Starting phenix.real_space_refine on Sun Dec 29 02:41:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uqx_26701/12_2024/7uqx_26701.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uqx_26701/12_2024/7uqx_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uqx_26701/12_2024/7uqx_26701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uqx_26701/12_2024/7uqx_26701.map" model { file = "/net/cci-nas-00/data/ceres_data/7uqx_26701/12_2024/7uqx_26701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uqx_26701/12_2024/7uqx_26701.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.53, per 1000 atoms: 0.69 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: 2.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.03 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: 3.32 Time building geometry restraints manager: 3.16 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.620 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.080 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:4.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.820 ------------------------------------------------------------------------------- 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 9746 Z= 0.170 Angle : 0.524 6.152 13252 Z= 0.297 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (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 TRP 0.008 0.001 TRP B 396 HIS 0.002 0.001 HIS B 623 PHE 0.009 0.001 PHE B 400 TYR 0.019 0.001 TYR B 399 ARG 0.001 0.000 ARG A 280 *********************** 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 : 1.163 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: 0.8325 (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: 0.7553 (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: 0.5460 (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: 0.7180 (m) outliers start: 2 outliers final: 1 residues processed: 286 average time/residue: 0.2837 time to fit residues: 107.4179 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 : 1.156 ------------------------------------------------------------------------------- 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 97 optimal weight: 7.9990 chunk 87 optimal weight: 0.0770 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 67 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.4744 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9746 Z= 0.316 Angle : 0.590 8.396 13252 Z= 0.303 Chirality : 0.046 0.169 1448 Planarity : 0.004 0.036 1675 Dihedral : 9.417 87.595 1414 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.94 % Allowed : 9.51 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1138 helix: 0.91 (0.27), residues: 373 sheet: -1.09 (0.43), residues: 141 loop : -0.19 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 374 HIS 0.006 0.001 HIS A 448 PHE 0.020 0.002 PHE A 579 TYR 0.017 0.002 TYR A 319 ARG 0.007 0.001 ARG A 595 *********************** 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: 20 poor density : 269 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7371 (mmtt) cc_final: 0.6979 (mmtt) REVERT: A 132 GLN cc_start: 0.7940 (tp40) cc_final: 0.7704 (tp40) REVERT: A 142 ARG cc_start: 0.8441 (ptt90) cc_final: 0.8012 (ptt90) REVERT: A 210 ASP cc_start: 0.7823 (t70) cc_final: 0.7228 (t70) REVERT: A 216 LEU cc_start: 0.6680 (pt) cc_final: 0.6406 (mt) REVERT: A 365 GLU cc_start: 0.6583 (tp30) cc_final: 0.6304 (tp30) REVERT: A 433 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7762 (ttp-170) REVERT: A 436 LYS cc_start: 0.8482 (mmmm) cc_final: 0.7984 (mmtm) REVERT: A 480 PHE cc_start: 0.8143 (p90) cc_final: 0.7831 (p90) REVERT: A 546 MET cc_start: 0.4733 (ppp) cc_final: 0.4123 (ppp) REVERT: A 603 LYS cc_start: 0.7573 (ttpt) cc_final: 0.7309 (ttpt) REVERT: A 631 HIS cc_start: 0.7516 (m170) cc_final: 0.7096 (m170) REVERT: A 645 MET cc_start: 0.7001 (tpp) cc_final: 0.6669 (tpp) REVERT: A 706 ASN cc_start: 0.7732 (m-40) cc_final: 0.7256 (m110) REVERT: A 715 MET cc_start: 0.6728 (tpp) cc_final: 0.5819 (tpp) REVERT: B 135 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6743 (mpp) REVERT: B 182 