Starting phenix.real_space_refine on Wed Feb 14 19:50:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui6_26540/02_2024/7ui6_26540.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui6_26540/02_2024/7ui6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui6_26540/02_2024/7ui6_26540.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui6_26540/02_2024/7ui6_26540.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui6_26540/02_2024/7ui6_26540.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui6_26540/02_2024/7ui6_26540.pdb" } 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 Residue "B TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.72, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 4.13 Conformation dependent library (CDL) restraints added in 1.8 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: 1.19 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: 3.05 Time building geometry restraints manager: 4.41 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: 96.39 - 103.95: 129 103.95 - 111.52: 4347 111.52 - 119.08: 4024 119.08 - 126.64: 5436 126.64 - 134.21: 196 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 2.520 nonbonded pdb=" O LYS A 748 " pdb=" OG1 THR A 751 " model vdw 2.124 2.440 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 2.520 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 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.920 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.230 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10422 Z= 0.297 Angle : 0.971 10.787 14132 Z= 0.546 Chirality : 0.057 0.284 1522 Planarity : 0.007 0.121 1784 Dihedral : 14.981 87.902 3822 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.79 % Favored : 94.96 % Rotamer: Outliers : 1.09 % Allowed : 2.91 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.23), residues: 1210 helix: -0.67 (0.24), residues: 424 sheet: -2.03 (0.39), residues: 154 loop : -0.93 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP B 679 HIS 0.011 0.002 HIS B 171 PHE 0.036 0.002 PHE A 734 TYR 0.038 0.002 TYR A 702 ARG 0.056 0.001 ARG A 673 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 290 time to evaluate : 1.136 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: 0.2739 time to fit residues: 107.0511 Evaluate side-chains 278 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 273 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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: 0.0770 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.2980 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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 532 HIS A 684 HIS ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS B 532 HIS ** B 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 10422 Z= 0.215 Angle : 0.660 11.613 14132 Z= 0.333 Chirality : 0.044 0.206 1522 Planarity : 0.005 0.109 1784 Dihedral : 5.017 55.277 1365 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.64 % Allowed : 10.20 % Favored : 88.16 % 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: -0.77 (0.24), residues: 1210 helix: 0.16 (0.25), residues: 440 sheet: -1.65 (0.39), residues: 150 loop : -0.60 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 316 HIS 0.011 0.001 HIS A 553 PHE 0.019 0.002 PHE B 338 TYR 