Starting phenix.real_space_refine on Mon Jul 28 09:23:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ui6_26540/07_2025/7ui6_26540.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ui6_26540/07_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_26540/07_2025/7ui6_26540.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ui6_26540/07_2025/7ui6_26540.map" model { file = "/net/cci-nas-00/data/ceres_data/7ui6_26540/07_2025/7ui6_26540.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ui6_26540/07_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.78, per 1000 atoms: 0.67 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: 2.70 Conformation dependent library (CDL) restraints added in 1.2 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: 1.24 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: 3.22 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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: 0.05 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: 1.320 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.030 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.300 ------------------------------------------------------------------------------- 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 10426 Z= 0.243 Angle : 0.972 10.787 14140 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 Details of bonding type rmsd hydrogen bonds : bond 0.16656 ( 355) hydrogen bonds : angle 6.83782 ( 978) SS BOND : bond 0.00115 ( 4) SS BOND : angle 1.40007 ( 8) covalent geometry : bond 0.00454 (10422) covalent geometry : angle 0.97143 (14132) *********************** 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 : 1.048 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: 0.2758 time to fit residues: 108.5733 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 : 1.093 ------------------------------------------------------------------------------- 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 = 0.173547 restraints weight = 17808.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.179341 restraints weight = 10368.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.183497 restraints weight = 7003.925| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 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 10426 Z= 0.138 Angle : 0.653 11.416 14140 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 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 355) hydrogen bonds : angle 5.18007 ( 978) SS BOND : bond 0.00078 ( 4) SS BOND : angle 0.44365 ( 8) covalent geometry : bond 0.00307 (10422) covalent geometry : angle 0.65330 (14132) *********************** 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 : 1.173 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: 0.6324 (m-30) REVERT: A 260 LYS cc_start: 0.9066 (mmtm) cc_final: 0.8711 (mmtm) REVERT: A 261 PHE cc_start: 0.6866 (m-80) cc_final: 0.5925 (m-80) REVERT: A 397 PHE cc_start: 0.8317 (m-10) cc_final: 0.7927 (m-10) REVERT: A 428 GLU cc_start: 0.8242 (pm20) cc_final: 0.7749 (pm20) REVERT: A 432 LYS cc_start: 0.8666 (ptpp) cc_final: 0.7994 (ptpp) REVERT: A 449 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6393 (mm-30) REVERT: A 450 ARG cc_start: 0.7259 (tmm-80) cc_final: 0.7000 (tmm-80) REVERT: A 460 PHE cc_start: 0.7201 (t80) cc_final: 0.6841 (m-80) REVERT: A 472 THR cc_start: 0.6808 (p) cc_final: 0.6602 (t) REVERT: A 493 LYS cc_start: 0.8260 (ptpt) cc_final: 0.7777 (ptpt) REVERT: A 515 ARG cc_start: 0.7732 (mpp80) cc_final: 0.7337 (mpp80) REVERT: A 619 MET cc_start: 0.7701 (tmm) cc_final: 0.7193 (tmm) REVERT: A 652 GLU cc_start: 0.7907 (mp0) cc_final: 0.7690 (mp0) REVERT: A 669 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6809 (mt-10) REVERT: A 691 GLN cc_start: 0.8316 (mm110) cc_final: 0.8030 (mm110) REVERT: A 736 GLN cc_start: 0.8015 (mp10) cc_final: 0.7804 (mp10) REVERT: A 738 MET cc_start: 0.8181 (ttt) cc_final: 0.7908 (ttt) REVERT: B 179 GLU cc_start: 0.7521 (pt0) cc_final: 0.6944 (pt0) REVERT: B 223 MET cc_start: 0.6770 (tmm) cc_final: 0.6520 (tmm) REVERT: B 229 LYS cc_start: 0.8028 (tmtt) cc_final: 0.7444 (tmtt) REVERT: B 349 VAL cc_start: 0.6589 (m) cc_final: 0.6095 (p) REVERT: B 407 TYR cc_start: 0.7105 (t80) cc_final: 0.6904 (t80) REVERT: B 489 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7795 (mm-30) REVERT: B 512 GLN cc_start: 0.8159 (mt0) cc_final: 0.7936 (mt0) REVERT: B 515 ARG cc_start: 0.8167 (ptp-110) cc_final: 0.7650 (ttp-110) REVERT: B 516 TYR cc_start: 0.8639 (t80) cc_final: 0.8435 (t80) REVERT: B 536 LYS cc_start: 0.7734 (ttmm) cc_final: 0.7453 (mttm) REVERT: B 547 ARG cc_start: 0.8028 (ptm160) cc_final: 0.7254 (ptm160) REVERT: B 559 MET cc_start: 0.5692 (ppp) cc_final: 0.5043 (ppp) REVERT: B 560 PHE cc_start: 0.6307 (t80) cc_final: 0.6038 (t80) REVERT: B 626 ARG cc_start: 0.6929 (tpp80) cc_final: 0.6477 (tpp80) REVERT: B 653 TRP cc_start: 0.7528 (t60) cc_final: 0.7037 (t60) REVERT: B 708 HIS cc_start: 0.6062 (t-90) cc_final: 0.5646 (t-90) outliers start: 15 outliers final: 9 residues processed: 277 average time/residue: 0.2941 time to fit residues: 108.6213 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 : 1.035 ------------------------------------------------------------------------------- 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: 0.9980 chunk 63 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4587 r_free = 0.4587 target = 0.202256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.166091 restraints weight = 17914.