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.7970 (mtp85) REVERT: B 275 LYS cc_start: 0.8513 (tmtt) cc_final: 0.8101 (tmtt) REVERT: B 310 GLN cc_start: 0.7743 (mp10) cc_final: 0.7279 (mp10) REVERT: B 370 MET cc_start: 0.7626 (tpt) cc_final: 0.7264 (tpp) REVERT: B 372 ASP cc_start: 0.7461 (t0) cc_final: 0.6984 (t0) REVERT: B 427 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6712 (mm-30) REVERT: B 431 ASP cc_start: 0.6885 (m-30) cc_final: 0.6656 (m-30) REVERT: B 517 ASN cc_start: 0.6816 (t0) cc_final: 0.6300 (t0) REVERT: B 583 GLU cc_start: 0.6213 (tm-30) cc_final: 0.5610 (tm-30) REVERT: B 589 GLU cc_start: 0.6641 (pm20) cc_final: 0.6261 (pm20) outliers start: 20 outliers final: 14 residues processed: 277 average time/residue: 0.2586 time to fit residues: 95.5718 Evaluate side-chains 272 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 257 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 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 184 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 233 TYR 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 58 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 HIS B 412 GLN ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9746 Z= 0.210 Angle : 0.560 8.444 13252 Z= 0.286 Chirality : 0.044 0.146 1448 Planarity : 0.004 0.036 1675 Dihedral : 8.444 89.111 1413 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.81 % Allowed : 11.45 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1138 helix: 1.01 (0.27), residues: 366 sheet: -1.13 (0.43), residues: 140 loop : -0.26 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 374 HIS 0.004 0.001 HIS A 631 PHE 0.027 0.002 PHE A 577 TYR 0.027 0.002 TYR A 714 ARG 0.005 0.000 ARG B 383 *********************** 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 294 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7360 (mmtt) cc_final: 0.7000 (mmtt) REVERT: A 142 ARG cc_start: 0.8414 (ptt90) cc_final: 0.8031 (ptt90) REVERT: A 181 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8406 (mm) REVERT: A 216 LEU cc_start: 0.6631 (pt) cc_final: 0.6395 (mt) REVERT: A 223 THR cc_start: 0.8244 (p) cc_final: 0.7894 (t) REVERT: A 256 ILE cc_start: 0.8305 (tp) cc_final: 0.8083 (tp) REVERT: A 267 LYS cc_start: 0.7028 (tttm) cc_final: 0.6732 (tttp) REVERT: A 346 ARG cc_start: 0.6312 (ttm170) cc_final: 0.5903 (mmt90) REVERT: A 436 LYS cc_start: 0.8463 (mmmm) cc_final: 0.8022 (mmtm) REVERT: A 454 VAL cc_start: 0.7469 (t) cc_final: 0.7166 (m) REVERT: A 546 MET cc_start: 0.4774 (ppp) cc_final: 0.4165 (ppp) REVERT: A 603 LYS cc_start: 0.7594 (ttpt) cc_final: 0.7300 (ttpt) REVERT: A 645 MET cc_start: 0.6966 (tpp) cc_final: 0.6629 (tpp) REVERT: A 706 ASN cc_start: 0.7734 (m-40) cc_final: 0.7256 (m110) REVERT: A 715 MET cc_start: 0.6740 (tpp) cc_final: 0.5918 (tpp) REVERT: B 131 ASN cc_start: 0.7947 (t0) cc_final: 0.6737 (t0) REVERT: B 135 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6437 (mpp) REVERT: B 182 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.7984 (mtp85) REVERT: B 275 LYS cc_start: 0.8539 (tmtt) cc_final: 0.8050 (tmtt) REVERT: B 310 GLN cc_start: 0.7638 (mp10) cc_final: 0.7192 (mp10) REVERT: B 344 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.7052 (mm) REVERT: B 370 MET cc_start: 0.7535 (tpt) cc_final: 0.7177 (tpp) REVERT: B 372 ASP cc_start: 0.7510 (t0) cc_final: 0.7032 (t0) REVERT: B 428 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6782 (tm-30) REVERT: B 484 LYS cc_start: 0.7217 (ttmt) cc_final: 0.6865 (ttmt) REVERT: B 517 ASN cc_start: 0.6894 (t0) cc_final: 0.6410 (t0) REVERT: B 541 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7238 (mm) REVERT: B 583 GLU cc_start: 0.6199 (tm-30) cc_final: 0.5779 (tm-30) REVERT: B 589 GLU cc_start: 0.6606 (pm20) cc_final: 0.6255 (pm20) outliers start: 29 outliers final: 17 residues processed: 281 average time/residue: 0.2731 time to fit residues: 101.0996 Evaluate side-chains 273 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 181 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 211 ILE 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 