Starting phenix.real_space_refine on Fri Feb 14 12:54:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ui6_26540/02_2025/7ui6_26540.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ui6_26540/02_2025/7ui6_26540.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ui6_26540/02_2025/7ui6_26540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ui6_26540/02_2025/7ui6_26540.map" model { file = "/net/cci-nas-00/data/ceres_data/7ui6_26540/02_2025/7ui6_26540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ui6_26540/02_2025/7ui6_26540.cif" } resolution = 3.7 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= 0.029 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: 5 Type Number sf(0) Gaussians Mn 4 7.51 5 S 52 5.16 5 C 6568 2.51 5 N 1736 2.21 5 O 1788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10148 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 5072 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 23, 'TRANS': 585} Chain breaks: 1 Chain: "B" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 5072 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 23, 'TRANS': 585} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.29, per 1000 atoms: 0.62 Number of scatterers: 10148 At special positions: 0 Unit cell: (106.6, 113.012, 113.012, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 4 24.99 S 52 16.00 O 1788 8.00 N 1736 7.00 C 6568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 726 " distance=2.03 Simple disulfide: pdb=" SG CYS B 354 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 443 " - pdb=" SG CYS B 726 " 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 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 8 sheets defined 48.4% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 145 through 163 removed outlier: 4.064A pdb=" N ALA A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N HIS A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.660A pdb=" N THR A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.606A pdb=" N LYS A 224 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 250 through 256 removed outlier: 4.162A pdb=" N LEU A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.020A pdb=" N LYS A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.635A pdb=" N MET A 315 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.712A pdb=" N ASN A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.994A pdb=" N CYS A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 393 through 406 removed outlier: 3.822A pdb=" N PHE A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 427 through 435 Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.695A pdb=" N PHE A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 452 " --> pdb=" O ARG A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 487 through 495 Processing helix chain 'A' and resid 506 through 520 Processing helix chain 'A' and resid 520 through 526 removed outlier: 3.962A pdb=" N MET A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.880A pdb=" N HIS A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 584 Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.524A pdb=" N GLY A 633 " --> pdb=" O TRP A 630 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A 634 " --> pdb=" O THR A 631 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA A 635 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Proline residue: A 636 - end of helix No H-bonds generated for 'chain 'A' and resid 630 through 637' Processing helix chain 'A' and resid 638 through 644 removed outlier: 3.606A pdb=" N TRP A 642 " --> pdb=" O ASN A 638 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 691 removed outlier: 3.620A pdb=" N GLN A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 718 removed outlier: 3.613A pdb=" N THR A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 743 removed outlier: 4.090A pdb=" N ARG A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 756 removed outlier: 3.702A pdb=" N LEU A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 163 removed outlier: 4.015A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N HIS B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 190 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.544A pdb=" N VAL B 208 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 250 through 257 removed outlier: 4.137A pdb=" N LEU B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 303 through 310 Processing helix chain 'B' and resid 311 through 323 removed outlier: 4.024A pdb=" N MET B 315 " --> pdb=" O LYS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.609A pdb=" N ASN B 339 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.556A pdb=" N ASN B 357 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.644A pdb=" N TYR B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.940A pdb=" N VAL B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 406 removed outlier: 3.664A pdb=" N PHE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 427 through 437 removed outlier: 3.770A pdb=" N GLU B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 451 removed outlier: 4.055A pdb=" N PHE B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 485 removed outlier: 3.695A pdb=" N ARG B 484 " --> pdb=" O SER B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 495 removed outlier: 4.431A pdb=" N ALA B 490 " --> pdb=" O GLN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 520 Processing helix chain 'B' and resid 520 through 526 removed outlier: 3.538A pdb=" N ARG B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 553 removed outlier: 3.829A pdb=" N HIS B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 584 removed outlier: 3.620A pdb=" N TYR B 575 " --> pdb=" O GLY B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 619 Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.636A pdb=" N HIS B 634 " --> pdb=" O THR B 631 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA B 635 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Proline residue: B 636 - end of helix Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.922A pdb=" N TRP B 642 " --> pdb=" O ASN B 638 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 643' Processing helix chain 'B' and resid 680 through 691 removed outlier: 4.038A pdb=" N HIS B 684 " --> pdb=" O ASN B 680 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 720 removed outlier: 3.970A pdb=" N THR B 715 " --> pdb=" O SER B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 743 removed outlier: 3.545A pdb=" N ARG B 724 " --> pdb=" O ASN B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 756 removed outlier: 3.676A pdb=" N LEU