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.171824 restraints weight = 10325.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.175802 restraints weight = 6960.369| |-----------------------------------------------------------------------------| r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10426 Z= 0.182 Angle : 0.655 12.439 14140 Z= 0.334 Chirality : 0.045 0.209 1522 Planarity : 0.004 0.047 1784 Dihedral : 4.867 48.935 1360 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.19 % Allowed : 13.21 % Favored : 84.61 % 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: -0.59 (0.24), residues: 1210 helix: 0.41 (0.25), residues: 436 sheet: -1.37 (0.40), residues: 144 loop : -0.65 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 316 HIS 0.008 0.001 HIS A 163 PHE 0.021 0.002 PHE A 657 TYR 0.028 0.002 TYR B 350 ARG 0.006 0.001 ARG B 626 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 355) hydrogen bonds : angle 5.04118 ( 978) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.47961 ( 8) covalent geometry : bond 0.00380 (10422) covalent geometry : angle 0.65528 (14132) *********************** 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 305 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 281 time to evaluate : 1.016 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: 0.7062 (m-30) cc_final: 0.6603 (m-30) REVERT: A 184 THR cc_start: 0.8650 (p) cc_final: 0.8216 (t) REVERT: A 260 LYS cc_start: 0.9177 (mmtm) cc_final: 0.8725 (mmtm) REVERT: A 261 PHE cc_start: 0.6981 (m-80) cc_final: 0.5999 (m-80) REVERT: A 397 PHE cc_start: 0.8396 (m-10) cc_final: 0.7937 (m-10) REVERT: A 428 GLU cc_start: 0.8198 (pm20) cc_final: 0.7705 (pm20) REVERT: A 432 LYS cc_start: 0.8690 (ptpp) cc_final: 0.8059 (ptpp) REVERT: A 449 GLU cc_start: 0.6693 (mm-30) cc_final: 0.6374 (mm-30) REVERT: A 450 ARG cc_start: 0.7627 (tmm-80) cc_final: 0.7376 (ttp-170) REVERT: A 493 LYS cc_start: 0.8289 (ptpt) cc_final: 0.7872 (ptpt) REVERT: A 511 GLN cc_start: 0.7494 (mm-40) cc_final: 0.7018 (mm-40) REVERT: A 515 ARG cc_start: 0.7935 (mpp80) cc_final: 0.7379 (mpp80) REVERT: A 559 MET cc_start: 0.6880 (ppp) cc_final: 0.6415 (ppp) REVERT: A 617 LEU cc_start: 0.8457 (mp) cc_final: 0.8217 (mp) REVERT: A 619 MET cc_start: 0.7807 (tmm) cc_final: 0.7198 (tmm) REVERT: A 657 PHE cc_start: 0.6341 (t80) cc_final: 0.5889 (t80) REVERT: A 691 GLN cc_start: 0.8403 (mm110) cc_final: 0.8161 (mm110) REVERT: A 703 MET cc_start: 0.5129 (mtm) cc_final: 0.4902 (mtm) REVERT: A 736 GLN cc_start: 0.8109 (mt0) cc_final: 0.7831 (mp10) REVERT: B 151 ARG cc_start: 0.7859 (mtm180) cc_final: 0.6935 (ptt-90) REVERT: B 179 GLU cc_start: 0.7611 (pt0) cc_final: 0.7052 (pt0) REVERT: B 223 MET cc_start: 0.6888 (tmm) cc_final: 0.6258 (tmm) REVERT: B 229 LYS cc_start: 0.8328 (tmtt) cc_final: 0.7895 (tmtt) REVERT: B 245 ILE cc_start: 0.8256 (mm) cc_final: 0.7904 (mm) REVERT: B 349 VAL cc_start: 0.6759 (m) cc_final: 0.6234 (p) REVERT: B 489 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7856 (mm-30) REVERT: B 509 GLU cc_start: 0.7919 (mt-10) cc_final: 0.6852 (mt-10) REVERT: B 512 GLN cc_start: 0.8275 (mt0) cc_final: 0.8031 (mt0) REVERT: B 515 ARG cc_start: 0.8294 (ptp-110) cc_final: 0.7896 (ttm110) REVERT: B 536 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7690 (mmtp) REVERT: B 547 ARG cc_start: 0.7989 (ptm160) cc_final: 0.7377 (ptm160) REVERT: B 559 MET cc_start: 0.5610 (ppp) cc_final: 0.5332 (ppp) REVERT: B 569 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7767 (mtm) REVERT: B 626 ARG cc_start: 0.7152 (tpp80) cc_final: 0.6885 (tpp80) REVERT: B 653 TRP cc_start: 0.7651 (t60) cc_final: 0.6980 (t60) REVERT: B 708 HIS cc_start: 0.6289 (t-90) cc_final: 0.5850 (t-90) REVERT: B 740 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7293 (mtm-85) outliers start: 24 outliers final: 15 residues processed: 294 average time/residue: 0.2619 time to fit residues: 102.0512 Evaluate side-chains 289 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 273 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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: 5.9990 chunk 95 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 87 optimal weight: 0.0970 chunk 22 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 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 = 0.4630 r_free = 0.4630 target = 0.207202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.168747 restraints weight = 17725.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.174884 restraints weight = 10217.