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 184 THR Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 402 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 92 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 719 HIS B 412 GLN B 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9746 Z= 0.184 Angle : 0.552 8.727 13252 Z= 0.281 Chirality : 0.043 0.139 1448 Planarity : 0.004 0.036 1675 Dihedral : 7.963 88.535 1413 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.39 % Allowed : 12.51 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1138 helix: 0.96 (0.27), residues: 366 sheet: -1.02 (0.46), residues: 128 loop : -0.34 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 396 HIS 0.004 0.001 HIS A 241 PHE 0.036 0.001 PHE A 577 TYR 0.023 0.002 TYR A 319 ARG 0.006 0.000 ARG B 383 *********************** 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 288 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7335 (mmtt) cc_final: 0.6988 (mmtt) REVERT: A 142 ARG cc_start: 0.8422 (ptt90) cc_final: 0.8134 (ptt90) REVERT: A 181 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8376 (mm) REVERT: A 210 ASP cc_start: 0.7860 (t0) cc_final: 0.7360 (t70) REVERT: A 223 THR cc_start: 0.8182 (p) cc_final: 0.7967 (t) REVERT: A 256 ILE cc_start: 0.8299 (tp) cc_final: 0.8079 (tp) REVERT: A 267 LYS cc_start: 0.7026 (tttm) cc_final: 0.6733 (tttp) REVERT: A 346 ARG cc_start: 0.6234 (ttm170) cc_final: 0.5873 (mmt90) REVERT: A 436 LYS cc_start: 0.8449 (mmmm) cc_final: 0.7991 (mmtm) REVERT: A 464 ASP cc_start: 0.6676 (m-30) cc_final: 0.6424 (m-30) REVERT: A 546 MET cc_start: 0.4825 (ppp) cc_final: 0.4183 (ppp) REVERT: A 603 LYS cc_start: 0.7629 (ttpt) cc_final: 0.7340 (ttpt) REVERT: A 645 MET cc_start: 0.6937 (tpp) cc_final: 0.6596 (tpp) REVERT: A 706 ASN cc_start: 0.7752 (m-40) cc_final: 0.7388 (m-40) REVERT: A 715 MET cc_start: 0.6767 (tpp) cc_final: 0.5974 (tpp) REVERT: B 131 ASN cc_start: 0.7907 (t0) cc_final: 0.7317 (t0) REVERT: B 135 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6702 (mpp) REVERT: B 182 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.7995 (mtp85) REVERT: B 275 LYS cc_start: 0.8533 (tmtt) cc_final: 0.8069 (tmtt) REVERT: B 310 GLN cc_start: 0.7605 (mp10) cc_final: 0.7101 (mp10) REVERT: B 344 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.7052 (mm) REVERT: B 370 MET cc_start: 0.7522 (tpt) cc_final: 0.7265 (tpp) REVERT: B 372 ASP cc_start: 0.7523 (t0) cc_final: 0.7013 (t0) REVERT: B 386 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6997 (mt-10) REVERT: B 428 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6909 (tm-30) REVERT: B 516 GLU cc_start: 0.6655 (mp0) cc_final: 0.6443 (mp0) REVERT: B 517 ASN cc_start: 0.6886 (t0) cc_final: 0.6374 (t0) REVERT: B 541 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7236 (mm) REVERT: B 583 GLU cc_start: 0.6187 (tm-30) cc_final: 0.5516 (tm-30) REVERT: B 589 GLU cc_start: 0.6576 (pm20) cc_final: 0.6236 (pm20) REVERT: B 693 GLU cc_start: 0.7448 (mp0) cc_final: 0.7104 (mp0) outliers start: 35 outliers final: 24 residues processed: 274 average time/residue: 0.2695 time to fit residues: 98.2906 Evaluate side-chains 273 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 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 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 618 MET 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 466 VAL 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 63 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 56 optimal weight: 0.3980 chunk 99 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN B 162 GLN B 412 GLN B 430 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9746 Z= 0.194 Angle : 0.560 8.573 13252 Z= 0.284 Chirality : 0.044 0.181 1448 Planarity : 0.004 0.036 1675 Dihedral : 7.659 88.762 1413 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.98 % Allowed : 13.19 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1138 helix: 0.93 (0.27), residues: 366 sheet: -1.03 (0.46), residues: 128 loop : -0.38 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 