0.017 0.002 TYR B 350 ARG 0.010 0.001 ARG A 673 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 272 time to evaluate : 1.232 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: 0.6904 (m-30) cc_final: 0.6370 (m-30) REVERT: A 260 LYS cc_start: 0.9051 (mmtm) cc_final: 0.8685 (mmtm) REVERT: A 261 PHE cc_start: 0.6891 (m-80) cc_final: 0.5946 (m-80) REVERT: A 397 PHE cc_start: 0.8384 (m-10) cc_final: 0.7953 (m-10) REVERT: A 428 GLU cc_start: 0.8016 (pm20) cc_final: 0.7587 (pm20) REVERT: A 432 LYS cc_start: 0.8510 (ptpp) cc_final: 0.7968 (ptpp) REVERT: A 472 THR cc_start: 0.6707 (p) cc_final: 0.6471 (t) REVERT: A 493 LYS cc_start: 0.8234 (ptpt) cc_final: 0.7796 (ptpt) REVERT: A 515 ARG cc_start: 0.7476 (mpp80) cc_final: 0.7097 (mpp80) REVERT: A 619 MET cc_start: 0.7363 (tmm) cc_final: 0.6976 (tmm) REVERT: A 691 GLN cc_start: 0.8126 (mm110) cc_final: 0.7874 (mm110) REVERT: A 732 GLU cc_start: 0.7915 (pt0) cc_final: 0.7662 (pt0) REVERT: A 738 MET cc_start: 0.7953 (ttt) cc_final: 0.7706 (ttt) REVERT: B 179 GLU cc_start: 0.7758 (pt0) cc_final: 0.7069 (pt0) REVERT: B 182 LEU cc_start: 0.8459 (mm) cc_final: 0.8251 (mm) REVERT: B 229 LYS cc_start: 0.8214 (tmtt) cc_final: 0.7618 (tmtt) REVERT: B 245 ILE cc_start: 0.8119 (mm) cc_final: 0.7769 (mm) REVERT: B 315 MET cc_start: 0.8420 (ptp) cc_final: 0.8119 (ptp) REVERT: B 349 VAL cc_start: 0.6330 (m) cc_final: 0.5865 (p) REVERT: B 407 TYR cc_start: 0.7359 (t80) cc_final: 0.6939 (t80) REVERT: B 489 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7985 (mm-30) REVERT: B 512 GLN cc_start: 0.8531 (mt0) cc_final: 0.8255 (mt0) REVERT: B 515 ARG cc_start: 0.8452 (ptp-110) cc_final: 0.7951 (ttp-110) REVERT: B 516 TYR cc_start: 0.8821 (t80) cc_final: 0.8615 (t80) REVERT: B 536 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7515 (mttm) REVERT: B 547 ARG cc_start: 0.8074 (ptm160) cc_final: 0.7616 (ptm160) REVERT: B 551 MET cc_start: 0.8148 (mmt) cc_final: 0.7944 (mmm) REVERT: B 559 MET cc_start: 0.5510 (ppp) cc_final: 0.4909 (ppp) REVERT: B 626 ARG cc_start: 0.7113 (tpp80) cc_final: 0.6640 (tpp80) REVERT: B 653 TRP cc_start: 0.7567 (t60) cc_final: 0.7097 (t60) outliers start: 18 outliers final: 11 residues processed: 281 average time/residue: 0.2739 time to fit residues: 101.3414 Evaluate side-chains 284 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 273 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 166 ASN Chi-restraints excluded: chain B residue 244 ASP 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 60 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 37 optimal weight: 0.0980 chunk 87 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 GLN A 684 HIS ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS ** B 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN B 708 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10422 Z= 0.198 Angle : 0.606 12.664 14132 Z= 0.305 Chirality : 0.043 0.194 1522 Planarity : 0.004 0.047 1784 Dihedral : 4.707 51.077 1360 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.82 % Allowed : 13.11 % Favored : 85.06 % 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: -0.53 (0.24), residues: 1210 helix: 0.44 (0.25), residues: 438 sheet: -1.25 (0.42), residues: 140 loop : -0.63 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 316 HIS 0.010 