.03890 ( 297) hydrogen bonds : angle 4.98339 ( 816) link_BETA1-4 : bond 0.00392 ( 2) link_BETA1-4 : angle 2.15775 ( 6) link_NAG-ASN : bond 0.00317 ( 2) link_NAG-ASN : angle 0.98292 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7613 (mmtt) cc_final: 0.7174 (mmtt) REVERT: A 142 ARG cc_start: 0.8516 (ptt90) cc_final: 0.8164 (ptt90) REVERT: A 147 ASP cc_start: 0.7856 (t0) cc_final: 0.7464 (t0) REVERT: A 181 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8383 (mm) REVERT: A 210 ASP cc_start: 0.8130 (t70) cc_final: 0.7370 (t70) REVERT: A 223 THR cc_start: 0.8768 (m) cc_final: 0.8301 (t) REVERT: A 365 GLU cc_start: 0.7107 (tp30) cc_final: 0.6671 (tp30) REVERT: A 394 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7557 (mtt-85) REVERT: A 436 LYS cc_start: 0.8386 (mmmm) cc_final: 0.7967 (mmtt) REVERT: A 439 SER cc_start: 0.8063 (p) cc_final: 0.7742 (m) REVERT: A 464 ASP cc_start: 0.7222 (m-30) cc_final: 0.6945 (m-30) REVERT: A 580 THR cc_start: 0.8246 (t) cc_final: 0.8005 (p) REVERT: A 595 ARG cc_start: 0.7629 (mmt-90) cc_final: 0.7248 (mmt-90) REVERT: A 600 ASP cc_start: 0.6976 (t0) cc_final: 0.6565 (t0) REVERT: A 603 LYS cc_start: 0.7750 (ttpt) cc_final: 0.7239 (tttt) REVERT: A 615 ASP cc_start: 0.7458 (m-30) cc_final: 0.7201 (m-30) REVERT: A 645 MET cc_start: 0.7802 (tpp) cc_final: 0.7173 (tpp) REVERT: A 705 MET cc_start: 0.8347 (mtp) cc_final: 0.8078 (mtp) REVERT: A 706 ASN cc_start: 0.8010 (m-40) cc_final: 0.7589 (m-40) REVERT: A 715 MET cc_start: 0.7090 (tpp) cc_final: 0.6790 (tpp) REVERT: B 105 LYS cc_start: 0.8161 (mttm) cc_final: 0.7870 (mttp) REVERT: B 131 ASN cc_start: 0.8064 (t0) cc_final: 0.7699 (t0) REVERT: B 135 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7214 (mpp) REVERT: B 212 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8142 (mt) REVERT: B 251 GLN cc_start: 0.7831 (pt0) cc_final: 0.7607 (pt0) REVERT: B 275 LYS cc_start: 0.8658 (tmtt) cc_final: 0.8198 (tmtt) REVERT: B 282 VAL cc_start: 0.8896 (t) cc_final: 0.8525 (m) REVERT: B 310 GLN cc_start: 0.8015 (mp10) cc_final: 0.7455 (mp10) REVERT: B 344 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7594 (mm) REVERT: B 359 LYS cc_start: 0.8213 (mppt) cc_final: 0.7808 (mppt) REVERT: B 370 MET cc_start: 0.8067 (tpt) cc_final: 0.7711 (tpp) REVERT: B 372 ASP cc_start: 0.7880 (t0) cc_final: 0.7294 (t0) REVERT: B 466 VAL cc_start: 0.8221 (p) cc_final: 0.8012 (t) REVERT: B 475 GLU cc_start: 0.7272 (tp30) cc_final: 0.7017 (tp30) REVERT: B 516 GLU cc_start: 0.7237 (mp0) cc_final: 0.6943 (mp0) REVERT: B 541 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7309 (mm) REVERT: B 554 GLU cc_start: 0.6477 (mm-30) cc_final: 0.6225 (mm-30) REVERT: B 583 GLU cc_start: 0.6714 (tm-30) cc_final: 0.6007 (tm-30) REVERT: B 612 MET cc_start: 0.7404 (tpt) cc_final: 0.6659 (tpp) outliers start: 38 outliers final: 29 residues processed: 279 average time/residue: 0.1065 time to fit residues: 40.1104 Evaluate side-chains 285 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 558 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 6 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 0.0040 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS A 431 GLN A 448 HIS ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.149461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128057 restraints weight = 14300.064| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.56 r_work: 0.3515 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9759 Z= 0.137 Angle : 0.586 8.044 13282 Z= 0.299 Chirality : 0.044 0.189 1448 Planarity : 0.004 0.050 1675 Dihedral : 7.107 88.470 1413 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.39 % Allowed : 15.71 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.25), residues: 1138 helix: 0.74 (0.27), residues: 365 sheet: -1.02 (0.45), residues: 141 loop : -0.33 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 383 TYR 0.027 0.002 TYR B 582 PHE 0.028 0.001 PHE A 577 TRP 0.015 0.001 TRP A 711 HIS 0.004 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9746) covalent geometry : angle 0.58327 (13252) SS BOND : bond 0.00187 ( 9) SS BOND : angle 0.84245 ( 18) hydrogen bonds : bond 0.03933 ( 297) hydrogen bonds : angle 5.01305 ( 816) link_BETA1-4 : bond 0.00369 ( 2) link_BETA1-4 : angle 2.16816 ( 6) link_NAG-ASN : bond 0.00303 ( 2) link_NAG-ASN : angle 0.97223 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 256 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7624 (mmtt) cc_final: 0.7165 (mmtt) REVERT: A 142 ARG cc_start: 0.8515 (ptt90) cc_final: 0.8149 (ptt90) REVERT: A 147 ASP cc_start: 0.7850 (t0) cc_final: 0.7458 (t0) REVERT: A 181 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8382 (mm) REVERT: A 210 ASP cc_start: 0.8127 (t70) cc_final: 0.7355 (t70) REVERT: A 223 THR cc_start: 0.8747 (m) cc_final: 0.8314 (t) REVERT: A 365 GLU cc_start: 0.7099 (tp30) cc_final: 0.6670 (tp30) REVERT: A 394 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7567 (mtt-85) REVERT: A 436 LYS cc_start: 0.8386 (mmmm) cc_final: 0.8033 (mmtt) REVERT: A 439 SER cc_start: 0.8057 (p) cc_final: 0.7735 (m) REVERT: A 464 ASP cc_start: 0.7213 (m-30) cc_final: 0.6979 (m-30) REVERT: A 595 ARG cc_start: 0.7643 (mmt-90) cc_final: 0.7254 (mmt-90) REVERT: A 600 ASP cc_start: 0.6968 (t0) cc_final: 0.6552 (t0) REVERT: A 603 LYS cc_start: 0.7760 (ttpt) cc_final: 0.7247 (tttt) REVERT: A 615 ASP cc_start: 0.7466 (m-30) cc_final: 0.7199 (m-30) REVERT: A 645 MET cc_start: 0.7786 (tpp) cc_final: 0.7152 (tpp) REVERT: A 705 MET cc_start: 0.8338 (mtp) cc_final: 0.8088 (mtp) REVERT: A 706 ASN cc_start: 0.8008 (m-40) cc_final: 0.7587 (m-40) REVERT: A 715 MET cc_start: 0.7103 (tpp) cc_final: 0.6811 (tpp) REVERT: B 135 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7165 (mpp) REVERT: B 212 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8128 (mt) REVERT: B 251 GLN cc_start: 0.7815 (pt0) cc_final: 0.7598 (pt0) REVERT: B 275 LYS cc_start: 0.8660 (tmtt) cc_final: 0.8248 (tmtt) REVERT: B 310 GLN cc_start: 0.8016 (mp10) cc_final: 0.7443 (mp10) REVERT: B 344 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7598 (mm) REVERT: B 359 LYS cc_start: 0.8221 (mppt) cc_final: 0.7816 (mppt) REVERT: B 370 MET cc_start: 0.8059 (tpt) cc_final: 0.7738 (tpp) REVERT: B 372 ASP cc_start: 0.7880 (t0) cc_final: 0.7331 (t0) REVERT: B 466 VAL cc_start: 0.8231 (p) cc_final: 0.8020 (t) REVERT: B 475 GLU cc_start: 0.7290 (tp30) cc_final: 0.7060 (tp30) REVERT: B 516 GLU cc_start: 0.7265 (mp0) cc_final: 0.6963 (mp0) REVERT: B 541 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7300 (mm) REVERT: B 554 GLU cc_start: 0.6513 (mm-30) cc_final: 0.6247 (mm-30) REVERT: B 583 GLU cc_start: 0.6731 (tm-30) cc_final: 0.5997 (tm-30) REVERT: B 672 GLU cc_start: 0.6473 (tp30) cc_final: 0.6016 (tm-30) REVERT: B 693 GLU cc_start: 0.7702 (mp0) cc_final: 0.7432 (mp0) outliers start: 35 outliers final: 27 residues processed: 277 average time/residue: 0.0996 time to fit residues: 37.7563 Evaluate side-chains 283 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 646 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.0980 chunk 13 optimal weight: 0.0170 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.5220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS A 631 HIS ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.149927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128640 restraints weight = 14208.756| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.57 r_work: 0.3521 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9759 Z= 0.126 Angle : 0.588 9.454 13282 Z= 0.298 Chirality : 0.044 0.184 1448 Planarity : 0.004 0.037 1675 Dihedral : 6.989 88.543 1413 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.39 % Allowed : 15.62 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.25), residues: 1138 helix: 0.77 (0.27), residues: 365 sheet: -1.01 (0.45), residues: 141 loop : -0.30 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 383 TYR 0.027 0.002 TYR B 582 PHE 0.027 0.001 PHE A 577 TRP 0.031 0.001 TRP A 711 HIS 0.004 0.001 HIS A 397 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9746) covalent geometry : angle 0.58577 (13252) SS BOND : bond 0.00165 ( 9) SS BOND : angle 0.74867 ( 18) hydrogen bonds : bond 0.03855 ( 297) hydrogen bonds : angle 4.97231 ( 816) link_BETA1-4 : bond 0.00369 ( 2) link_BETA1-4 : angle 2.14739 ( 6) link_NAG-ASN : bond 0.00330 ( 2) link_NAG-ASN : angle 0.96791 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7602 (mmtt) cc_final: 0.7155 (mmtt) REVERT: A 142 ARG cc_start: 0.8506 (ptt90) cc_final: 0.8183 (ptt90) REVERT: A 147 ASP cc_start: 0.7854 (t0) cc_final: 0.7464 (t0) REVERT: A 181 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8401 (mm) REVERT: A 210 ASP cc_start: 0.8109 (t70) cc_final: 0.7335 (t70) REVERT: A 223 THR cc_start: 0.8738 (m) cc_final: 0.8321 (t) REVERT: A 267 LYS cc_start: 0.6785 (tttm) cc_final: 0.6535 (tttm) REVERT: A 365 GLU cc_start: 0.7073 (tp30) cc_final: 0.6657 (tp30) REVERT: A 428 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6961 (mm-30) REVERT: A 436 LYS cc_start: 0.8371 (mmmm) cc_final: 0.8027 (mmtt) REVERT: A 439 SER cc_start: 0.8059 (p) cc_final: 0.7699 (m) REVERT: A 464 ASP cc_start: 0.7228 (m-30) cc_final: 0.6969 (m-30) REVERT: A 595 ARG cc_start: 0.7647 (mmt-90) cc_final: 0.7257 (mmt-90) REVERT: A 600 ASP cc_start: 0.6980 (t0) cc_final: 0.6572 (t0) REVERT: A 603 LYS cc_start: 0.7774 (ttpt) cc_final: 0.7219 (tttt) REVERT: A 615 ASP cc_start: 0.7438 (m-30) cc_final: 0.6985 (m-30) REVERT: A 645 MET cc_start: 0.7795 (tpp) cc_final: 0.7155 (tpp) REVERT: A 705 MET cc_start: 0.8301 (mtp) cc_final: 0.8028 (mtp) REVERT: A 706 ASN cc_start: 0.8001 (m-40) cc_final: 0.7547 (m-40) REVERT: B 83 LEU cc_start: 0.7832 (tp) cc_final: 0.7624 (tt) REVERT: B 131 ASN cc_start: 0.8078 (t0) cc_final: 0.7705 (t0) REVERT: B 135 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.7166 (mpp) REVERT: B 212 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8129 (mt) REVERT: B 251 GLN cc_start: 0.7810 (pt0) cc_final: 0.7589 (pt0) REVERT: B 275 LYS cc_start: 0.8656 (tmtt) cc_final: 0.8221 (tmtt) REVERT: B 310 GLN cc_start: 0.8013 (mp10) cc_final: 0.7436 (mp10) REVERT: B 344 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7598 (mm) REVERT: B 359 LYS cc_start: 0.8179 (mppt) cc_final: 0.7759 (mppt) REVERT: B 370 MET cc_start: 0.8033 (tpt) cc_final: 0.7701 (tpp) REVERT: B 372 ASP cc_start: 0.7864 (t0) cc_final: 0.7322 (t0) REVERT: B 466 VAL cc_start: 0.8223 (p) cc_final: 0.8012 (t) REVERT: B 475 GLU cc_start: 0.7281 (tp30) cc_final: 0.7068 (tp30) REVERT: B 516 GLU cc_start: 0.7251 (mp0) cc_final: 0.6948 (mp0) REVERT: B 541 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7325 (mm) REVERT: B 554 GLU cc_start: 0.6500 (mm-30) cc_final: 0.6239 (mm-30) REVERT: B 672 GLU cc_start: 0.6428 (tp30) cc_final: 0.6007 (tm-30) REVERT: B 673 ARG cc_start: 0.6295 (mtp-110) cc_final: 0.6006 (ttp80) REVERT: B 693 GLU cc_start: 0.7709 (mp0) cc_final: 0.7439 (mp0) outliers start: 35 outliers final: 26 residues processed: 276 average time/residue: 0.1021 time to fit residues: 38.4615 Evaluate side-chains 281 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 646 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 60 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 97 optimal weight: 0.0870 chunk 96 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 3 optimal weight: 0.0010 chunk 111 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 HIS ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 276 HIS ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.150776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.129566 restraints weight = 14374.741| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.59 r_work: 0.3531 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9759 Z= 0.116 Angle : 0.586 8.072 13282 Z= 0.297 Chirality : 0.043 0.182 1448 Planarity : 0.004 0.042 1675 Dihedral : 6.862 88.066 1413 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.10 % Allowed : 16.59 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1138 helix: 0.84 (0.27), residues: 365 sheet: -1.00 (0.45), residues: 141 loop : -0.27 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 383 TYR 0.025 0.002 TYR B 582 PHE 0.025 0.001 PHE A 577 TRP 0.027 0.001 TRP A 711 HIS 0.003 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9746) covalent geometry : angle 0.58377 (13252) SS BOND : bond 0.00149 ( 9) SS BOND : angle 0.69445 ( 18) hydrogen bonds : bond 0.03721 ( 297) hydrogen bonds : angle 4.93275 ( 816) link_BETA1-4 : bond 0.00428 ( 2) link_BETA1-4 : angle 2.07465 ( 6) link_NAG-ASN : bond 0.00338 ( 2) link_NAG-ASN : angle 1.01637 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2052.97 seconds wall clock time: 36 minutes 2.68 seconds (2162.68 seconds total)