374 HIS 0.004 0.001 HIS A 631 PHE 0.037 0.002 PHE A 577 TYR 0.023 0.002 TYR A 319 ARG 0.006 0.000 ARG B 383 *********************** 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 294 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7373 (mmtt) cc_final: 0.7022 (mmtt) REVERT: A 142 ARG cc_start: 0.8425 (ptt90) cc_final: 0.8052 (ptt90) REVERT: A 181 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8400 (mm) REVERT: A 210 ASP cc_start: 0.8003 (t0) cc_final: 0.7446 (t70) REVERT: A 256 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8084 (tp) REVERT: A 267 LYS cc_start: 0.7016 (tttm) cc_final: 0.6816 (tttp) REVERT: A 346 ARG cc_start: 0.6217 (ttm170) cc_final: 0.5872 (mmt90) REVERT: A 433 ARG cc_start: 0.8040 (ttp-170) cc_final: 0.7576 (ttm170) REVERT: A 436 LYS cc_start: 0.8426 (mmmm) cc_final: 0.7998 (mmtm) REVERT: A 464 ASP cc_start: 0.6675 (m-30) cc_final: 0.6447 (m-30) REVERT: A 546 MET cc_start: 0.4875 (ppp) cc_final: 0.4158 (ppp) REVERT: A 603 LYS cc_start: 0.7634 (ttpt) cc_final: 0.7326 (ttpt) REVERT: A 645 MET cc_start: 0.6914 (tpp) cc_final: 0.6572 (tpp) REVERT: A 705 MET cc_start: 0.7968 (mtp) cc_final: 0.7753 (mtp) REVERT: A 706 ASN cc_start: 0.7762 (m-40) cc_final: 0.7405 (m-40) REVERT: B 106 VAL cc_start: 0.8310 (m) cc_final: 0.8109 (t) REVERT: B 131 ASN cc_start: 0.7897 (t0) cc_final: 0.7312 (t0) REVERT: B 135 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6673 (mpp) REVERT: B 182 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.8005 (mtp85) REVERT: B 275 LYS cc_start: 0.8537 (tmtt) cc_final: 0.8073 (tmtt) REVERT: B 310 GLN cc_start: 0.7627 (mp10) cc_final: 0.7111 (mp10) REVERT: B 344 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7133 (mm) REVERT: B 370 MET cc_start: 0.7540 (tpt) cc_final: 0.7277 (tpp) REVERT: B 372 ASP cc_start: 0.7524 (t0) cc_final: 0.6995 (t0) REVERT: B 386 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6991 (mt-10) REVERT: B 516 GLU cc_start: 0.6662 (mp0) cc_final: 0.6448 (mp0) REVERT: B 517 ASN cc_start: 0.6920 (t0) cc_final: 0.6378 (t0) REVERT: B 541 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7204 (mm) REVERT: B 583 GLU cc_start: 0.6167 (tm-30) cc_final: 0.5543 (tm-30) REVERT: B 589 GLU cc_start: 0.6586 (pm20) cc_final: 0.6225 (pm20) REVERT: B 693 GLU cc_start: 0.7454 (mp0) cc_final: 0.7096 (mp0) outliers start: 41 outliers final: 31 residues processed: 276 average time/residue: 0.2583 time to fit residues: 94.9020 Evaluate side-chains 286 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 256 ILE 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 589 ILE Chi-restraints excluded: chain A residue 618 MET 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 281 LEU Chi-restraints excluded: chain B residue 282 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 466 VAL 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 100 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.0770 chunk 111 optimal weight: 6.9990 chunk 92 optimal weight: 0.0030 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 overall best weight: 0.3348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 GLN B 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9746 Z= 0.158 Angle : 0.546 8.302 13252 Z= 0.277 Chirality : 0.043 0.172 1448 Planarity : 0.004 0.043 1675 Dihedral : 7.275 88.767 1413 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.88 % Allowed : 13.97 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1138 helix: 0.95 (0.27), residues: 367 sheet: -1.02 (0.46), residues: 129 loop : -0.38 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 396 HIS 0.004 0.001 HIS B 88 PHE 0.033 0.001 PHE A 577 TYR 0.025 0.001 TYR B 582 ARG 0.007 0.000 ARG B 383 *********************** 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 296 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 256 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7350 (mmtt) cc_final: 0.7020 (mmtt) REVERT: A 142 ARG cc_start: 0.8414 (ptt90) cc_final: 0.8135 (ptt90) REVERT: A 181 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8389 (mm) REVERT: A 210 ASP cc_start: 0.8021 (t0) cc_final: 0.7610 (t70) REVERT: A 223 THR cc_start: 0.8486 (t) cc_final: 0.8255 (t) REVERT: A 394 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7327 (mtt-85) REVERT: A 436 LYS cc_start: 0.8385 (mmmm) cc_final: 0.7922 (mmtt) REVERT: A 464 ASP cc_start: 0.6651 (m-30) cc_final: 0.6439 (m-30) REVERT: A 546 MET cc_start: 0.4874 (ppp) cc_final: 0.4148 (ppp) REVERT: A 600 ASP cc_start: 0.6752 (t0) cc_final: 0.6405 (t0) REVERT: A 603 LYS cc_start: 0.7649 (ttpt) cc_final: 0.7272 (ttpt) REVERT: A 645 MET cc_start: 0.6892 (tpp) cc_final: 0.6593 (tpp) REVERT: A 706 ASN cc_start: 0.7739 (m-40) cc_final: 0.7364 (m-40) REVERT: B 106 VAL cc_start: 0.8323 (m) cc_final: 0.8118 (t) REVERT: B 131 ASN cc_start: 0.7887 (t0) cc_final: 0.6597 (t0) REVERT: B 135 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6327 (mpp) REVERT: B 182 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.8005 (mtp85) REVERT: B 275 LYS cc_start: 0.8530 (tmtt) cc_final: 0.8087 (tmtt) REVERT: B 310 GLN cc_start: 0.7603 (mp10) cc_final: 0.7077 (mp10) REVERT: B 344 ILE cc_start: 0.7293 (OUTLIER) cc_final: 0.7063 (mm) REVERT: B 370 MET cc_start: 0.7533 (tpt) cc_final: 0.7216 (tpp) REVERT: B 372 ASP cc_start: 0.7531 (t0) cc_final: 0.6986 (t0) REVERT: B 517 ASN cc_start: 0.6766 (t0) cc_final: 0.6293 (t0) REVERT: B 541 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7151 (mm) REVERT: B 589 GLU cc_start: 0.6583 (pm20) cc_final: 0.6209 (pm20) REVERT: B 693 GLU cc_start: 0.7415 (mp0) cc_final: 0.7114 (mp0) outliers start: 40 outliers final: 29 residues processed: 277 average time/residue: 0.2616 time to fit residues: 96.2490 Evaluate side-chains 281 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 248 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 160 THR Chi-restraints excluded: chain A residue 181 LEU 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 474 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 721 GLN 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 281 LEU Chi-restraints excluded: chain B residue 282 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 466 VAL 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 12 optimal weight: 8.9990 chunk 63 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 68 optimal weight: 0.3980 chunk 44 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9746 Z= 0.188 Angle : 0.564 9.017 13252 Z= 0.285 Chirality : 0.043 0.166 1448 Planarity : 0.004 0.041 1675 Dihedral : 7.134 89.994 1413 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.49 % Allowed : 15.42 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1138 helix: 0.90 (0.27), residues: 367 sheet: -0.98 (0.46), residues: 127 loop : -0.37 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 396 HIS 0.004 0.001 HIS A 397 PHE 0.027 0.001 PHE A 577 TYR 0.024 0.002 TYR A 629 ARG 0.007 0.001 ARG B 383 *********************** 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 294 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8217 (m-80) cc_final: 0.7789 (m-80) REVERT: A 115 LYS cc_start: 0.7366 (mmtt) cc_final: 0.7019 (mmtt) REVERT: A 142 ARG cc_start: 0.8415 (ptt90) cc_final: 0.8129 (ptt90) REVERT: A 147 ASP cc_start: 0.7369 (t0) cc_final: 0.7129 (t70) REVERT: A 181 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8395 (mm) REVERT: A 223 THR cc_start: 0.8524 (t) cc_final: 0.8132 (t) REVERT: A 256 ILE cc_start: 0.8309 (tp) cc_final: 0.8075 (tp) REVERT: A 346 ARG cc_start: 0.6178 (ttm170) cc_final: 0.5856 (mmt-90) REVERT: A 365 GLU cc_start: 0.6613 (tp30) cc_final: 0.6259 (tp30) REVERT: A 394 ARG cc_start: 0.7883 (mtm-85) cc_final: 0.7349 (mtt-85) REVERT: A 436 LYS cc_start: 0.8394 (mmmm) cc_final: 0.7951 (mmtt) REVERT: A 464 ASP cc_start: 0.6676 (m-30) cc_final: 0.6469 (m-30) REVERT: A 600 ASP cc_start: 0.6755 (t0) cc_final: 0.6398 (t0) REVERT: A 603 LYS cc_start: 0.7653 (ttpt) cc_final: 0.7260 (ttpt) REVERT: A 645 MET cc_start: 0.6898 (tpp) cc_final: 0.6620 (tpp) REVERT: A 705 MET cc_start: 0.7937 (mtp) cc_final: 0.7705 (mtp) REVERT: A 706 ASN cc_start: 0.7758 (m-40) cc_final: 0.7374 (m-40) REVERT: B 131 ASN cc_start: 0.7894 (t0) cc_final: 0.7307 (t0) REVERT: B 135 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6684 (mpp) REVERT: B 182 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.7987 (mtp85) REVERT: B 275 LYS cc_start: 0.8530 (tmtt) cc_final: 0.8099 (tmtt) REVERT: B 310 GLN cc_start: 0.7659 (mp10) cc_final: 0.7092 (mp10) REVERT: B 344 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.7111 (mm) REVERT: B 359 LYS cc_start: 0.7986 (mppt) cc_final: 0.7643 (mppt) REVERT: B 370 MET cc_start: 0.7534 (tpt) cc_final: 0.7285 (tpp) REVERT: B 372 ASP cc_start: 0.7529 (t0) cc_final: 0.7004 (t0) REVERT: B 516 GLU cc_start: 0.6673 (mp0) cc_final: 0.6457 (mp0) REVERT: B 517 ASN cc_start: 0.6779 (t0) cc_final: 0.6368 (t0) REVERT: B 541 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7151 (mm) REVERT: B 589 GLU cc_start: 0.6576 (pm20) cc_final: 0.6206 (pm20) outliers start: 36 outliers final: 29 residues processed: 278 average time/residue: 0.2703 time to fit residues: 101.0271 Evaluate side-chains 286 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 253 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 474 LEU Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 721 GLN 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 281 LEU Chi-restraints excluded: chain B residue 282 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 466 VAL Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 329 HIS A 397 HIS A 431 GLN ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 452 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9746 Z= 0.306 Angle : 0.606 7.943 13252 Z= 0.308 Chirality : 0.045 0.172 1448 Planarity : 0.005 0.040 1675 Dihedral : 7.268 88.368 1413 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.98 % Allowed : 15.52 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1138 helix: 0.70 (0.27), residues: 366 sheet: -0.96 (0.47), residues: 126 loop : -0.38 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 374 HIS 0.005 0.001 HIS A 448 PHE 0.029 0.002 PHE A 577 TYR 0.022 0.002 TYR A 319 ARG 0.009 0.001 ARG A 243 *********************** 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 291 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.8284 (m-80) cc_final: 0.7863 (m-80) REVERT: A 115 LYS cc_start: 0.7412 (mmtt) cc_final: 0.7052 (mmtt) REVERT: A 131 TYR cc_start: 0.7290 (t80) cc_final: 0.7037 (t80) REVERT: A 142 ARG cc_start: 0.8459 (ptt90) cc_final: 0.8026 (ptt90) REVERT: A 147 ASP cc_start: 0.7440 (t0) cc_final: 0.7129 (t0) REVERT: A 181 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8379 (mm) REVERT: A 202 ASP cc_start: 0.6694 (t0) cc_final: 0.6478 (m-30) REVERT: A 256 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8054 (tp) REVERT: A 291 ASP cc_start: 0.6393 (p0) cc_final: 0.6155 (p0) REVERT: A 365 GLU cc_start: 0.6666 (tp30) cc_final: 0.6417 (tp30) REVERT: A 394 ARG cc_start: 0.7937 (mtm-85) cc_final: 0.7397 (mtt-85) REVERT: A 436 LYS cc_start: 0.8396 (mmmm) cc_final: 0.8131 (mmtt) REVERT: A 464 ASP cc_start: 0.6727 (m-30) cc_final: 0.6508 (m-30) REVERT: A 600 ASP cc_start: 0.6766 (t0) cc_final: 0.6368 (t0) REVERT: A 603 LYS cc_start: 0.7672 (ttpt) cc_final: 0.7311 (ttpt) REVERT: A 615 ASP cc_start: 0.7302 (m-30) cc_final: 0.6783 (t0) REVERT: A 645 MET cc_start: 0.6924 (tpp) cc_final: 0.6640 (tpp) REVERT: A 705 MET cc_start: 0.7966 (mtp) cc_final: 0.7745 (mtp) REVERT: A 706 ASN cc_start: 0.7798 (m-40) cc_final: 0.7427 (m-40) REVERT: B 131 ASN cc_start: 0.7987 (t0) cc_final: 0.7502 (t0) REVERT: B 135 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6777 (mpp) REVERT: B 212 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7940 (mt) REVERT: B 275 LYS cc_start: 0.8546 (tmtt) cc_final: 0.8105 (tmtt) REVERT: B 310 GLN cc_start: 0.7742 (mp10) cc_final: 0.7218 (mp10) REVERT: B 344 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7257 (mm) REVERT: B 359 LYS cc_start: 0.8005 (mppt) cc_final: 0.7658 (mppt) REVERT: B 370 MET cc_start: 0.7533 (tpt) cc_final: 0.7260 (tpp) REVERT: B 372 ASP cc_start: 0.7568 (t0) cc_final: 0.7013 (t0) REVERT: B 516 