0.001 HIS A 163 PHE 0.021 0.002 PHE A 657 TYR 0.021 0.002 TYR A 516 ARG 0.006 0.001 ARG A 673 *********************** 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 299 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 279 time to evaluate : 1.217 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: 0.6959 (m-30) cc_final: 0.6429 (m-30) REVERT: A 260 LYS cc_start: 0.9130 (mmtm) cc_final: 0.8919 (mmtm) REVERT: A 261 PHE cc_start: 0.6874 (m-80) cc_final: 0.5904 (m-80) REVERT: A 397 PHE cc_start: 0.8416 (m-10) cc_final: 0.7956 (m-10) REVERT: A 432 LYS cc_start: 0.8571 (ptpp) cc_final: 0.8348 (pttp) REVERT: A 450 ARG cc_start: 0.7280 (tmm-80) cc_final: 0.7060 (ttp-170) REVERT: A 487 MET cc_start: 0.7667 (pmm) cc_final: 0.7467 (pmm) REVERT: A 493 LYS cc_start: 0.8216 (ptpt) cc_final: 0.7802 (ptpt) REVERT: A 515 ARG cc_start: 0.7444 (mpp80) cc_final: 0.7071 (mpp80) REVERT: A 559 MET cc_start: 0.6741 (ppp) cc_final: 0.6422 (ppp) REVERT: A 619 MET cc_start: 0.7528 (tmm) cc_final: 0.7192 (tmm) REVERT: A 657 PHE cc_start: 0.6132 (t80) cc_final: 0.5723 (t80) REVERT: A 732 GLU cc_start: 0.7880 (pt0) cc_final: 0.7621 (pt0) REVERT: B 175 ASP cc_start: 0.7275 (p0) cc_final: 0.6833 (p0) REVERT: B 179 GLU cc_start: 0.7735 (pt0) cc_final: 0.7085 (pt0) REVERT: B 197 ASP cc_start: 0.7492 (t0) cc_final: 0.7167 (t0) REVERT: B 223 MET cc_start: 0.6828 (tmm) cc_final: 0.6485 (tmm) REVERT: B 229 LYS cc_start: 0.8352 (tmtt) cc_final: 0.7928 (tmtt) REVERT: B 245 ILE cc_start: 0.8067 (mm) cc_final: 0.7687 (mm) REVERT: B 311 LYS cc_start: 0.8529 (tmmt) cc_final: 0.8240 (tmmt) REVERT: B 349 VAL cc_start: 0.6319 (m) cc_final: 0.5851 (p) REVERT: B 489 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8117 (mm-30) REVERT: B 512 GLN cc_start: 0.8525 (mt0) cc_final: 0.8219 (mt0) REVERT: B 515 ARG cc_start: 0.8483 (ptp-110) cc_final: 0.7933 (ttp-110) REVERT: B 536 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7651 (mmtp) REVERT: B 559 MET cc_start: 0.5382 (ppp) cc_final: 0.5056 (ppp) REVERT: B 572 LEU cc_start: 0.8643 (tp) cc_final: 0.8425 (tt) REVERT: B 653 TRP cc_start: 0.7561 (t60) cc_final: 0.6901 (t60) REVERT: B 740 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7283 (mtm-85) outliers start: 20 outliers final: 14 residues processed: 288 average time/residue: 0.2883 time to fit residues: 109.9461 Evaluate side-chains 283 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 269 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 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 689 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 188 THR 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 107 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 10422 Z= 0.408 Angle : 0.766 12.183 14132 Z= 0.398 Chirality : 0.049 0.211 1522 Planarity : 0.005 0.044 1784 Dihedral : 5.544 51.001 1360 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.28 % Allowed : 14.66 % Favored : 82.06 % 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: -1.06 (0.23), residues: 1210 helix: -0.01 (0.25), residues: 436 sheet: -1.76 (0.39), residues: 154 loop : -0.84 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 189 HIS 0.012 0.002 HIS A 457 PHE 0.024 0.002 PHE A 657 TYR 0.038 0.003 TYR B 350 ARG 0.010 0.001 ARG B 650 *********************** 