B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS B 748 " --> pdb=" O PHE B 744 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TYR B 749 " --> pdb=" O ALA B 745 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 200 removed outlier: 6.656A pdb=" N LEU A 168 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASP A 197 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 170 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N TYR A 199 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 172 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N HIS A 139 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU A 241 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA A 141 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL A 270 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLY A 298 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N GLY A 268 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N LEU A 267 " --> pdb=" O TYR A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 247 removed outlier: 3.783A pdb=" N ILE A 379 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 456 through 457 removed outlier: 3.528A pdb=" N ILE A 533 " --> pdb=" O HIS A 457 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE A 499 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N HIS A 532 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 501 " --> pdb=" O HIS A 532 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 534 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 503 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N SER A 500 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU A 476 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ALA A 502 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA A 478 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N THR A 475 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 661 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ARG A 664 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N LYS A 590 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE A 695 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 651 " --> pdb=" O PHE A 695 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR A 649 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 597 through 599 Processing sheet with id=AA5, first strand: chain 'B' and resid 194 through 200 removed outlier: 6.674A pdb=" N HIS B 139 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU B 241 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA B 141 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL B 299 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N VAL B 270 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 352 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU B 269 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 246 through 247 removed outlier: 3.617A pdb=" N HIS B 380 " --> pdb=" O VAL B 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 456 through 457 removed outlier: 3.555A pdb=" N ILE B 533 " --> pdb=" O HIS B 457 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 474 through 477 removed outlier: 6.093A pdb=" N THR B 475 " --> pdb=" O PHE B 560 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 661 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TYR B 660 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ARG B 664 " --> pdb=" O LYS B 590 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N LYS B 590 " --> pdb=" O ARG B 664 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA B 591 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE B 695 " --> pdb=" O VAL B 651 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 978 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: 3.09 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1782 1.32 - 1.45: 2884 1.45 - 1.57: 5666 1.57 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 10422 Sorted by residual: bond pdb=" CA SER B 500 " pdb=" CB SER B 500 " ideal model delta sigma weight residual 1.534 1.461 0.073 1.77e-02 3.19e+03 1.72e+01 bond pdb=" N ALA B 701 " pdb=" CA ALA B 701 " ideal model delta sigma weight residual 1.454 1.500 -0.045 1.16e-02 7.43e+03 1.53e+01 bond pdb=" N GLU B 598 " pdb=" CA GLU B 598 " ideal model delta sigma weight residual 1.455 1.500 -0.044 1.18e-02 7.18e+03 1.41e+01 bond pdb=" C ALA B 502 " pdb=" N LEU B 503 " ideal model delta sigma weight residual 1.331 1.285 0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" N THR B 599 " pdb=" CA THR B 599 " ideal model delta sigma weight residual 1.454 1.499 -0.045 1.29e-02 6.01e+03 1.24e+01 ... (remaining 10417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 13542 2.16 - 4.31: 476 4.31 - 6.47: 82 6.47 - 8.63: 22 8.63 - 10.79: 10 Bond angle restraints: 14132 Sorted by residual: angle pdb=" N ASP A 305 " pdb=" CA ASP A 305 " pdb=" C ASP A 305 " ideal model delta sigma weight residual 111.90 102.14 9.76 1.32e+00 5.74e-01 5.46e+01 angle pdb=" N PRO B 595 " pdb=" CA PRO B 595 " pdb=" C PRO B 595 " ideal model delta sigma weight residual 110.50 121.01 -10.51 1.57e+00 4.06e-01 4.48e+01 angle pdb=" C PHE B 186 " pdb=" N GLN B 187 " pdb=" CA GLN B 187 " ideal model delta sigma weight residual 120.38 112.92 7.46 1.46e+00 4.69e-01 2.61e+01 angle pdb=" C PHE B 566 " pdb=" N LEU B 567 " pdb=" CA LEU B 567 " ideal model delta sigma weight residual 122.37 117.67 4.70 9.30e-01 1.16e+00 2.55e+01 angle pdb=" C THR B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta sigma weight residual 120.63 114.31 6.32 1.36e+00 5.41e-01 2.16e+01 ... (remaining 14127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 5440 17.58 - 35.16: 589 35.16 - 52.74: 120 52.74 - 70.32: 28 70.32 - 87.90: 9 Dihedral angle restraints: 6186 sinusoidal: 2554 harmonic: 3632 Sorted by residual: dihedral pdb=" CB CYS B 443 " pdb=" SG CYS B 443 " pdb=" SG CYS B 726 " pdb=" CB CYS B 726 " ideal model delta sinusoidal sigma weight residual 93.00 163.18 -70.18 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CB CYS A 443 " pdb=" SG CYS A 443 " pdb=" SG CYS A 726 " pdb=" CB CYS A 726 " ideal model delta sinusoidal sigma weight residual 93.00 136.26 -43.26 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CB CYS A 354 " pdb=" SG CYS A 354 " pdb=" SG CYS A 369 " pdb=" CB CYS A 369 " ideal model delta sinusoidal sigma weight residual -86.00 -129.23 43.23 1 1.00e+01 1.00e-02 2.61e+01 ... (remaining 6183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1136 0.057 - 0.114: 288 0.114 - 0.170: 83 0.170 - 0.227: 13 0.227 - 0.284: 2 Chirality restraints: 1522 Sorted by residual: chirality pdb=" CA PHE B 597 " pdb=" N PHE B 597 " pdb=" C PHE B 597 " pdb=" CB PHE B 597 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CG LEU A 505 " pdb=" CB LEU A 505 " pdb=" CD1 LEU A 505 " pdb=" CD2 LEU A 505 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE B 300 " pdb=" N ILE B 300 " pdb=" C ILE B 300 " pdb=" CB ILE B 300 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1519 not shown) Planarity restraints: 1784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 345 " -0.080 5.00e-02 4.00e+02 1.21e-01 2.36e+01 pdb=" N PRO B 346 " 0.210 5.00e-02 4.00e+02 pdb=" CA PRO B 346 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 346 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 704 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C ILE B 704 " 0.073 2.00e-02 2.50e+03 pdb=" O ILE B 704 " -0.028 2.00e-02 2.50e+03 pdb=" N HIS B 705 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 302 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C LEU A 302 " 0.067 2.00e-02 2.50e+03 pdb=" O LEU A 302 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A 303 " -0.023 2.00e-02 2.50e+03 ... (remaining 1781 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 146 2.61 - 3.19: 9153 3.19 - 3.76: 15228 3.76 - 4.33: 21364 4.33 - 4.90: 34076 Nonbonded interactions: 79967 Sorted by model distance: nonbonded pdb=" N LYS B 608 " pdb=" OE2 GLU B 612 " model vdw 2.044 3.120 nonbonded pdb=" O LYS A 748 " pdb=" OG1 THR A 751 " model vdw 2.124 3.040 nonbonded pdb=" OD2 ASP B 244 " pdb="MN MN B 801 " model vdw 2.142 2.320 nonbonded pdb=" OD2 ASP A 671 " pdb=" NH1 ARG A 673 " model vdw 2.163 3.120 nonbonded pdb=" OD2 ASP A 244 " pdb="MN MN A 801 " model vdw 2.166 2.320 ... (remaining 79962 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.930 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10422 Z= 0.297 Angle : 0.971 10.787 14132 Z= 0.546 Chirality : 0.057 0.284 1522 Planarity : 0.007 0.121 1784 Dihedral : 14.981 87.902 3822 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.79 % Favored : 94.96 % Rotamer: Outliers : 1.09 % Allowed : 2.91 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.57 (0.23), residues: 1210 helix: -0.67 (0.24), residues: 424 sheet: -2.03 (0.39), residues: 154 loop : -0.93 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP B 679 HIS 0.011 0.002 HIS B 171 PHE 0.036 0.002 PHE A 734 TYR 0.038 0.002 TYR A 702 ARG 0.056 0.001 ARG A 673 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 290 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.6789 (m-30) cc_final: 0.6346 (m-30) REVERT: A 260 LYS cc_start: 0.9015 (mmtm) cc_final: 0.8693 (mmtm) REVERT: A 261 PHE cc_start: 0.6815 (m-80) cc_final: 0.6063 (m-80) REVERT: A 377 LYS cc_start: 0.7190 (mptt) cc_final: 0.6978 (mmtm) REVERT: A 397 PHE cc_start: 0.8386 (m-10) cc_final: 0.8094 (m-10) REVERT: A 428 GLU cc_start: 0.8156 (pm20) cc_final: 0.7796 (pm20) REVERT: A 432 LYS cc_start: 0.8413 (ptpp) cc_final: 0.8209 (ptpp) REVERT: A 493 LYS cc_start: 0.8170 (ptpt) cc_final: 0.7635 (ptpt) REVERT: A 515 ARG cc_start: 0.7506 (mpp80) cc_final: 0.7204 (mpp80) REVERT: A 619 MET cc_start: 0.7428 (tmm) cc_final: 0.6811 (tmm) REVERT: A 691 GLN cc_start: 0.8098 (mm110) cc_final: 0.7877 (mm110) REVERT: A 734 PHE cc_start: 0.7592 (t80) cc_final: 0.7359 (t80) REVERT: A 738 MET cc_start: 0.8041 (ttt) cc_final: 0.7706 (ttt) REVERT: B 179 GLU cc_start: 0.7666 (pt0) cc_final: 0.7187 (pt0) REVERT: B 223 MET cc_start: 0.7006 (tmm) cc_final: 0.6491 (tmm) REVERT: B 229 LYS cc_start: 0.8180 (tmtt) cc_final: 0.7613 (tmtt) REVERT: B 315 MET cc_start: 0.8460 (ptp) cc_final: 0.8085 (ptp) REVERT: B 407 TYR cc_start: 0.7309 (t80) cc_final: 0.6855 (t80) REVERT: B 482 MET cc_start: 0.5001 (tpt) cc_final: 0.4676 (tpt) REVERT: B 489 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7990 (mm-30) REVERT: B 512 GLN cc_start: 0.8456 (mt0) cc_final: 0.8198 (mt0) REVERT: B 515 ARG cc_start: 0.8430 (ptp-110) cc_final: 0.7940 (ttp-110) REVERT: B 531 TYR cc_start: 0.7846 (m-10) cc_final: 0.7479 (m-10) REVERT: B 547 ARG cc_start: 0.8077 (ptm160) cc_final: 0.7652 (ptm160) REVERT: B 559 MET cc_start: 0.5376 (ppp) cc_final: 0.4706 (ppp) REVERT: B 560 PHE cc_start: 0.6031 (t80) cc_final: 0.5761 (t80) REVERT: B 626 ARG cc_start: 0.6960 (tpp80) cc_final: 0.6579 (tpp80) REVERT: B 708 HIS cc_start: 0.5965 (t-90) cc_final: 0.5569 (t-90) outliers start: 12 outliers final: 5 residues processed: 297 average time/residue: 0.2859 time to fit residues: 111.9422 Evaluate side-chains 278 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 273 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 597 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.0870 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN A 532 HIS A 684 HIS B 285 HIS ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS B 532 HIS ** B 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.209424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.173546 restraints weight = 17808.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.179282 restraints weight = 10368.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.183504 restraints weight = 7015.544| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10422 Z= 0.199 Angle : 0.653 11.416 14132 Z= 0.334 Chirality : 0.044 0.200 1522 Planarity : 0.005 0.103 1784 Dihedral : 4.988 56.299 1365 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.37 % Allowed : 9.47 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.24), residues: 1210 helix: 0.13 (0.25), residues: 442 sheet: -1.66 (0.39), residues: 150 loop : -0.60 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 679 HIS 0.012 0.001 HIS A 163 PHE 0.019 0.002 PHE B 338 TYR 0.017 0.002 TYR A 370 ARG 0.008 0.001 ARG A 673 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 270 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.6869 (m-30) cc_final: 0.6325 (m-30) REVERT: A 260 LYS cc_start: 0.9067 (mmtm) cc_final: 0.8711 (mmtm) REVERT: A 261 PHE cc_start: 0.6868 (m-80) cc_final: 0.5926 (m-80) REVERT: A 397 PHE cc_start: 0.8324 (m-10) cc_final: 0.7932 (m-10) REVERT: A 428 GLU cc_start: 0.8247 (pm20) cc_final: 0.7754 (pm20) REVERT: A 432 LYS cc_start: 0.8669 (ptpp) cc_final: 0.7997 (ptpp) REVERT: A 449 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6397 (mm-30) REVERT: A 450 ARG cc_start: 0.7265 (tmm-80) cc_final: 0.7003 (tmm-80) REVERT: A 460 PHE cc_start: 0.7204 (t80) cc_final: 0.6842 (m-80) REVERT: A 472 THR cc_start: 0.6808 (p) cc_final: 0.6601 (t) REVERT: A 493 LYS cc_start: 0.8261 (ptpt) cc_final: 0.7775 (ptpt) REVERT: A 515 ARG cc_start: 0.7730 (mpp80) cc_final: 0.7335 (mpp80) REVERT: A 619 MET cc_start: 0.7701 (tmm) cc_final: 0.7193 (tmm) REVERT: A 652 GLU cc_start: 0.7904 (mp0) cc_final: 