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.179218 restraints weight = 6914.512| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10426 Z= 0.128 Angle : 0.628 12.710 14140 Z= 0.312 Chirality : 0.044 0.260 1522 Planarity : 0.004 0.047 1784 Dihedral : 4.604 40.612 1360 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.09 % Allowed : 15.94 % Favored : 81.97 % 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: -0.48 (0.24), residues: 1210 helix: 0.51 (0.25), residues: 440 sheet: -1.33 (0.40), residues: 140 loop : -0.59 (0.24), 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 0.018 0.001 PHE A 657 TYR 0.027 0.002 TYR B 407 ARG 0.007 0.000 ARG B 413 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 355) hydrogen bonds : angle 4.81948 ( 978) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.45010 ( 8) covalent geometry : bond 0.00283 (10422) covalent geometry : angle 0.62812 (14132) *********************** 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: 23 poor density : 278 time to evaluate : 1.043 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: 0.7060 (m-30) cc_final: 0.6567 (m-30) REVERT: A 260 LYS cc_start: 0.9184 (mmtm) cc_final: 0.8784 (mmtm) REVERT: A 261 PHE cc_start: 0.6998 (m-80) cc_final: 0.5956 (m-80) REVERT: A 356 TRP cc_start: 0.7791 (m100) cc_final: 0.7473 (m100) REVERT: A 397 PHE cc_start: 0.8402 (m-10) cc_final: 0.7938 (m-10) REVERT: A 428 GLU cc_start: 0.8209 (pm20) cc_final: 0.7437 (pm20) REVERT: A 431 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7743 (mm-40) REVERT: A 432 LYS cc_start: 0.8699 (ptpp) cc_final: 0.8015 (ptpp) REVERT: A 449 GLU cc_start: 0.6772 (mm-30) cc_final: 0.6428 (mm-30) REVERT: A 450 ARG cc_start: 0.7611 (tmm-80) cc_final: 0.7383 (ttp-170) REVERT: A 493 LYS cc_start: 0.8283 (ptpt) cc_final: 0.7842 (ptpt) REVERT: A 515 ARG cc_start: 0.7973 (mpp80) cc_final: 0.7379 (mpp80) REVERT: A 559 MET cc_start: 0.6917 (ppp) cc_final: 0.6439 (ppp) REVERT: A 560 PHE cc_start: 0.7006 (t80) cc_final: 0.6740 (t80) REVERT: A 617 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8254 (mp) REVERT: A 619 MET cc_start: 0.7835 (tmm) cc_final: 0.7241 (tmm) REVERT: A 658 GLU cc_start: 0.7771 (pt0) cc_final: 0.7341 (pt0) REVERT: A 691 GLN cc_start: 0.8306 (mm110) cc_final: 0.8040 (mm110) REVERT: A 703 MET cc_start: 0.5028 (mtm) cc_final: 0.4692 (mtm) REVERT: A 735 GLN cc_start: 0.8715 (mt0) cc_final: 0.8253 (mt0) REVERT: B 151 ARG cc_start: 0.7806 (mtm180) cc_final: 0.6834 (mpp80) REVERT: B 179 GLU cc_start: 0.7548 (pt0) cc_final: 0.6982 (pt0) REVERT: B 223 MET cc_start: 0.6842 (tmm) cc_final: 0.6155 (tmm) REVERT: B 229 LYS cc_start: 0.8251 (tmtt) cc_final: 0.7818 (tmtt) REVERT: B 245 ILE cc_start: 0.8211 (mm) cc_final: 0.7901 (mm) REVERT: B 349 VAL cc_start: 0.6779 (m) cc_final: 0.6235 (p) REVERT: B 357 ASN cc_start: 0.7702 (p0) cc_final: 0.7369 (p0) REVERT: B 489 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7844 (mm-30) REVERT: B 509 GLU cc_start: 0.7789 (mt-10) cc_final: 0.6995 (mt-10) REVERT: B 512 GLN cc_start: 0.8137 (mt0) cc_final: 0.7879 (mt0) REVERT: B 515 ARG cc_start: 0.8246 (ptp-110) cc_final: 0.7816 (ttm110) REVERT: B 547 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7495 (ptm160) REVERT: B 559 MET cc_start: 0.5512 (ppp) cc_final: 0.5304 (ppp) REVERT: B 568 PRO cc_start: 0.8548 (Cg_endo) cc_final: 0.7458 (Cg_exo) REVERT: B 569 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7412 (mtm) REVERT: B 626 ARG cc_start: 0.7132 (tpp80) cc_final: 0.6838 (tpp80) REVERT: B 653 TRP cc_start: 0.7636 (t60) cc_final: 0.6824 (t60) REVERT: B 708 HIS cc_start: 0.6299 (t-90) cc_final: 0.5868 (t-90) REVERT: B 740 ARG cc_start: 0.7648 (mtm-85) cc_final: 0.7249 (mtm-85) outliers start: 23 outliers final: 16 residues processed: 289 average time/residue: 0.2726 time to fit residues: 105.4799 Evaluate side-chains 280 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 262 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 617 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 7 optimal weight: 30.0000 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.206060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.167058 restraints weight = 17817.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.173132 restraints weight = 10260.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.177400 restraints weight = 6956.975| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10426 Z= 0.139 Angle : 0.615 12.316 14140 Z= 0.308 Chirality : 0.044 0.224 1522 Planarity : 0.004 0.058 1784 Dihedral : 4.540 41.407 1359 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.01 % Allowed : 15.57 % Favored : 81.42 % 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: -0.48 (0.24), residues: 1210 helix: 0.50 (0.25), residues: 440 sheet: -1.49 (0.39), residues: 148 loop : -0.53 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 316 HIS 0.009 0.001 HIS A 494 PHE 0.018 0.001 PHE A 355 TYR 0.030 0.002 TYR B 407 ARG 0.007 0.000 ARG B 413 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 355) hydrogen bonds : angle 4.76935 ( 978) SS BOND : bond 0.00087 ( 4) SS BOND : angle 0.44395 ( 8) covalent geometry : bond 0.00303 (10422) covalent geometry : angle 0.61476 (14132) *********************** 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 300 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 267 time to evaluate : 0.976 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: 0.7107 (m-30) cc_final: 0.6655 (m-30) REVERT: A 260 LYS cc_start: 0.9183 (mmtm) cc_final: 0.8776 (mmtm) REVERT: A 261 PHE cc_start: 0.7035 (m-80) cc_final: 0.5964 (m-80) REVERT: A 356 TRP cc_start: 0.7837 (m100) cc_final: 0.7598 (m100) REVERT: A 397 PHE cc_start: 0.8399 (m-10) cc_final: 0.7949 (m-80) REVERT: A 428 GLU cc_start: 0.8224 (pm20) cc_final: 0.7498 (pm20) REVERT: A 432 LYS cc_start: 0.8694 (ptpp) cc_final: 0.8009 (ptpp) REVERT: A 449 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6421 (mm-30) REVERT: A 450 ARG cc_start: 0.7643 (tmm-80) cc_final: 0.7434 (ttp-170) REVERT: A 493 LYS cc_start: 0.8315 (ptpt) cc_final: 0.7878 (ptpt) REVERT: A 515 ARG cc_start: 0.7970 (mpp80) cc_final: 0.7351 (mpp80) REVERT: A 535 TYR cc_start: 0.8001 (m-10) cc_final: 0.7027 (m-10) REVERT: A 559 MET cc_start: 0.6919 (ppp) cc_final: 0.6394 (ppp) REVERT: A 560 PHE cc_start: 0.6998 (t80) cc_final: 0.6700 (t80) REVERT: A 617 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8270 (mp) REVERT: A 619 MET cc_start: 0.7864 (tmm) cc_final: 0.7343 (tmm) REVERT: A 658 GLU cc_start: 0.7817 (pt0) cc_final: 0.7322 (pt0) REVERT: A 691 GLN cc_start: 0.8328 (mm110) cc_final: 0.8054 (mm110) REVERT: A 735 GLN cc_start: 0.8719 (mt0) cc_final: 0.8277 (mt0) REVERT: B 179 GLU cc_start: 0.7522 (pt0) cc_final: 0.6942 (pt0) REVERT: B 223 MET cc_start: 0.6903 (tmm) cc_final: 0.6138 (tmm) REVERT: B 229 LYS cc_start: 0.8293 (tmtt) cc_final: 0.7855 (tmtt) REVERT: B 245 ILE cc_start: 0.8211 (mm) cc_final: 0.7959 (mm) REVERT: B 349 VAL cc_start: 0.6605 (m) cc_final: 0.6060 (p) REVERT: B 357 ASN cc_start: 0.7685 (p0) cc_final: 0.7308 (p0) REVERT: B 489 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7785 (mm-30) REVERT: B 509 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7041 (mt-10) REVERT: B 512 GLN cc_start: 0.8138 (mt0) cc_final: 0.7851 (mt0) REVERT: B 515 ARG cc_start: 0.8207 (ptp-110) cc_final: 0.7800 (ttm110) REVERT: B 547 ARG cc_start: 0.7775 (ptm160) cc_final: 0.7181 (ptm160) REVERT: B 559 MET cc_start: 0.5590 (ppp) cc_final: 0.5259 (ppp) REVERT: B 569 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7340 (mtm) REVERT: B 626 ARG cc_start: 0.7223 (tpp80) cc_final: 0.6924 (tpp80) REVERT: B 653 TRP cc_start: 0.7726 (t60) cc_final: 0.6882 (t60) REVERT: B 670 TYR cc_start: 0.5621 (m-80) cc_final: 0.5421 (m-80) REVERT: B 708 HIS cc_start: 0.6361 (t-90) cc_final: 0.5896 (t-90) REVERT: B 740 ARG cc_start: 0.7645 (mtm-85) cc_final: 0.7255 (mtm-85) outliers start: 33 outliers final: 19 residues processed: 284 average time/residue: 0.2753 time to fit residues: 103.4883 Evaluate side-chains 284 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 263 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL 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 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: 0.9990 chunk 75 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 78 optimal weight: 0.0370 chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 ** A 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4620 r_free = 0.4620 target = 0.206175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.169406 restraints weight = 17765.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.175397 restraints weight = 10243.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.179608 restraints weight = 6871.081| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10426 Z= 0.117 Angle : 0.621 12.977 14140 Z= 0.309 Chirality : 0.043 0.238 1522 Planarity : 0.004 0.057 1784 Dihedral : 4.447 40.730 1359 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.82 % Allowed : 16.76 % Favored : 80.42 % 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: -0.33 (0.24), residues: 1210 helix: 0.56 (0.25), residues: 440 sheet: -1.20 (0.40), residues: 138 loop : -0.45 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 189 HIS 0.013 0.001 HIS A 553 PHE 0.027 0.001 PHE A 657 TYR 0.027 0.001 TYR B 407 ARG 0.006 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 355) hydrogen bonds : angle 4.68796 ( 978) SS BOND : bond 0.00072 ( 4) SS BOND : angle 0.37181 ( 8) covalent geometry : bond 0.00265 (10422) covalent geometry : angle 0.62151 (14132) *********************** 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 301 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 0.961 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: 0.7086 (m-30) cc_final: 0.6645 (m-30) REVERT: A 260 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8846 (mmtm) REVERT: A 261 PHE cc_start: 0.6992 (m-80) cc_final: 0.5913 (m-80) REVERT: A 356 TRP cc_start: 0.7793 (m100) cc_final: 0.7580 (m100) REVERT: A 397 PHE cc_start: 0.8352 (m-10) cc_final: 0.7921 (m-80) REVERT: A 428 GLU cc_start: 0.8211 (pm20) cc_final: 0.7457 (pm20) REVERT: A 432 LYS cc_start: 0.8703 (ptpp) cc_final: 0.7938 (ptpp) REVERT: A 449 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6409 (mm-30) REVERT: A 450 ARG cc_start: 0.7618 (tmm-80) cc_final: 0.7418 (ttp-170) REVERT: A 493 LYS cc_start: 0.8297 (ptpt) cc_final: 0.7842 (ptpt) REVERT: A 505 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6555 (mt) REVERT: A 515 ARG cc_start: 0.7980 (mpp80) cc_final: 0.7376 (mpp80) REVERT: A 559 MET cc_start: 0.6919 (ppp) cc_final: 0.6402 (ppp) REVERT: A 560 PHE cc_start: 0.6956 (t80) cc_final: 0.6676 (t80) REVERT: A 617 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8270 (mp) REVERT: A 619 MET cc_start: 0.7821 (tmm) cc_final: 0.7317 (tmm) REVERT: A 658 GLU cc_start: 0.7788 (pt0) cc_final: 0.7310 (pt0) REVERT: A 691 GLN cc_start: 0.8309 (mm110) cc_final: 0.8005 (mm110) REVERT: A 735 GLN cc_start: 0.8708 (mt0) cc_final: 0.8300 (mt0) REVERT: B 179 GLU cc_start: 0.7612 (pt0) cc_final: 0.6940 (pt0) REVERT: B 223 MET cc_start: 0.6836 (tmm) cc_final: 0.5981 (tmm) REVERT: B 229 LYS cc_start: 0.8297 (tmtt) cc_final: 0.7851 (tmtt) REVERT: B 245 ILE cc_start: 0.8175 (mm) cc_final: 0.7932 (mm) REVERT: B 349 VAL cc_start: 0.6625 (m) cc_final: 0.6083 (p) REVERT: B 357 ASN cc_start: 0.7630 (p0) cc_final: 