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 311 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 275 time to evaluate : 1.034 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: 0.7083 (m-30) cc_final: 0.6633 (m-30) REVERT: A 182 LEU cc_start: 0.8878 (mt) cc_final: 0.8662 (mm) REVERT: A 261 PHE cc_start: 0.6967 (m-80) cc_final: 0.5993 (m-80) REVERT: A 397 PHE cc_start: 0.8468 (m-10) cc_final: 0.7972 (m-80) REVERT: A 432 LYS cc_start: 0.8746 (ptpp) cc_final: 0.8378 (ptpp) REVERT: A 450 ARG cc_start: 0.7492 (tmm-80) cc_final: 0.7229 (ttt180) REVERT: A 493 LYS cc_start: 0.8407 (ptpt) cc_final: 0.8030 (ptpt) REVERT: A 559 MET cc_start: 0.6760 (ppp) cc_final: 0.6368 (ppp) REVERT: A 560 PHE cc_start: 0.6985 (t80) cc_final: 0.6619 (t80) REVERT: A 567 LEU cc_start: 0.8406 (tp) cc_final: 0.8136 (tp) REVERT: A 619 MET cc_start: 0.7642 (tmm) cc_final: 0.7246 (tmm) REVERT: A 650 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7063 (tmt-80) REVERT: A 652 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: A 657 PHE cc_start: 0.6666 (t80) cc_final: 0.6316 (t80) REVERT: A 732 GLU cc_start: 0.8034 (pt0) cc_final: 0.7747 (pt0) REVERT: A 735 GLN cc_start: 0.8571 (mt0) cc_final: 0.8325 (mt0) REVERT: B 151 ARG cc_start: 0.8539 (ttm110) cc_final: 0.7964 (ttp80) REVERT: B 179 GLU cc_start: 0.7890 (pt0) cc_final: 0.7121 (pt0) REVERT: B 197 ASP cc_start: 0.7438 (t0) cc_final: 0.7129 (t0) REVERT: B 223 MET cc_start: 0.7213 (tmm) cc_final: 0.6900 (tmm) REVERT: B 245 ILE cc_start: 0.8087 (mm) cc_final: 0.7737 (mm) REVERT: B 300 ILE cc_start: 0.7573 (mm) cc_final: 0.7231 (mm) REVERT: B 311 LYS cc_start: 0.8832 (tmmt) cc_final: 0.8585 (tmmt) REVERT: B 349 VAL cc_start: 0.6664 (m) cc_final: 0.6153 (p) REVERT: B 453 VAL cc_start: 0.7899 (p) cc_final: 0.7678 (p) REVERT: B 486 GLN cc_start: 0.8101 (pm20) cc_final: 0.7571 (pm20) REVERT: B 489 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8350 (mm-30) REVERT: B 504 TYR cc_start: 0.8326 (t80) cc_final: 0.8009 (t80) REVERT: B 509 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7927 (mt-10) REVERT: B 532 HIS cc_start: 0.7627 (m90) cc_final: 0.7390 (m170) REVERT: B 534 VAL cc_start: 0.7872 (t) cc_final: 0.7331 (p) REVERT: B 547 ARG cc_start: 0.8323 (ptp-110) cc_final: 0.8117 (ptp-170) REVERT: B 551 MET cc_start: 0.8195 (mmt) cc_final: 0.7754 (mmm) REVERT: B 653 TRP cc_start: 0.8130 (t60) cc_final: 0.7576 (t60) REVERT: B 667 CYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7770 (p) outliers start: 36 outliers final: 19 residues processed: 290 average time/residue: 0.2699 time to fit residues: 103.5859 Evaluate side-chains 287 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 265 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 652 GLU 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 166 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 667 CYS 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 96 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 0.0470 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN ** B 285 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10422 Z= 0.183 Angle : 0.658 13.170 14132 Z= 0.322 Chirality : 0.043 0.192 1522 Planarity : 0.004 0.045 1784 Dihedral : 4.590 23.690 1356 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.01 % Allowed : 17.12 % Favored : 