0.7687 (mp0) REVERT: A 669 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6807 (mt-10) REVERT: A 691 GLN cc_start: 0.8319 (mm110) cc_final: 0.8031 (mm110) REVERT: A 736 GLN cc_start: 0.8019 (mp10) cc_final: 0.7809 (mp10) REVERT: A 738 MET cc_start: 0.8194 (ttt) cc_final: 0.7919 (ttt) REVERT: B 179 GLU cc_start: 0.7521 (pt0) cc_final: 0.6943 (pt0) REVERT: B 223 MET cc_start: 0.6770 (tmm) cc_final: 0.6520 (tmm) REVERT: B 229 LYS cc_start: 0.8033 (tmtt) cc_final: 0.7448 (tmtt) REVERT: B 315 MET cc_start: 0.7964 (ptp) cc_final: 0.7762 (ptp) REVERT: B 349 VAL cc_start: 0.6588 (m) cc_final: 0.6095 (p) REVERT: B 407 TYR cc_start: 0.7108 (t80) cc_final: 0.6905 (t80) REVERT: B 489 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7796 (mm-30) REVERT: B 512 GLN cc_start: 0.8157 (mt0) cc_final: 0.7934 (mt0) REVERT: B 515 ARG cc_start: 0.8163 (ptp-110) cc_final: 0.7647 (ttp-110) REVERT: B 516 TYR cc_start: 0.8637 (t80) cc_final: 0.8434 (t80) REVERT: B 536 LYS cc_start: 0.7734 (ttmm) cc_final: 0.7454 (mttm) REVERT: B 547 ARG cc_start: 0.8028 (ptm160) cc_final: 0.7254 (ptm160) REVERT: B 559 MET cc_start: 0.5695 (ppp) cc_final: 0.5046 (ppp) REVERT: B 560 PHE cc_start: 0.6303 (t80) cc_final: 0.6034 (t80) REVERT: B 626 ARG cc_start: 0.6930 (tpp80) cc_final: 0.6478 (tpp80) REVERT: B 653 TRP cc_start: 0.7531 (t60) cc_final: 0.7038 (t60) REVERT: B 708 HIS cc_start: 0.6064 (t-90) cc_final: 0.5647 (t-90) outliers start: 15 outliers final: 9 residues processed: 277 average time/residue: 0.2904 time to fit residues: 105.6456 Evaluate side-chains 277 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 268 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 689 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 chunk 3 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.204329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.168283 restraints weight = 17782.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.174107 restraints weight = 10322.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.178141 restraints weight = 6958.482| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10422 Z= 0.229 Angle : 0.636 12.697 14132 Z= 0.323 Chirality : 0.044 0.207 1522 Planarity : 0.004 0.044 1784 Dihedral : 4.783 49.723 1360 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.09 % Allowed : 13.02 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1210 helix: 0.44 (0.25), residues: 436 sheet: -1.37 (0.40), residues: 144 loop : -0.62 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 316 HIS 0.008 0.001 HIS A 163 PHE 0.022 0.002 PHE A 657 TYR 0.025 0.002 TYR B 350 ARG 0.006 0.001 ARG B 626 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 273 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7072 (m-30) cc_final: 0.6543 (m-30) REVERT: A 260 LYS cc_start: 0.9159 (mmtm) cc_final: 0.8768 (mmtm) REVERT: A 261 PHE cc_start: 0.6970 (m-80) cc_final: 0.5993 (m-80) REVERT: A 397 PHE cc_start: 0.8413 (m-10) cc_final: 0.7957 (m-10) REVERT: A 428 GLU cc_start: 0.8199 (pm20) cc_final: 0.7588 (pm20) REVERT: A 431 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7749 (mm-40) REVERT: A 432 LYS cc_start: 0.8684 (ptpp) cc_final: 0.8040 (ptpp) REVERT: A 449 GLU cc_start: 0.6670 (mm-30) cc_final: 0.6358 (mm-30) REVERT: A 493 LYS cc_start: 0.8269 (ptpt) cc_final: 0.7819 (ptpt) REVERT: A 515 ARG cc_start: 0.7933 (mpp80) cc_final: 0.7396 (mpp80) REVERT: A 559 MET cc_start: 0.6886 (ppp) cc_final: 0.6435 (ppp) REVERT: A 617 LEU cc_start: 0.8452 (mp) cc_final: 0.8210 (mp) REVERT: A 619 MET cc_start: 0.7843 (tmm) cc_final: 0.7231 (tmm) REVERT: A 691 GLN cc_start: 0.8419 (mm110) cc_final: 0.8145 (mm110) REVERT: A 736 GLN cc_start: 0.8093 (mt0) cc_final: 0.7814 (mp10) REVERT: B 179 GLU cc_start: 0.7619 (pt0) cc_final: 0.7035 (pt0) REVERT: B 223 MET cc_start: 0.6861 (tmm) cc_final: 0.6234 (tmm) REVERT: B 229 LYS cc_start: 0.8302 (tmtt) cc_final: 0.7875 (tmtt) REVERT: B 245 ILE cc_start: 0.8233 (mm) cc_final: 0.7874 (mm) REVERT: B 349 VAL cc_start: 0.6692 (m) cc_final: 0.6176 (p) REVERT: B 407 TYR cc_start: 0.7210 (t80) cc_final: 0.6984 (t80) REVERT: B 489 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7854 (mm-30) REVERT: B 509 GLU cc_start: 0.7877 (mt-10) cc_final: 0.6822 (mt-10) REVERT: B 512 GLN cc_start: 0.8244 (mt0) cc_final: 0.7987 (mt0) REVERT: B 515 ARG cc_start: 0.8256 (ptp-110) cc_final: 0.7825 (ttm110) REVERT: B 536 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7692 (mmtp) REVERT: B 547 ARG cc_start: 0.8007 (ptm160) cc_final: 0.7419 (ptm160) REVERT: B 559 MET cc_start: 0.5566 (ppp) cc_final: 0.5255 (ppp) REVERT: B 626 ARG cc_start: 0.7116 (tpp80) cc_final: 0.6821 (tpp80) REVERT: B 653 TRP cc_start: 0.7588 (t60) cc_final: 0.6928 (t60) REVERT: B 708 HIS cc_start: 0.6278 (t-90) cc_final: 0.5823 (t-90) REVERT: B 740 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7288 (mtm-85) outliers start: 23 outliers final: 16 residues processed: 285 average time/residue: 0.2817 time to fit residues: 106.1509 Evaluate side-chains 281 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 265 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 738 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 8 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 HIS ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.207184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.168964 restraints weight = 17795.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.175149 restraints weight = 10228.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.179444 restraints weight = 6888.610| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10422 Z= 0.196 Angle : 0.621 12.018 14132 Z= 0.310 Chirality : 0.044 0.289 1522 Planarity : 0.004 0.044 1784 Dihedral : 4.599 42.312 1360 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.28 % Allowed : 15.39 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.24), residues: 1210 helix: 0.59 (0.25), residues: 436 sheet: -1.32 (0.40), residues: 140 loop : -0.58 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 316 HIS 0.008 0.001 HIS A 163 PHE 0.014 0.001 PHE A 355 TYR 0.019 0.001 TYR B 516 ARG 0.007 0.000 ARG B 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7063 (m-30) cc_final: 0.6580 (m-30) REVERT: A 260 LYS cc_start: 0.9185 (mmtm) cc_final: 0.8785 (mmtm) REVERT: A 261 PHE cc_start: 0.6999 (m-80) cc_final: 0.5989 (m-80) REVERT: A 397 PHE cc_start: 0.8395 (m-10) cc_final: 0.7923 (m-10) REVERT: A 428 GLU cc_start: 0.8277 (pm20) cc_final: 0.7613 (pm20) REVERT: A 432 LYS cc_start: 0.8708 (ptpp) cc_final: 0.8058 (ptpp) REVERT: A 449 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6455 (mm-30) REVERT: A 493 LYS