0.7261 (p0) REVERT: B 408 ASP cc_start: 0.7416 (t0) cc_final: 0.7081 (t0) REVERT: B 489 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7806 (mm-30) REVERT: B 512 GLN cc_start: 0.8174 (mt0) cc_final: 0.7882 (mt0) REVERT: B 515 ARG cc_start: 0.8256 (ptp-110) cc_final: 0.7836 (ttm110) REVERT: B 547 ARG cc_start: 0.7817 (ptm160) cc_final: 0.7421 (ptm160) REVERT: B 559 MET cc_start: 0.5556 (ppp) cc_final: 0.5137 (ppp) REVERT: B 569 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7439 (mtm) REVERT: B 626 ARG cc_start: 0.6791 (tpp80) cc_final: 0.6545 (tpp80) REVERT: B 653 TRP cc_start: 0.7679 (t60) cc_final: 0.6858 (t60) REVERT: B 708 HIS cc_start: 0.6362 (t-90) cc_final: 0.5883 (t-90) REVERT: B 740 ARG cc_start: 0.7611 (mtm-85) cc_final: 0.7202 (mtm-85) outliers start: 31 outliers final: 19 residues processed: 285 average time/residue: 0.2714 time to fit residues: 102.3445 Evaluate side-chains 287 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 265 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL 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 574 GLU 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 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 339 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 339 ASN B 532 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.205115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.167831 restraints weight = 17768.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.173712 restraints weight = 10266.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.177897 restraints weight = 6928.061| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10426 Z= 0.139 Angle : 0.653 12.337 14140 Z= 0.327 Chirality : 0.045 0.291 1522 Planarity : 0.004 0.058 1784 Dihedral : 4.530 42.251 1359 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.46 % Allowed : 17.30 % Favored : 80.24 % 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: -0.49 (0.24), residues: 1210 helix: 0.33 (0.25), residues: 454 sheet: -1.29 (0.39), residues: 150 loop : -0.46 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 316 HIS 0.009 0.001 HIS A 494 PHE 0.015 0.001 PHE A 460 TYR 0.023 0.002 TYR B 516 ARG 0.007 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 355) hydrogen bonds : angle 4.76608 ( 978) SS BOND : bond 0.00132 ( 4) SS BOND : angle 0.37059 ( 8) covalent geometry : bond 0.00307 (10422) covalent geometry : angle 0.65280 (14132) *********************** 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 302 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 275 time to evaluate : 1.171 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: 0.7088 (m-30) cc_final: 0.6639 (m-30) REVERT: A 260 LYS cc_start: 0.9161 (mmtm) cc_final: 0.8819 (mmtm) REVERT: A 261 PHE cc_start: 0.6902 (m-80) cc_final: 0.5957 (m-80) REVERT: A 397 PHE cc_start: 0.8342 (m-10) cc_final: 0.7883 (m-80) REVERT: A 428 GLU cc_start: 0.8230 (pm20) cc_final: 0.7462 (pm20) REVERT: A 432 LYS cc_start: 0.8690 (ptpp) cc_final: 0.8069 (ptpp) REVERT: A 449 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6448 (mm-30) REVERT: A 493 LYS cc_start: 0.8298 (ptpt) cc_final: 0.7900 (ptpt) REVERT: A 515 ARG cc_start: 0.7992 (mpp80) cc_final: 0.7416 (mpp80) REVERT: A 535 TYR cc_start: 0.7963 (m-10) cc_final: 0.7084 (m-10) REVERT: A 559 MET cc_start: 0.6925 (ppp) cc_final: 0.6414 (ppp) REVERT: A 560 PHE cc_start: 0.6966 (t80) cc_final: 0.6704 (t80) REVERT: A 567 LEU cc_start: 0.8066 (tp) cc_final: 0.7724 (tp) REVERT: A 574 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: A 617 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8260 (mp) REVERT: A 619 MET cc_start: 0.7837 (tmm) cc_final: 0.7337 (tmm) REVERT: A 658 GLU cc_start: 0.7786 (pt0) cc_final: 0.7314 (pt0) REVERT: A 673 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.5788 (ttp-110) REVERT: A 691 GLN cc_start: 0.8321 (mm110) cc_final: 0.8019 (mm110) REVERT: A 735 GLN cc_start: 0.8727 (mt0) cc_final: 0.8310 (mt0) REVERT: B 179 GLU cc_start: 0.7638 (pt0) cc_final: 0.7008 (pt0) REVERT: B 223 MET cc_start: 0.6897 (tmm) cc_final: 0.6012 (tmm) REVERT: B 229 LYS cc_start: 0.8334 (tmtt) cc_final: 0.7906 (tmtt) REVERT: B 245 ILE cc_start: 0.8204 (mm) cc_final: 0.7950 (mm) REVERT: B 349 VAL cc_start: 0.6633 (m) cc_final: 0.6116 (p) REVERT: B 408 ASP cc_start: 0.7372 (t0) cc_final: 0.7039 (t0) REVERT: B 413 ARG cc_start: 0.7550 (ttm-80) cc_final: 0.7202 (ttm-80) REVERT: B 484 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7152 (mtt180) REVERT: B 489 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7764 (mm-30) REVERT: B 504 TYR cc_start: 0.7966 (t80) cc_final: 0.7510 (t80) REVERT: B 512 GLN cc_start: 0.8175 (mt0) cc_final: 0.7893 (mt0) REVERT: B 515 ARG cc_start: 0.8234 (ptp-110) cc_final: 0.7824 (ttm110) REVERT: B 547 ARG cc_start: 0.7848 (ptm160) cc_final: 0.7197 (ptm160) REVERT: B 559 MET cc_start: 0.5617 (ppp) cc_final: 0.5207 (ppp) REVERT: B 626 ARG cc_start: 0.6996 (tpp80) cc_final: 0.6682 (tpp80) REVERT: B 670 TYR cc_start: 0.5517 (m-80) cc_final: 0.5311 (m-80) REVERT: B 708 HIS cc_start: 0.6390 (t-90) cc_final: 0.5863 (t-90) outliers start: 27 outliers final: 21 residues processed: 287 average time/residue: 0.2753 time to fit residues: 104.3085 Evaluate side-chains 297 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 273 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 227 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 574 GLU 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 453 VAL Chi-restraints excluded: chain B residue 487 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: 0.9990 chunk 25 optimal weight: 7.9990 chunk 23 optimal weight: 0.0970 chunk 110 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 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 = 0.4618 r_free = 0.4618 target = 0.206339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.167326 restraints weight = 17888.