79.87 % 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: -0.72 (0.23), residues: 1210 helix: 0.28 (0.24), residues: 442 sheet: -1.24 (0.40), residues: 144 loop : -0.77 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 189 HIS 0.007 0.001 HIS A 163 PHE 0.022 0.001 PHE A 657 TYR 0.028 0.002 TYR B 407 ARG 0.007 0.000 ARG B 626 *********************** 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 306 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 273 time to evaluate : 1.143 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: 0.7045 (m-30) cc_final: 0.6584 (m-30) REVERT: A 190 MET cc_start: 0.6328 (mtp) cc_final: 0.6034 (mtp) REVERT: A 261 PHE cc_start: 0.6876 (m-80) cc_final: 0.6042 (m-80) REVERT: A 303 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6388 (mt) REVERT: A 356 TRP cc_start: 0.7732 (m100) cc_final: 0.7360 (m100) REVERT: A 397 PHE cc_start: 0.8421 (m-10) cc_final: 0.7925 (m-80) REVERT: A 428 GLU cc_start: 0.8222 (pm20) cc_final: 0.7631 (pm20) REVERT: A 431 GLN cc_start: 0.8259 (mm-40) cc_final: 0.8015 (mm-40) REVERT: A 432 LYS cc_start: 0.8627 (ptpp) cc_final: 0.8237 (ptpp) REVERT: A 493 LYS cc_start: 0.8294 (ptpt) cc_final: 0.7906 (ptpt) REVERT: A 535 TYR cc_start: 0.8200 (m-10) cc_final: 0.6515 (m-10) REVERT: A 547 ARG cc_start: 0.7973 (ttm170) cc_final: 0.7646 (tpp80) REVERT: A 559 MET cc_start: 0.6711 (ppp) cc_final: 0.6367 (ppp) REVERT: A 560 PHE cc_start: 0.6858 (t80) cc_final: 0.6540 (t80) REVERT: A 567 LEU cc_start: 0.8232 (tp) cc_final: 0.7789 (tp) REVERT: A 574 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6734 (tp30) REVERT: A 619 MET cc_start: 0.7621 (tmm) cc_final: 0.7406 (tmm) REVERT: A 650 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7023 (tmt-80) REVERT: A 652 GLU cc_start: 0.7912 (mp0) cc_final: 0.6976 (mp0) REVERT: A 663 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.6992 (t) REVERT: A 673 ARG cc_start: 0.6604 (ptp90) cc_final: 0.6011 (mtm110) REVERT: A 735 GLN cc_start: 0.8475 (mt0) cc_final: 0.8271 (mt0) REVERT: B 151 ARG cc_start: 0.8620 (ttm110) cc_final: 0.7890 (ttp-110) REVERT: B 173 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6290 (tt) REVERT: B 175 ASP cc_start: 0.7186 (p0) cc_final: 0.6459 (p0) REVERT: B 179 GLU cc_start: 0.7732 (pt0) cc_final: 0.6969 (pt0) REVERT: B 182 LEU cc_start: 0.8480 (mm) cc_final: 0.8258 (mm) REVERT: B 197 ASP cc_start: 0.7345 (t0) cc_final: 0.7089 (t0) REVERT: B 245 ILE cc_start: 0.8050 (mm) cc_final: 0.7693 (mm) REVERT: B 311 LYS cc_start: 0.8645 (tmmt) cc_final: 0.8400 (tmmt) REVERT: B 349 VAL cc_start: 0.6409 (m) cc_final: 0.5915 (p) REVERT: B 476 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6462 (mp) REVERT: B 486 GLN cc_start: 0.7997 (pm20) cc_final: 0.7452 (pm20) REVERT: B 489 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8320 (mm-30) REVERT: B 504 TYR cc_start: 0.8257 (t80) cc_final: 0.7497 (t80) REVERT: B 509 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7633 (mt-10) REVERT: B 547 ARG cc_start: 0.8273 (ptp-110) cc_final: 0.7872 (ptp-170) REVERT: B 551 MET cc_start: 0.7952 (mmt) cc_final: 0.7737 (tpp) REVERT: B 569 MET cc_start: 0.7818 (mpp) cc_final: 0.7608 (mtm) REVERT: B 613 LEU cc_start: 0.8572 (tt) cc_final: 0.8354 (tp) REVERT: B 653 TRP cc_start: 0.7913 (t60) cc_final: 0.7173 (t60) outliers