cc_start: 0.8297 (ptpt) cc_final: 0.7871 (ptpt) REVERT: A 515 ARG cc_start: 0.7972 (mpp80) cc_final: 0.7379 (mpp80) REVERT: A 559 MET cc_start: 0.6914 (ppp) cc_final: 0.6429 (ppp) REVERT: A 560 PHE cc_start: 0.7040 (t80) cc_final: 0.6771 (t80) REVERT: A 617 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8272 (mp) REVERT: A 619 MET cc_start: 0.7857 (tmm) cc_final: 0.7250 (tmm) REVERT: A 658 GLU cc_start: 0.7829 (pt0) cc_final: 0.7366 (pt0) REVERT: A 691 GLN cc_start: 0.8355 (mm110) cc_final: 0.8102 (mm110) REVERT: A 735 GLN cc_start: 0.8729 (mt0) cc_final: 0.8266 (mt0) REVERT: B 179 GLU cc_start: 0.7555 (pt0) cc_final: 0.6995 (pt0) REVERT: B 223 MET cc_start: 0.6831 (tmm) cc_final: 0.6165 (tmm) REVERT: B 229 LYS cc_start: 0.8237 (tmtt) cc_final: 0.7813 (tmtt) REVERT: B 245 ILE cc_start: 0.8213 (mm) cc_final: 0.7903 (mm) REVERT: B 300 ILE cc_start: 0.7851 (mm) cc_final: 0.7609 (mm) REVERT: B 311 LYS cc_start: 0.8195 (tmmt) cc_final: 0.7792 (tmmt) REVERT: B 349 VAL cc_start: 0.6784 (m) cc_final: 0.6242 (p) REVERT: B 357 ASN cc_start: 0.7703 (p0) cc_final: 0.7384 (p0) REVERT: B 489 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7798 (mm-30) REVERT: B 509 GLU cc_start: 0.7788 (mt-10) cc_final: 0.6981 (mt-10) REVERT: B 512 GLN cc_start: 0.8140 (mt0) cc_final: 0.7872 (mt0) REVERT: B 515 ARG cc_start: 0.8241 (ptp-110) cc_final: 0.7811 (ttm110) REVERT: B 559 MET cc_start: 0.5517 (ppp) cc_final: 0.5315 (ppp) REVERT: B 568 PRO cc_start: 0.8542 (Cg_endo) cc_final: 0.7478 (Cg_exo) REVERT: B 653 TRP cc_start: 0.7626 (t60) cc_final: 0.6872 (t60) REVERT: B 708 HIS cc_start: 0.6283 (t-90) cc_final: 0.5853 (t-90) REVERT: B 740 ARG cc_start: 0.7641 (mtm-85) cc_final: 0.7245 (mtm-85) outliers start: 25 outliers final: 19 residues processed: 288 average time/residue: 0.2932 time to fit residues: 111.9718 Evaluate side-chains 284 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 264 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 738 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 7 optimal weight: 0.0570 chunk 32 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 HIS ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.208186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.170183 restraints weight = 17738.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.176353 restraints weight = 10175.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.180661 restraints weight = 6843.401| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10422 Z= 0.168 Angle : 0.603 12.648 14132 Z= 0.301 Chirality : 0.043 0.239 1522 Planarity : 0.004 0.058 1784 Dihedral : 4.410 40.766 1359 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.01 % Allowed : 15.66 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.24), residues: 1210 helix: 0.55 (0.25), residues: 440 sheet: -1.26 (0.40), residues: 140 loop : -0.51 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 316 HIS 0.009 0.001 HIS A 494 PHE 0.016 0.001 PHE A 355 TYR 0.031 0.001 TYR B 407 ARG 0.005 0.000 ARG A 398 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 260 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7099 (m-30) cc_final: 0.6607 (m-30) REVERT: A 261 PHE cc_start: 0.6989 (m-80) cc_final: 0.5894 (m-80) REVERT: A 356 TRP cc_start: 0.7769 (m100) cc_final: 0.7501 (m100) REVERT: A 397 PHE cc_start: 0.8385 (m-10) cc_final: 0.7898 (m-10) REVERT: A 428 GLU cc_start: 0.8257 (pm20) cc_final: 0.7580 (pm20) REVERT: A 432 LYS cc_start: 0.8698 (ptpp) cc_final: 0.8029 (ptpp) REVERT: A 449 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6438 (mm-30) REVERT: A 487 MET cc_start: 0.7336 (pmm) cc_final: 0.7113 (pmm) REVERT: A 493 LYS cc_start: 0.8279 (ptpt) cc_final: 0.7842 (ptpt) REVERT: A 515 ARG cc_start: 0.7991 (mpp80) cc_final: 0.7390 (mpp80) REVERT: A 559 MET cc_start: 0.6893 (ppp) cc_final: 0.6400 (ppp) REVERT: A 560 PHE cc_start: 0.6997 (t80) cc_final: 0.6705 (t80) REVERT: A 617 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8275 (mp) REVERT: A 619 MET cc_start: 0.7879 (tmm) cc_final: 0.7346 (tmm) REVERT: A 658 GLU cc_start: 0.7800 (pt0) cc_final: 0.7308 (pt0) REVERT: A 686 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6684 (mpp) REVERT: A 691 GLN cc_start: 0.8315 (mm110) cc_final: 0.8012 (mm110) REVERT: A 735 GLN cc_start: 0.8720 (mt0) cc_final: 0.8269 (mt0) REVERT: B 179 GLU cc_start: 0.7536 (pt0) cc_final: 0.6949 (pt0) REVERT: B 223 MET cc_start: 0.6833 (tmm) cc_final: 0.6085 (tmm) REVERT: B 229 LYS cc_start: 0.8237 (tmtt) cc_final: 0.7792 (tmtt) REVERT: B 245 ILE cc_start: 0.8184 (mm) cc_final: 0.7937 (mm) REVERT: B 315 MET cc_start: 0.7928 (ptp) cc_final: 0.7616 (ptp) REVERT: B 349 VAL cc_start: 0.6682 (m) cc_final: 0.6136 (p) REVERT: B 357 ASN cc_start: 0.7640 (p0) cc_final: 0.7291 (p0) REVERT: B 489 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7795 (mm-30) REVERT: B 509 GLU cc_start: 0.7753 (mt-10) cc_final: 0.6970 (mt-10) REVERT: B 547 ARG cc_start: 0.8111 (ptp-110) cc_final: 0.7723 (ptp-170) REVERT: B 559 MET cc_start: 0.5603 (ppp) cc_final: 0.5227 (ppp) REVERT: B 569 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7547 (mtm) REVERT: B 612 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8017 (mt-10) REVERT: B 653 TRP cc_start: 0.7621 (t60) cc_final: 0.6810 (t60) REVERT: B 708 HIS cc_start: 0.6352 (t-90) cc_final: 0.5880 (t-90) outliers start: 33 outliers final: 22 residues processed: 277 average time/residue: 0.2744 time to fit residues: 100.9172 Evaluate side-chains 283 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 738 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 66 optimal weight: 0.8980 chunk 75 optimal weight: 0.1980 chunk 56 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 98 optimal weight: 0.0980 chunk 40 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 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 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 HIS ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 532 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.207001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.169508 restraints weight = 17892.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.175497 restraints weight = 10321.