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.173617 restraints weight = 10206.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.177848 restraints weight = 6886.675| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10426 Z= 0.139 Angle : 0.686 12.904 14140 Z= 0.336 Chirality : 0.045 0.263 1522 Planarity : 0.004 0.055 1784 Dihedral : 4.320 22.186 1356 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.64 % Allowed : 18.12 % Favored : 79.23 % 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: -0.48 (0.24), residues: 1210 helix: 0.24 (0.25), residues: 452 sheet: -1.09 (0.39), residues: 154 loop : -0.41 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 356 HIS 0.009 0.001 HIS A 494 PHE 0.026 0.001 PHE A 657 TYR 0.024 0.001 TYR B 516 ARG 0.007 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 355) hydrogen bonds : angle 4.76609 ( 978) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.48921 ( 8) covalent geometry : bond 0.00309 (10422) covalent geometry : angle 0.68643 (14132) *********************** 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 303 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 274 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: A 152 ASP cc_start: 0.7091 (m-30) cc_final: 0.6647 (m-30) REVERT: A 260 LYS cc_start: 0.9150 (mmtm) cc_final: 0.8832 (mmtm) REVERT: A 261 PHE cc_start: 0.6907 (m-80) cc_final: 0.5959 (m-80) REVERT: A 397 PHE cc_start: 0.8361 (m-10) cc_final: 0.7894 (m-80) REVERT: A 402 LEU cc_start: 0.7825 (mt) cc_final: 0.7555 (mp) REVERT: A 428 GLU cc_start: 0.8210 (pm20) cc_final: 0.7691 (pm20) REVERT: A 432 LYS cc_start: 0.8699 (ptpp) cc_final: 0.8250 (ptpp) REVERT: A 449 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6489 (mm-30) REVERT: A 450 ARG cc_start: 0.7625 (ttp-170) cc_final: 0.7412 (ttp-170) REVERT: A 493 LYS cc_start: 0.8297 (ptpt) cc_final: 0.7872 (ptpt) REVERT: A 515 ARG cc_start: 0.8011 (mpp80) cc_final: 0.7395 (mpp80) REVERT: A 559 MET cc_start: 0.6939 (ppp) cc_final: 0.6401 (ppp) REVERT: A 560 PHE cc_start: 0.6979 (t80) cc_final: 0.6722 (t80) REVERT: A 574 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6955 (tp30) REVERT: A 617 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8298 (mp) REVERT: A 619 MET cc_start: 0.7861 (tmm) cc_final: 0.7403 (tmm) REVERT: A 658 GLU cc_start: 0.7792 (pt0) cc_final: 0.7306 (pt0) REVERT: A 673 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.5989 (ttp-110) REVERT: A 691 GLN cc_start: 0.8344 (mm110) cc_final: 0.8031 (mm110) REVERT: A 735 GLN cc_start: 0.8682 (mt0) cc_final: 0.8309 (mt0) REVERT: B 179 GLU cc_start: 0.7585 (pt0) cc_final: 0.7023 (pt0) REVERT: B 223 MET cc_start: 0.6893 (tmm) cc_final: 0.5979 (tmm) REVERT: B 229 LYS cc_start: 0.8332 (tmtt) cc_final: 0.7863 (tmtt) REVERT: B 245 ILE cc_start: 0.8214 (mm) cc_final: 0.7983 (mm) REVERT: B 349 VAL cc_start: 0.6636 (m) cc_final: 0.6108 (p) REVERT: B 408 ASP cc_start: 0.7324 (t0) cc_final: 0.7025 (t0) REVERT: B 484 ARG cc_start: 0.7517 (mtt180) cc_final: 0.7218 (mtt180) REVERT: B 489 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7734 (mm-30) REVERT: B 504 TYR cc_start: 0.7891 (t80) cc_final: 0.7425 (t80) REVERT: B 512 GLN cc_start: 0.8115 (mt0) cc_final: 0.7852 (mt0) REVERT: B 515 ARG cc_start: 0.8232 (ptp-110) cc_final: 0.7804 (ttm110) REVERT: B 547 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7449 (ptm160) REVERT: B 559 MET cc_start: 0.5649 (ppp) cc_final: 0.5176 (ppp) REVERT: B 612 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7981 (mt-10) REVERT: B 703 MET cc_start: 0.4131 (mpp) cc_final: 0.3676 (mpp) REVERT: B 708 HIS cc_start: 0.6360 (t-90) cc_final: 0.5846 (t-90) outliers start: 29 outliers final: 23 residues processed: 285 average time/residue: 0.2650 time to fit residues: 99.9628 Evaluate side-chains 297 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 271 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 227 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 574 GLU 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 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 224 LYS Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 487 MET 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 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: 8.9990 chunk 13 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4605 r_free = 0.4605 target = 0.205254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.166924 restraints weight = 17784.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.173130 restraints weight = 10101.