start: 33 outliers final: 16 residues processed: 292 average time/residue: 0.2747 time to fit residues: 106.1019 Evaluate side-chains 290 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 268 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 663 VAL 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 166 ASN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 637 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 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** B 684 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10422 Z= 0.248 Angle : 0.695 13.916 14132 Z= 0.342 Chirality : 0.044 0.182 1522 Planarity : 0.004 0.046 1784 Dihedral : 4.728 22.827 1356 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.46 % Allowed : 17.94 % Favored : 78.60 % 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: -0.69 (0.24), residues: 1210 helix: 0.30 (0.25), residues: 440 sheet: -1.39 (0.38), residues: 150 loop : -0.69 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 189 HIS 0.008 0.001 HIS B 171 PHE 0.021 0.002 PHE A 460 TYR 0.028 0.002 TYR B 407 ARG 0.009 0.001 ARG B 455 *********************** 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 306 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 268 time to evaluate : 1.113 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: 0.7028 (m-30) cc_final: 0.6580 (m-30) REVERT: A 190 MET cc_start: 0.6357 (mtp) cc_final: 0.6011 (mtp) REVERT: A 261 PHE cc_start: 0.6923 (m-80) cc_final: 0.6027 (m-80) REVERT: A 303 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6415 (mt) REVERT: A 356 TRP cc_start: 0.7814 (m100) cc_final: 0.7609 (m100) REVERT: A 397 PHE cc_start: 0.8446 (m-10) cc_final: 0.7976 (m-80) REVERT: A 428 GLU cc_start: 0.8285 (pm20) cc_final: 0.7582 (pm20) REVERT: A 432 LYS cc_start: 0.8643 (ptpp) cc_final: 0.8227 (ptpp) REVERT: A 450 ARG cc_start: 0.7431 (tmm-80) cc_final: 0.7214 (tmm-80) REVERT: A 493 LYS cc_start: 0.8349 (ptpt) cc_final: 0.7889 (ptpt) REVERT: A 547 ARG cc_start: 0.8084 (ttm170) cc_final: 0.7711 (tpp80) REVERT: A 559 MET cc_start: 0.6732 (ppp) cc_final: 0.6338 (ppp) REVERT: A 560 PHE cc_start: 0.6905 (t80) cc_final: 0.6594 (t80) REVERT: A 574 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6864 (tp30) REVERT: A 619 MET cc_start: 0.7665 (tmm) cc_final: 0.7258 (tmm) REVERT: A 650 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7021 (tmt170) REVERT: A 652 GLU cc_start: 0.7916 (mp0) cc_final: 0.6967 (mp0) REVERT: A 657 PHE cc_start: 0.6464 (t80) cc_final: 0.6196 (t80) REVERT: A 663 VAL cc_start: 0.7305 (OUTLIER) cc_final: 0.7087 (t) REVERT: A 673 ARG cc_start: 0.6782 (ptp90) cc_final: 0.6422 (mtm110) REVERT: A 735 GLN cc_start: 0.8522 (mt0) cc_final: 0.8298 (mt0) REVERT: B 173 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6357 (tt) REVERT: B 179 GLU cc_start: 0.7743 (pt0) cc_final: 0.6951 (pt0) REVERT: B 197 ASP cc_start: 0.7345 (t0) cc_final: 0.7136 (t0) REVERT: B 223 MET cc_start: 0.7136 (tmm) cc_final: 0.6771 (tmm) REVERT: B 245 ILE cc_start: 0.8043 (mm) cc_final: 0.7716 (mm) REVERT: B 300 ILE cc_start: 0.7465 (mm) cc_final: 0.7262 (mm) REVERT: B 311 LYS cc_start: 0.8750 (tmmt) cc_final: 0.8486 (tmmt) REVERT: B 349 VAL cc_start: 0.6483 (m) cc_final: 0.5999 (p) REVERT: B 484 ARG cc_start: 0.8028 (mtt180) cc_final: 0.7604 (mtt180) REVERT: B 486 GLN cc_start: 0.8040 (pm20) cc_final: 0.7515 (pm20) REVERT: B 489 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8256 (mm-30) REVERT: B 504 TYR cc_start: 0.8231 (t80) cc_final: 0.7560 (t80) REVERT: B 509 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7744 (mt-10) REVERT: B 515 ARG cc_start: 0.8534 (ptp-110) cc_final: 0.8160 (ttm110) REVERT: B 547 ARG cc_start: 0.8353 (ptp-110) cc_final: 0.8003 (ptp-170) REVERT: B 569 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7649 (mtm) REVERT: B 613 LEU cc_start: 0.8525 (tt) cc_final: 0.8293 (tp) REVERT: B 653 TRP cc_start: 0.8069 (t60) cc_final: 0.7255 (t60) outliers start: 38 outliers final: 26 residues processed: 284 average time/residue: 0.3145 time to fit residues: 119.1207 Evaluate side-chains 298 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 266 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 650 ARG Chi-restraints excluded: chain A residue 663 VAL 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 173 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 597 PHE Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 658 GLU 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 111 optimal weight: 0.0770 chunk 13 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 0.0270 chunk 97 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10422 Z= 0.184 Angle : 0.691 13.933 14132 Z= 0.335 Chirality : 0.044 0.249 1522 Planarity : 0.004 0.043 1784 Dihedral : 4.458 22.617 1356 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.10 % Allowed : 19.40 % Favored : 77.50 % 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: -0.60 (0.24), residues: 1210 helix: 0.32 (0.25), residues: 446 sheet: -1.37 (0.36), residues: 170 loop : -0.53 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 316 HIS 0.011 0.001 HIS A 494 PHE 0.015 0.001 PHE A 657 TYR 0.024 0.002 TYR B 516 ARG 0.007 0.000 ARG B 455 *********************** 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 fitting. rotamer outliers: 34 poor density : 268 time to evaluate : 1.218 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: A 152 ASP cc_start: 0.7065 (m-30) cc_final: 0.6648 (m-30) REVERT: A 190 MET cc_start: 0.6275 (mtp) cc_final: 0.6047 (mtt) REVERT: A 260 LYS cc_start: 0.9185 (mmtm) cc_final: 0.8708 (mmtm) REVERT: A 261 PHE cc_start: 0.6923 (m-80) cc_final: 0.5983 (m-80) REVERT: A 356 TRP cc_start: 0.7806 (m100) cc_final: 0.7481 (m100) REVERT: A 397 PHE cc_start: 0.8419 (m-10) cc_final: 0.7939 (m-80) REVERT: A 399 ASN cc_start: 0.7717 (m-40) cc_final: 0.7353 (m-40) REVERT: A 428 GLU cc_start: 0.8174 (pm20) cc_final: 0.7403 (pm20) REVERT: A 432 LYS cc_start: 0.8582 (ptpp) cc_final: 0.8143 (ptpp) REVERT: A 450 ARG cc_start: 0.7347 (tmm-80) cc_final: 0.6668 (tmm-80) REVERT: A 493 LYS cc_start: 0.8258 (ptpt) cc_final: 0.7862 (ptpt) REVERT: A 535 TYR cc_start: 0.8118 (m-10) cc_final: 0.7134 (m-10) REVERT: A 547 ARG cc_start: 0.8009 (ttm170) cc_final: 0.7638 (tpp80) REVERT: A 559 MET cc_start: 0.6715 (ppp) cc_final: 0.6365 (ppp) REVERT: A 560 PHE cc_start: 0.6847 (t80) cc_final: 0.6517 (t80) REVERT: A 619 MET cc_start: 0.7659 (tmm) cc_final: 0.7289 (tmm) REVERT: A 650 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7029 (tmt170) REVERT: A 652 GLU cc_start: 0.7902 (mp0) cc_final: 0.7016 (mp0) REVERT: A 