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.179791 restraints weight = 6955.946| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10422 Z= 0.166 Angle : 0.615 13.115 14132 Z= 0.307 Chirality : 0.044 0.254 1522 Planarity : 0.004 0.058 1784 Dihedral : 4.353 36.536 1359 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.73 % Allowed : 16.12 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.24), residues: 1210 helix: 0.58 (0.25), residues: 440 sheet: -1.21 (0.39), residues: 150 loop : -0.41 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 189 HIS 0.010 0.001 HIS A 553 PHE 0.025 0.001 PHE A 657 TYR 0.023 0.001 TYR B 516 ARG 0.012 0.001 ARG B 740 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 267 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7109 (m-30) cc_final: 0.6622 (m-30) REVERT: A 260 LYS cc_start: 0.9178 (mmtm) cc_final: 0.8834 (mmtm) REVERT: A 261 PHE cc_start: 0.6941 (m-80) cc_final: 0.5824 (m-80) REVERT: A 397 PHE cc_start: 0.8411 (m-10) cc_final: 0.7973 (m-80) REVERT: A 402 LEU cc_start: 0.7873 (mt) cc_final: 0.7631 (mp) REVERT: A 428 GLU cc_start: 0.8273 (pm20) cc_final: 0.7604 (pm20) REVERT: A 432 LYS cc_start: 0.8695 (ptpp) cc_final: 0.7996 (ptpp) REVERT: A 449 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6467 (mm-30) REVERT: A 487 MET cc_start: 0.7298 (pmm) cc_final: 0.7076 (pmm) REVERT: A 493 LYS cc_start: 0.8280 (ptpt) cc_final: 0.7867 (ptpt) REVERT: A 515 ARG cc_start: 0.7996 (mpp80) cc_final: 0.7392 (mpp80) REVERT: A 559 MET cc_start: 0.6923 (ppp) cc_final: 0.6369 (ppp) REVERT: A 560 PHE cc_start: 0.6985 (t80) cc_final: 0.6711 (t80) REVERT: A 567 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7876 (tp) REVERT: A 574 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6843 (tp30) REVERT: A 617 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 619 MET cc_start: 0.7848 (tmm) cc_final: 0.7330 (tmm) REVERT: A 658 GLU cc_start: 0.7798 (pt0) cc_final: 0.7307 (pt0) REVERT: A 686 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6733 (mpp) REVERT: A 691 GLN cc_start: 0.8291 (mm110) cc_final: 0.7976 (mm110) REVERT: A 735 GLN cc_start: 0.8711 (mt0) cc_final: 0.8293 (mt0) REVERT: B 179 GLU cc_start: 0.7541 (pt0) cc_final: 0.6918 (pt0) REVERT: B 223 MET cc_start: 0.6835 (tmm) cc_final: 0.5966 (tmm) REVERT: B 229 LYS cc_start: 0.8270 (tmtt) cc_final: 0.7839 (tmtt) REVERT: B 245 ILE cc_start: 0.8163 (mm) cc_final: 0.7927 (mm) REVERT: B 349 VAL cc_start: 0.6586 (m) cc_final: 0.6058 (p) REVERT: B 489 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7791 (mm-30) REVERT: B 504 TYR cc_start: 0.7993 (t80) cc_final: 0.7472 (t80) REVERT: B 509 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7052 (mt-10) REVERT: B 515 ARG cc_start: 0.8274 (ptp-110) cc_final: 0.7868 (ttm110) REVERT: B 547 ARG cc_start: 0.8163 (ptp-110) cc_final: 0.7919 (ptm160) REVERT: B 559 MET cc_start: 0.5550 (ppp) cc_final: 0.5112 (ppp) REVERT: B 569 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7284 (mtm) REVERT: B 653 TRP cc_start: 0.7646 (t60) cc_final: 0.6814 (t60) REVERT: B 708 HIS cc_start: 0.6374 (t-90) cc_final: 0.5892 (t-90) REVERT: B 740 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7173 (mtm-85) outliers start: 30 outliers final: 19 residues processed: 279 average time/residue: 0.2818 time to fit residues: 103.8525 Evaluate side-chains 278 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 738 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 532 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS B 735 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.205870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.167826 restraints weight = 17721.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.173823 restraints weight = 10228.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.177905 restraints weight = 6903.481| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10422 Z= 0.187 Angle : 0.637 13.306 14132 Z= 0.316 Chirality : 0.044 0.256 1522 Planarity : 0.004 0.058 1784 Dihedral : 4.426 35.481 1359 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.82 % Allowed : 17.03 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.24), residues: 1210 helix: 0.55 (0.25), residues: 440 sheet: -1.20 (0.40), residues: 150 loop : -0.35 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 356 HIS 0.007 0.001 HIS A 494 PHE 0.013 0.001 PHE A 460 TYR 0.024 0.002 TYR B 516 ARG 0.009 0.001 ARG B 626 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 274 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7123 (m-30) cc_final: 0.6664 (m-30) REVERT: A 260 LYS cc_start: 0.9169 (mmtm) cc_final: 0.8825 (mmtm) REVERT: A 261 PHE cc_start: 0.6983 (m-80) cc_final: 0.5878 (m-80) REVERT: A 356 TRP cc_start: 0.7698 (m100) cc_final: 0.7421 (m100) REVERT: A 397 PHE cc_start: 0.8371 (m-10) cc_final: 0.7897 (m-80) REVERT: A 402 LEU cc_start: 0.7913 (mt) cc_final: 0.7692 (mp) REVERT: A 428 GLU cc_start: 0.8255 (pm20) cc_final: 0.7640 (pm20) REVERT: A 432 LYS cc_start: 0.8690 (ptpp) cc_final: 0.8089 (ptpp) REVERT: A 449 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6508 (mm-30) REVERT: A 487 MET cc_start: 0.7358 (pmm) cc_final: 0.7132 (pmm) REVERT: A 493 LYS cc_start: 0.8297 (ptpt) cc_final: 0.7891 (ptpt) REVERT: A 515 ARG cc_start: 0.8007 (mpp80) cc_final: 0.7426 (mpp80) REVERT: A 535 TYR cc_start: 0.7971 (m-10) cc_final: 0.7039 (m-10) REVERT: A 559 MET cc_start: 0.6956 (ppp) cc_final: 0.6383 (ppp) REVERT: A 560 PHE cc_start: 0.6974 (t80) cc_final: 0.6692 (t80) REVERT: A 574 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6893 (tp30) REVERT: A 617 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8273 (mp) REVERT: A 619 MET cc_start: 0.7857 (tmm) cc_final: 0.7375 (tmm) REVERT: A 658 GLU cc_start: 0.7792 (pt0) cc_final: 0.7314 (pt0) REVERT: A 673 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.5866 (ttp-110) REVERT: A 691 GLN cc_start: 0.8306 (mm110) cc_final: 0.7984 (mm110) REVERT: A 706 MET cc_start: 0.6408 (mpp) cc_final: 0.6074 (mpp) REVERT: A 735 GLN cc_start: 0.8703 (mt0) cc_final: 0.8272 (mt0) REVERT: B 151 ARG cc_start: 0.8460 (ttp-110) cc_final: 0.8139 (ttp-110) REVERT: B 179 GLU cc_start: 0.7546 (pt0) cc_final: 0.6928 (pt0) REVERT: B 223 MET cc_start: 0.6852 (tmm) cc_final: 0.5977 (tmm) REVERT: B 229 LYS cc_start: 0.8314 (tmtt) cc_final: 0.7881 (tmtt) REVERT: B 245 ILE cc_start: 0.8193 (mm) cc_final: 0.7967 (mm) REVERT: B 349 VAL cc_start: 0.6619 (m) cc_final: 0.6083 (p) REVERT: B 489 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7754 (mm-30) REVERT: B 504 TYR cc_start: 0.8007 (t80) cc_final: 0.7430 (t80) REVERT: B 515 ARG cc_start: 0.8253 (ptp-110) cc_final: 0.7821 (ttm110) REVERT: B 547 ARG cc_start: 0.8165 (ptp-110) cc_final: 0.7901 (ptm160) REVERT: B 559 MET cc_start: 0.5597 (ppp) cc_final: 0.5166 (ppp) REVERT: B 569 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7469 (mtm) REVERT: B 653 TRP cc_start: 0.7734 (t60) cc_final: 0.6909 (t60) REVERT: B 708 HIS cc_start: 0.6395 (t-90) cc_final: 0.5905 (t-90) REVERT: B 740 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7234 (mtm-85) outliers start: 31 outliers final: 23 residues processed: 288 average time/residue: 0.2770 time to fit residues: 105.6237 Evaluate side-chains 293 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 189 TRP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 738 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 23 optimal weight: 0.0970 chunk 110 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 532 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.204913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.165995 restraints weight = 17708.