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.177358 restraints weight = 6772.009| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10426 Z= 0.160 Angle : 0.717 12.127 14140 Z= 0.349 Chirality : 0.046 0.288 1522 Planarity : 0.004 0.052 1784 Dihedral : 4.483 21.341 1356 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.91 % Allowed : 19.76 % Favored : 78.32 % 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: 0.13 (0.25), residues: 454 sheet: -1.11 (0.40), residues: 152 loop : -0.44 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 316 HIS 0.011 0.001 HIS A 494 PHE 0.027 0.001 PHE A 657 TYR 0.023 0.002 TYR B 516 ARG 0.011 0.001 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 355) hydrogen bonds : angle 4.84270 ( 978) SS BOND : bond 0.00169 ( 4) SS BOND : angle 0.53838 ( 8) covalent geometry : bond 0.00351 (10422) covalent geometry : angle 0.71707 (14132) *********************** 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 299 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 278 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: A 152 ASP cc_start: 0.7084 (m-30) cc_final: 0.6659 (m-30) REVERT: A 260 LYS cc_start: 0.9156 (mmtm) cc_final: 0.8866 (mmtm) REVERT: A 261 PHE cc_start: 0.6876 (m-80) cc_final: 0.5959 (m-80) REVERT: A 310 MET cc_start: 0.7202 (ppp) cc_final: 0.6753 (ppp) REVERT: A 397 PHE cc_start: 0.8386 (m-10) cc_final: 0.7883 (m-80) REVERT: A 399 ASN cc_start: 0.7978 (m-40) cc_final: 0.7635 (m-40) REVERT: A 402 LEU cc_start: 0.7868 (mt) cc_final: 0.7601 (mp) REVERT: A 428 GLU cc_start: 0.8255 (pm20) cc_final: 0.7789 (pm20) REVERT: A 432 LYS cc_start: 0.8759 (ptpp) cc_final: 0.8264 (ptpp) REVERT: A 449 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6532 (mm-30) REVERT: A 450 ARG cc_start: 0.7732 (ttp-170) cc_final: 0.7529 (ttp-170) REVERT: A 493 LYS cc_start: 0.8302 (ptpt) cc_final: 0.7848 (ptpt) REVERT: A 511 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6926 (mm-40) REVERT: A 515 ARG cc_start: 0.8039 (mpp80) cc_final: 0.7412 (mpp80) REVERT: A 535 TYR cc_start: 0.7995 (m-10) cc_final: 0.7322 (m-10) REVERT: A 559 MET cc_start: 0.6945 (ppp) cc_final: 0.6391 (ppp) REVERT: A 560 PHE cc_start: 0.6975 (t80) cc_final: 0.6716 (t80) REVERT: A 566 PHE cc_start: 0.7099 (m-80) cc_final: 0.6888 (m-80) REVERT: A 574 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6984 (tp30) REVERT: A 617 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8293 (mp) REVERT: A 619 MET cc_start: 0.7869 (tmm) cc_final: 0.7423 (tmm) REVERT: A 652 GLU cc_start: 0.7784 (mp0) cc_final: 0.7447 (mp0) REVERT: A 658 GLU cc_start: 0.7774 (pt0) cc_final: 0.7279 (pt0) REVERT: A 673 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.5926 (ttp-110) REVERT: A 691 GLN cc_start: 0.8329 (mm110) cc_final: 0.8018 (mm110) REVERT: A 692 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7369 (mt-10) REVERT: A 735 GLN cc_start: 0.8736 (mt0) cc_final: 0.8382 (mt0) REVERT: B 179 GLU cc_start: 0.7640 (pt0) cc_final: 0.7057 (pt0) REVERT: B 223 MET cc_start: 0.6908 (tmm) cc_final: 0.6058 (tmm) REVERT: B 245 ILE cc_start: 0.8244 (mm) cc_final: 0.8000 (mm) REVERT: B 349 VAL cc_start: 0.6670 (m) cc_final: 0.6147 (p) REVERT: B 381 TRP cc_start: 0.8002 (m100) cc_final: 0.7682 (m-90) REVERT: B 408 ASP cc_start: 0.7342 (t0) cc_final: 0.7049 (t0) REVERT: B 413 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7239 (ttm-80) REVERT: B 484 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7348 (mtt180) REVERT: B 489 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7747 (mm-30) REVERT: B 504 TYR cc_start: 0.7892 (t80) cc_final: 0.7356 (t80) REVERT: B 512 GLN cc_start: 0.8192 (mt0) cc_final: 0.7922 (mt0) REVERT: B 515 ARG cc_start: 0.8270 (ptp-110) cc_final: 0.7844 (ttm110) REVERT: B 547 ARG cc_start: 0.7893 (ptm160) cc_final: 0.7105 (ptm160) REVERT: B 559 MET cc_start: 0.5719 (ppp) cc_final: 0.5250 (ppp) REVERT: B 612 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7952 (mt-10) REVERT: B 626 ARG cc_start: 0.7010 (tpp80) cc_final: 0.6371 (ttm-80) REVERT: B 708 HIS cc_start: 0.6367 (t-90) cc_final: 0.5820 (t-90) outliers start: 21 outliers final: 18 residues processed: 284 average time/residue: 0.2871 time to fit residues: 108.2176 Evaluate side-chains 295 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 274 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 227 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 574 GLU 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 196 VAL Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 453 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 Chi-restraints excluded: chain B residue 738 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 0.0050 chunk 35 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 69 optimal weight: 0.0970 chunk 73 optimal weight: 0.0030 chunk 52 optimal weight: 1.9990 overall best weight: 0.4204 ------------------------------------------------------------------------------- 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 ** 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 = 0.4635 r_free = 0.4635 target = 0.207722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.169242 restraints weight = 17779.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.175575 restraints weight = 10157.