GLU cc_start: 0.6704 (mp0) cc_final: 0.6470 (mp0) REVERT: B 541 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7157 (mm) REVERT: B 589 GLU cc_start: 0.6603 (pm20) cc_final: 0.6245 (pm20) outliers start: 41 outliers final: 32 residues processed: 275 average time/residue: 0.2510 time to fit residues: 92.4091 Evaluate side-chains 284 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 246 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 160 THR 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 236 LEU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 256 ILE 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 618 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 721 GLN 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 217 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 282 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 466 VAL 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 103 optimal weight: 0.4980 chunk 106 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9746 Z= 0.193 Angle : 0.584 9.200 13252 Z= 0.295 Chirality : 0.044 0.172 1448 Planarity : 0.004 0.041 1675 Dihedral : 7.080 87.678 1413 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.39 % Allowed : 16.39 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1138 helix: 0.83 (0.27), residues: 366 sheet: -0.88 (0.47), residues: 129 loop : -0.35 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 711 HIS 0.004 0.001 HIS A 397 PHE 0.026 0.001 PHE A 480 TYR 0.032 0.002 TYR B 582 ARG 0.008 0.001 ARG B 383 *********************** 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 289 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7382 (mmtt) cc_final: 0.7004 (mmtt) REVERT: A 142 ARG cc_start: 0.8439 (ptt90) cc_final: 0.8063 (ptt90) REVERT: A 147 ASP cc_start: 0.7402 (t0) cc_final: 0.7113 (t0) REVERT: A 181 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8405 (mm) REVERT: A 291 ASP cc_start: 0.6382 (p0) cc_final: 0.6150 (p0) REVERT: A 365 GLU cc_start: 0.6640 (tp30) cc_final: 0.6393 (tp30) REVERT: A 394 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7375 (mtt-85) REVERT: A 428 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6628 (mm-30) REVERT: A 436 LYS cc_start: 0.8337 (mmmm) cc_final: 0.7974 (mmtt) REVERT: A 439 SER cc_start: 0.7943 (p) cc_final: 0.7563 (m) REVERT: A 464 ASP cc_start: 0.6698 (m-30) cc_final: 0.6482 (m-30) REVERT: A 600 ASP cc_start: 0.6747 (t0) cc_final: 0.6358 (t0) REVERT: A 603 LYS cc_start: 0.7674 (ttpt) cc_final: 0.7312 (ttpt) REVERT: A 645 MET cc_start: 0.6892 (tpp) cc_final: 0.6612 (tpp) REVERT: A 706 ASN cc_start: 0.7766 (m-40) cc_final: 0.7395 (m-40) REVERT: B 131 ASN cc_start: 0.7989 (t0) cc_final: 0.7426 (t0) REVERT: B 135 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6739 (mpp) REVERT: B 275 LYS cc_start: 0.8537 (tmtt) cc_final: 0.8096 (tmtt) REVERT: B 310 GLN cc_start: 0.7676 (mp10) cc_final: 0.7116 (mp10) REVERT: B 344 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7216 (mm) REVERT: B 359 LYS cc_start: 0.7997 (mppt) cc_final: 0.7624 (mppt) REVERT: B 372 ASP cc_start: 0.7549 (t0) cc_final: 0.7003 (t0) REVERT: B 386 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6848 (mm-30) REVERT: B 516 GLU cc_start: 0.6688 (mp0) cc_final: 0.6466 (mp0) REVERT: B 541 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7127 (mm) REVERT: B 589 GLU cc_start: 0.6578 (pm20) cc_final: 0.6214 (pm20) REVERT: B 612 MET cc_start: 0.7121 (tpt) cc_final: 0.6496 (tpp) outliers start: 35 outliers final: 28 residues processed: 277 average time/residue: 0.2678 time to fit residues: 98.4691 Evaluate side-chains 281 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 618 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 721 GLN 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 281 LEU 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 466 VAL Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.0670 chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 105 optimal weight: 0.0570 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- 