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.171971 restraints weight = 10233.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.176073 restraints weight = 6939.018| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10422 Z= 0.227 Angle : 0.692 13.859 14132 Z= 0.343 Chirality : 0.046 0.238 1522 Planarity : 0.004 0.058 1784 Dihedral : 4.573 35.633 1359 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.73 % Allowed : 18.31 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.50 (0.24), residues: 1210 helix: 0.28 (0.25), residues: 454 sheet: -1.21 (0.40), residues: 156 loop : -0.43 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 316 HIS 0.007 0.001 HIS B 171 PHE 0.026 0.001 PHE A 657 TYR 0.024 0.002 TYR B 516 ARG 0.009 0.000 ARG B 626 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 278 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7095 (m-30) cc_final: 0.6654 (m-30) REVERT: A 260 LYS cc_start: 0.9109 (mmtm) cc_final: 0.8810 (mmtm) REVERT: A 261 PHE cc_start: 0.6856 (m-80) cc_final: 0.6090 (m-80) REVERT: A 397 PHE cc_start: 0.8438 (m-10) cc_final: 0.7907 (m-80) REVERT: A 428 GLU cc_start: 0.8266 (pm20) cc_final: 0.7688 (pm20) REVERT: A 432 LYS cc_start: 0.8697 (ptpp) cc_final: 0.8189 (ptpp) REVERT: A 449 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6570 (mm-30) REVERT: A 493 LYS cc_start: 0.8275 (ptpt) cc_final: 0.7833 (ptpt) REVERT: A 505 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6767 (mp) REVERT: A 515 ARG cc_start: 0.8038 (mpp80) cc_final: 0.7425 (mpp80) REVERT: A 535 TYR cc_start: 0.8007 (m-10) cc_final: 0.6249 (m-10) REVERT: A 559 MET cc_start: 0.6962 (ppp) cc_final: 0.6399 (ppp) REVERT: A 560 PHE cc_start: 0.6964 (t80) cc_final: 0.6710 (t80) REVERT: A 574 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6932 (tp30) REVERT: A 617 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8286 (mp) REVERT: A 619 MET cc_start: 0.7891 (tmm) cc_final: 0.7427 (tmm) REVERT: A 658 GLU cc_start: 0.7807 (pt0) cc_final: 0.7320 (pt0) REVERT: A 673 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6109 (ttp-110) REVERT: A 691 GLN cc_start: 0.8310 (mm110) cc_final: 0.7990 (mm110) REVERT: A 706 MET cc_start: 0.6466 (mpp) cc_final: 0.5894 (mpp) REVERT: A 735 GLN cc_start: 0.8702 (mt0) cc_final: 0.8311 (mt0) REVERT: B 151 ARG cc_start: 0.8573 (ttp-110) cc_final: 0.7914 (mtm110) REVERT: B 179 GLU cc_start: 0.7605 (pt0) cc_final: 0.6981 (pt0) REVERT: B 223 MET cc_start: 0.6892 (tmm) cc_final: 0.6010 (tmm) REVERT: B 245 ILE cc_start: 0.8220 (mm) cc_final: 0.7964 (mm) REVERT: B 349 VAL cc_start: 0.6680 (m) cc_final: 0.6156 (p) REVERT: B 489 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7749 (mm-30) REVERT: B 504 TYR cc_start: 0.7982 (t80) cc_final: 0.7376 (t80) REVERT: B 515 ARG cc_start: 0.8289 (ptp-110) cc_final: 0.7875 (ttm110) REVERT: B 559 MET cc_start: 0.5680 (ppp) cc_final: 0.5207 (ppp) REVERT: B 569 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7446 (mtm) REVERT: B 612 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7988 (mt-10) REVERT: B 638 ASN cc_start: 0.6156 (t0) cc_final: 0.5134 (t0) REVERT: B 703 MET cc_start: 0.4109 (mpp) cc_final: 0.3879 (mpp) REVERT: B 708 HIS cc_start: 0.6400 (t-90) cc_final: 0.5941 (t-90) outliers start: 30 outliers final: 23 residues processed: 291 average time/residue: 0.2823 time to fit residues: 108.5175 Evaluate side-chains 303 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 276 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 189 TRP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 689 ASP Chi-restraints excluded: chain B residue 738 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 25 optimal weight: 0.2980 chunk 13 optimal weight: 20.0000 chunk 3 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 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 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 345 ASN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.206081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.167609 restraints weight = 17614.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.173540 restraints weight = 10219.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.177687 restraints weight = 6936.397| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10422 Z= 0.182 Angle : 0.692 13.708 14132 Z= 0.337 Chirality : 0.045 0.228 1522 Planarity : 0.004 0.058 1784 Dihedral : 4.479 39.986 1359 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.37 % Allowed : 19.22 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.31 (0.24), residues: 1210 helix: 0.36 (0.25), residues: 444 sheet: -1.05 (0.40), residues: 152 loop : -0.28 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 356 HIS 0.011 0.001 HIS A 494 PHE 0.026 0.001 PHE A 657 TYR 0.026 0.002 TYR B 516 ARG 0.009 0.000 ARG B 626 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7065 (m-30) cc_final: 0.6616 (m-30) REVERT: A 260 LYS cc_start: 0.9135 (mmtm) cc_final: 0.8877 (mmtm) REVERT: A 261 PHE cc_start: 0.6828 (m-80) cc_final: 0.5866 (m-80) REVERT: A 397 PHE cc_start: 0.8365 (m-10) cc_final: 0.7845 (m-80) REVERT: A 399 ASN cc_start: 0.7954 (m-40) cc_final: 0.7607 (m-40) REVERT: A 402 LEU cc_start: 0.7796 (mt) cc_final: 0.7551 (mp) REVERT: A 428 GLU cc_start: 0.8248 (pm20) cc_final: 0.7602 (pm20) REVERT: A 432 LYS cc_start: 0.8700 (ptpp) cc_final: 0.8172 (ptpp) REVERT: A 449 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6529 (mm-30) REVERT: A 450 ARG cc_start: 0.7688 (ttp-170) cc_final: 0.7446 (ttp-170) REVERT: A 493 LYS cc_start: 0.8260 (ptpt) cc_final: 0.7817 (ptpt) REVERT: A 505 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6640 (mp) REVERT: A 515 ARG cc_start: 0.8033 (mpp80) cc_final: 0.7429 (mpp80) REVERT: A 535 TYR cc_start: 0.7938 (m-10) cc_final: 0.7232 (m-10) REVERT: A 559 MET cc_start: 0.6977 (ppp) cc_final: 0.6384 (ppp) REVERT: A 560 PHE cc_start: 0.6949 (t80) cc_final: 0.6696 (t80) REVERT: A 574 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6865 (tp30) REVERT: A 617 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8292 (mp) REVERT: A 619 MET cc_start: 0.7846 (tmm) cc_final: 0.7398 (tmm) REVERT: A 658 GLU cc_start: 0.7768 (pt0) cc_final: 0.7322 (pt0) REVERT: A 673 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6131 (ttp-110) REVERT: A 691 GLN cc_start: 0.8295 (mm110) cc_final: 0.7969 (mm110) REVERT: A 735 GLN cc_start: 0.8716 (mt0) cc_final: 0.8333 (mt0) REVERT: B 151 ARG cc_start: 0.8552 (ttp-110) cc_final: 0.7960 (mtm110) REVERT: B 179 GLU cc_start: 0.7548 (pt0) cc_final: 0.6909 (pt0) REVERT: B 223 MET cc_start: 0.6857 (tmm) cc_final: 0.5964 (tmm) REVERT: B 245 ILE cc_start: 0.8203 (mm) cc_final: 0.8001 (mm) REVERT: B 309 LYS cc_start: 0.8231 (mttp) cc_final: 0.7713 (mttp) REVERT: B 349 VAL cc_start: 0.6775 (m) cc_final: 0.6237 (p) REVERT: B 408 ASP cc_start: 0.7460 (t0) cc_final: 0.7102 (t0) REVERT: B 414 ARG cc_start: 0.8154 (tpm170) cc_final: 0.7933 (tpm170) REVERT: B 489 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7722 (mm-30) REVERT: B 504 TYR cc_start: 0.7942 (t80) cc_final: 0.7352 (t80) REVERT: B 515 ARG cc_start: 0.8271 (ptp-110) cc_final: 0.7857 (ttm110) REVERT: B 549 VAL cc_start: 0.8410 (m) cc_final: 0.8209 (t) REVERT: B 559 MET cc_start: 0.5626 (ppp) cc_final: 0.5097 (ppp) REVERT: B 612 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7988 (mt-10) REVERT: B 625 PHE cc_start: 0.7218 (t80) cc_final: 0.6994 (t80) REVERT: B 703 MET cc_start: 0.3837 (mpp) cc_final: 0.3617 (mpp) REVERT: B 708 HIS cc_start: 0.6425 (t-90) cc_final: 0.5951 (t-90) outliers start: 26 outliers final: 17 residues processed: 289 average time/residue: 0.2846 time to fit residues: 107.9330 Evaluate side-chains 296 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 276 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 189 TRP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 689 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.201181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.164055 restraints weight = 17824.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.169725 restraints weight = 10471.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.173516 restraints weight = 7187.852| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10422 Z= 0.295 Angle : 0.775 13.973 14132 Z= 0.381 Chirality : 0.048 0.235 1522 Planarity : 0.004 0.053 1784 Dihedral : 4.727 33.219 1356 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.82 % Allowed : 20.04 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.24), residues: 1210 helix: 0.06 (0.24), residues: 452 sheet: -1.15 (0.40), residues: 154 loop : -0.53 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 356 HIS 0.010 0.001 HIS A 494 PHE 0.029 0.002 PHE A 657 TYR 0.030 0.002 TYR B 350 ARG 0.009 0.001 ARG B 626 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 278 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.6927 (m-30) cc_final: 0.6526 (m-30) REVERT: A 260 LYS cc_start: 0.9161 (mmtm) cc_final: 0.8881 (mmtm) REVERT: A 261 PHE cc_start: 0.6781 (m-80) cc_final: 0.6098 (m-80) REVERT: A 397 PHE cc_start: 0.8255 (m-10) cc_final: 0.7824 (m-80) REVERT: A 399 ASN cc_start: 0.8009 (m-40) cc_final: 0.7655 (m-40) REVERT: A 402 LEU cc_start: 0.7897 (mt) cc_final: 0.7646 (mp) REVERT: A 428 GLU cc_start: 0.8110 (pm20) cc_final: 0.7627 (pm20) REVERT: A 432 LYS cc_start: 0.8623 (ptpp) cc_final: 0.8043 (ptpp) REVERT: A 449 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6575 (mm-30) REVERT: A 493 LYS cc_start: 0.8287 (ptpt) cc_final: 0.7864 (ptpt) REVERT: A 505 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6551 (mp) REVERT: A 515 ARG cc_start: 0.7890 (mpp80) cc_final: 0.7346 (mpp80) REVERT: A 535 TYR cc_start: 0.8085 (m-10) cc_final: 0.7412 (m-10) REVERT: A 540 PHE cc_start: 0.5698 (m-10) cc_final: 0.5478 (m-10) REVERT: A 559 MET cc_start: 0.6900 (ppp) cc_final: 0.6378 (ppp) REVERT: A 560 PHE cc_start: 0.6880 (t80) cc_final: 0.6647 (t80) REVERT: A 617 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8318 (mp) REVERT: A 619 MET cc_start: 0.7690 (tmm) cc_final: 0.7316 (tmm) REVERT: A 652 GLU cc_start: 0.7715 (mp0) cc_final: 0.7466 (mp0) REVERT: A 673 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6362 (ttp-110) REVERT: A 691 GLN cc_start: 0.8189 (mm110) cc_final: 0.7937 (mm110) REVERT: A 735 GLN cc_start: 0.8654 (mt0) cc_final: 0.8352 (mt0) REVERT: B 151 ARG cc_start: 0.8619 (ttp-110) cc_final: 0.7992 (mtm110) REVERT: B 179 GLU cc_start: 0.7574 (pt0) cc_final: 0.7042 (pt0) REVERT: B 223 MET cc_start: 0.6896 (tmm) cc_final: 0.5959 (tmm) REVERT: B 245 ILE cc_start: 0.8321 (mm) cc_final: 0.8085 (mm) REVERT: B 381 TRP cc_start: 0.8023 (m100) cc_final: 0.7638 (m-90) REVERT: B 408 ASP cc_start: 0.7412 (t0) cc_final: 0.7207 (t0) REVERT: B 486 GLN cc_start: 0.7857 (pm20) cc_final: 0.7484 (pm20) REVERT: B 489 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7601 (mm-30) REVERT: B 504 TYR cc_start: 0.7883 (t80) cc_final: 0.7377 (t80) REVERT: B 515 ARG cc_start: 0.7994 (ptp-110) cc_final: 0.7543 (ttm110) REVERT: B 559 MET cc_start: 0.5853 (ppp) cc_final: 0.5408 (ppp) REVERT: B 703 MET cc_start: 0.3877 (mpp) cc_final: 0.3574 (mpp) REVERT: B 708 HIS cc_start: 0.6333 (t-90) cc_final: 0.5886 (t-90) outliers start: 20 outliers final: 15 residues processed: 288 average time/residue: 0.3199 time to fit residues: 121.3035 Evaluate side-chains 296 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 278 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 673 ARG Chi-restraints excluded: chain A residue 689 ASP Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 689 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 109 optimal weight: 0.0980 chunk 52 optimal weight: 0.0470 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN B 345 ASN B 532 HIS B 735 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.205041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.167433 restraints weight = 17482.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.173425 restraints weight = 10091.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.177555 restraints weight = 6815.211| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10422 Z= 0.183 Angle : 0.731 14.275 14132 Z= 0.356 Chirality : 0.047 0.312 1522 Planarity : 0.004 0.054 1784 Dihedral : 4.469 33.504 1356 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.28 % Allowed : 20.77 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1210 helix: 0.02 (0.24), residues: 458 sheet: -1.13 (0.41), residues: 152 loop : -0.43 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 642 HIS 0.010 0.001 HIS A 494 PHE 0.025 0.001 PHE A 657 TYR 0.027 0.002 TYR B 516 ARG 0.008 0.000 ARG B 626 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3823.93 seconds wall clock time: 68 minutes 59.70 seconds (4139.70 seconds total)