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.179905 restraints weight = 6823.048| |-----------------------------------------------------------------------------| r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10426 Z= 0.120 Angle : 0.713 12.691 14140 Z= 0.343 Chirality : 0.045 0.320 1522 Planarity : 0.004 0.054 1784 Dihedral : 4.287 20.513 1356 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.91 % Allowed : 19.85 % Favored : 78.23 % 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: -0.34 (0.24), residues: 1210 helix: 0.26 (0.25), residues: 446 sheet: -0.99 (0.41), residues: 152 loop : -0.25 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 316 HIS 0.009 0.001 HIS A 494 PHE 0.024 0.001 PHE A 657 TYR 0.026 0.001 TYR B 516 ARG 0.007 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 355) hydrogen bonds : angle 4.72784 ( 978) SS BOND : bond 0.00104 ( 4) SS BOND : angle 0.55440 ( 8) covalent geometry : bond 0.00274 (10422) covalent geometry : angle 0.71299 (14132) ********************** 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 304 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 283 time to evaluate : 1.109 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: 0.7086 (m-30) cc_final: 0.6654 (m-30) REVERT: A 260 LYS cc_start: 0.9166 (mmtm) cc_final: 0.8907 (mmtm) REVERT: A 261 PHE cc_start: 0.6840 (m-80) cc_final: 0.5926 (m-80) REVERT: A 310 MET cc_start: 0.7102 (ppp) cc_final: 0.6748 (ppp) REVERT: A 397 PHE cc_start: 0.8364 (m-10) cc_final: 0.7859 (m-80) REVERT: A 399 ASN cc_start: 0.7975 (m-40) cc_final: 0.7564 (m-40) REVERT: A 402 LEU cc_start: 0.7771 (mt) cc_final: 0.7525 (mp) REVERT: A 428 GLU cc_start: 0.8224 (pm20) cc_final: 0.7757 (pm20) REVERT: A 432 LYS cc_start: 0.8727 (ptpp) cc_final: 0.8233 (ptpp) REVERT: A 449 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6531 (mm-30) REVERT: A 450 ARG cc_start: 0.7658 (ttp-170) cc_final: 0.7433 (ttp-170) REVERT: A 493 LYS cc_start: 0.8256 (ptpt) cc_final: 0.7796 (ptpt) REVERT: A 515 ARG cc_start: 0.8006 (mpp80) cc_final: 0.7380 (mpp80) REVERT: A 535 TYR cc_start: 0.7923 (m-10) cc_final: 0.7278 (m-10) REVERT: A 559 MET cc_start: 0.6941 (ppp) cc_final: 0.6401 (ppp) REVERT: A 560 PHE cc_start: 0.6934 (t80) cc_final: 0.6680 (t80) REVERT: A 574 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6948 (tp30) REVERT: A 617 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8286 (mp) REVERT: A 619 MET cc_start: 0.7860 (tmm) cc_final: 0.7417 (tmm) REVERT: A 650 ARG cc_start: 0.7639 (tmt170) cc_final: 0.6845 (tmt-80) REVERT: A 652 GLU cc_start: 0.7784 (mp0) cc_final: 0.7485 (mp0) REVERT: A 673 ARG cc_start: 0.6816 (OUTLIER) cc_final: 0.5968 (ttp-110) REVERT: A 691 GLN cc_start: 0.8339 (mm110) cc_final: 0.8039 (mm110) REVERT: A 692 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7313 (mt-10) REVERT: A 735 GLN cc_start: 0.8720 (mt0) cc_final: 0.8372 (mt0) REVERT: B 179 GLU cc_start: 0.7584 (pt0) cc_final: 0.6942 (pt0) REVERT: B 223 MET cc_start: 0.6847 (tmm) cc_final: 0.5950 (tmm) REVERT: B 349 VAL cc_start: 0.6567 (m) cc_final: 0.6049 (p) REVERT: B 408 ASP cc_start: 0.7246 (t0) cc_final: 0.6927 (t0) REVERT: B 489 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7722 (mm-30) REVERT: B 504 TYR cc_start: 0.7842 (t80) cc_final: 0.7372 (t80) REVERT: B 512 GLN cc_start: 0.8139 (mt0) cc_final: 0.7857 (mt0) REVERT: B 515 ARG cc_start: 0.8220 (ptp-110) cc_final: 0.7791 (ttm110) REVERT: B 552 LYS cc_start: 0.8194 (mtpp) cc_final: 0.7898 (mtpp) REVERT: B 559 MET cc_start: 0.5645 (ppp) cc_final: 0.5105 (ppp) REVERT: B 612 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 708 HIS cc_start: 0.6397 (t-90) cc_final: 0.5923 (t-90) outliers start: 21 outliers final: 15 residues processed: 291 average time/residue: 0.2703 time to fit residues: 104.5179 Evaluate side-chains 297 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 279 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 227 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 574 GLU 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 196 VAL Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 453 VAL 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: 2.9990 chunk 52 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 0.0670 overall best weight: 0.9722 ------------------------------------------------------------------------------- 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 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.205658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.167124 restraints weight = 17758.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.173250 restraints weight = 10183.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.177503 restraints weight = 6867.916| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10426 Z= 0.150 Angle : 0.719 13.174 14140 Z= 0.351 Chirality : 0.045 0.253 1522 Planarity : 0.004 0.051 1784 Dihedral : 4.429 30.124 1356 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.91 % Allowed : 20.40 % Favored : 77.69 % 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: -0.45 (0.24), residues: 1210 helix: 0.16 (0.25), residues: 456 sheet: -0.97 (0.39), residues: 164 loop : -0.31 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 316 HIS 0.010 0.001 HIS A 494 PHE 0.029 0.001 PHE A 513 TYR 0.052 0.002 TYR B 693 ARG 0.010 0.000 ARG B 450 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 355) hydrogen bonds : angle 4.82287 ( 978) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.49215 ( 8) covalent geometry : bond 0.00330 (10422) covalent geometry : angle 0.71907 (14132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4099.78 seconds wall clock time: 71 minutes 45.09 seconds (4305.09 seconds total)