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 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9746 Z= 0.179 Angle : 0.586 8.343 13252 Z= 0.296 Chirality : 0.044 0.165 1448 Planarity : 0.004 0.051 1675 Dihedral : 6.922 87.598 1413 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.20 % Allowed : 16.59 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.25), residues: 1138 helix: 0.83 (0.27), residues: 366 sheet: -0.90 (0.45), residues: 139 loop : -0.30 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 711 HIS 0.003 0.001 HIS A 241 PHE 0.027 0.001 PHE A 480 TYR 0.036 0.002 TYR B 582 ARG 0.009 0.001 ARG B 383 ********************** 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 283 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7375 (mmtt) cc_final: 0.7009 (mmtt) REVERT: A 142 ARG cc_start: 0.8430 (ptt90) cc_final: 0.8067 (ptt90) REVERT: A 147 ASP cc_start: 0.7391 (t0) cc_final: 0.7103 (t0) REVERT: A 181 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8412 (mm) REVERT: A 428 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6544 (mm-30) REVERT: A 436 LYS cc_start: 0.8319 (mmmm) cc_final: 0.7955 (mmtt) REVERT: A 439 SER cc_start: 0.7940 (p) cc_final: 0.7537 (m) REVERT: A 464 ASP cc_start: 0.6682 (m-30) cc_final: 0.6474 (m-30) REVERT: A 595 ARG cc_start: 0.7335 (mmt-90) cc_final: 0.7017 (mmt-90) REVERT: A 600 ASP cc_start: 0.6723 (t0) cc_final: 0.6347 (t0) REVERT: A 603 LYS cc_start: 0.7684 (ttpt) cc_final: 0.7304 (ttpt) REVERT: A 645 MET cc_start: 0.6884 (tpp) cc_final: 0.6599 (tpp) REVERT: A 706 ASN cc_start: 0.7756 (m-40) cc_final: 0.7371 (m-40) REVERT: B 83 LEU cc_start: 0.7853 (tp) cc_final: 0.7645 (tt) REVERT: B 131 ASN cc_start: 0.7997 (t0) cc_final: 0.7417 (t0) REVERT: B 135 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6709 (mpp) REVERT: B 275 LYS cc_start: 0.8536 (tmtt) cc_final: 0.8089 (tmtt) REVERT: B 310 GLN cc_start: 0.7650 (mp10) cc_final: 0.7092 (mp10) REVERT: B 344 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7188 (mm) REVERT: B 359 LYS cc_start: 0.7994 (mppt) cc_final: 0.7624 (mppt) REVERT: B 372 ASP cc_start: 0.7573 (t0) cc_final: 0.7004 (t0) REVERT: B 386 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6823 (mm-30) REVERT: B 516 GLU cc_start: 0.6691 (mp0) cc_final: 0.6463 (mp0) REVERT: B 541 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.7125 (mm) REVERT: B 589 GLU cc_start: 0.6569 (pm20) cc_final: 0.6219 (pm20) REVERT: B 672 GLU cc_start: 0.6435 (tp30) cc_final: 0.6056 (tm-30) REVERT: B 673 ARG cc_start: 0.6353 (mtp-110) cc_final: 0.6020 (ttp80) outliers start: 33 outliers final: 28 residues processed: 271 average time/residue: 0.2548 time to fit residues: 92.8972 Evaluate side-chains 278 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 618 MET Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 721 GLN 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 281 LEU 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 466 VAL Chi-restraints excluded: chain B residue 541 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 chunk 38 optimal weight: 0.2980 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 412 GLN ** 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 = 0.3970 r_free = 0.3970 target = 0.151614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130676 restraints weight = 14226.648| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.57 r_work: 0.3530 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9746 Z= 0.170 Angle : 0.585 9.574 13252 Z= 0.296 Chirality : 0.043 0.158 1448 Planarity : 0.004 0.041 1675 Dihedral : 6.804 88.442 1413 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.49 % Allowed : 16.59 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1138 helix: 0.95 (0.27), residues: 359 sheet: -0.90 (0.46), residues: 139 loop : -0.29 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 711 HIS 0.003 0.001 HIS A 241 PHE 0.029 0.001 PHE A 480 TYR 0.029 0.002 TYR B 582 ARG 0.009 0.001 ARG B 383 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2668.47 seconds wall clock time: 49 minutes 32.39 seconds (2972.39 seconds total)