657 PHE cc_start: 0.6356 (t80) cc_final: 0.6090 (t80) REVERT: A 673 ARG cc_start: 0.6800 (ptp90) cc_final: 0.6393 (mtm110) REVERT: A 735 GLN cc_start: 0.8470 (mt0) cc_final: 0.8260 (mt0) REVERT: B 173 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6281 (tt) REVERT: B 179 GLU cc_start: 0.7709 (pt0) cc_final: 0.6934 (pt0) REVERT: B 197 ASP cc_start: 0.7277 (t0) cc_final: 0.7066 (t0) REVERT: B 223 MET cc_start: 0.7101 (tmm) cc_final: 0.6740 (tmm) REVERT: B 245 ILE cc_start: 0.8000 (mm) cc_final: 0.7737 (mm) REVERT: B 311 LYS cc_start: 0.8685 (tmmt) cc_final: 0.8425 (tmmt) REVERT: B 349 VAL cc_start: 0.6418 (m) cc_final: 0.5955 (p) REVERT: B 408 ASP cc_start: 0.7402 (t0) cc_final: 0.7037 (t0) REVERT: B 484 ARG cc_start: 0.7908 (mtt180) cc_final: 0.7514 (mtt180) REVERT: B 486 GLN cc_start: 0.7982 (pm20) cc_final: 0.7469 (pm20) REVERT: B 489 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8037 (mm-30) REVERT: B 504 TYR cc_start: 0.8183 (t80) cc_final: 0.7536 (t80) REVERT: B 509 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 515 ARG cc_start: 0.8495 (ptp-110) cc_final: 0.8120 (ttm110) REVERT: B 569 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7523 (mtm) REVERT: B 653 TRP cc_start: 0.7956 (t60) cc_final: 0.7101 (t60) outliers start: 34 outliers final: 24 residues processed: 283 average time/residue: 0.2639 time to fit residues: 99.2470 Evaluate side-chains 294 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 267 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 THR 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 173 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 637 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10422 Z= 0.228 Angle : 0.702 14.162 14132 Z= 0.345 Chirality : 0.044 0.186 1522 Planarity : 0.004 0.043 1784 Dihedral : 4.649 30.425 1356 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.46 % Allowed : 19.13 % Favored : 77.41 % 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: -0.52 (0.24), residues: 1210 helix: 0.40 (0.25), residues: 434 sheet: -1.26 (0.37), residues: 170 loop : -0.52 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 316 HIS 0.011 0.001 HIS A 494 PHE 0.020 0.001 PHE B 625 TYR 0.047 0.002 TYR B 693 ARG 0.006 0.001 ARG B 455 *********************** 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 fitting. rotamer outliers: 38 poor density : 265 time to evaluate : 1.169 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: 0.7115 (m-30) cc_final: 0.6678 (m-30) REVERT: A 190 MET cc_start: 0.6321 (mtp) cc_final: 0.5999 (mtp) REVERT: A 261 PHE cc_start: 0.6862 (m-80) cc_final: 0.6054 (m-80) REVERT: A 356 TRP cc_start: 0.7742 (m100) cc_final: 0.7494 (m100) REVERT: A 397 PHE cc_start: 0.8406 (m-10) cc_final: 0.7924 (m-80) REVERT: A 399 ASN cc_start: 0.7724 (m-40) cc_final: 0.7354 (m-40) REVERT: A 428 GLU cc_start: 0.8212 (pm20) cc_final: 0.7296 (pm20) REVERT: A 432 LYS cc_start: 0.8586 (ptpp) cc_final: 0.8084 (ptpp) REVERT: A 450 ARG cc_start: 0.7438 (tmm-80) cc_final: 0.7145 (ttt180) REVERT: A 493 LYS cc_start: 0.8299 (ptpt) cc_final: 0.7885 (ptpt) REVERT: A 495 TRP cc_start: 0.5306 (OUTLIER) cc_final: 0.4841 (t60) REVERT: A 511 GLN cc_start: 0.7052 (mm-40) cc_final: 0.6775 (mm-40) REVERT: A 535 TYR cc_start: 0.8136 (m-10) cc_final: 0.7140 (m-10) REVERT: A 547 ARG cc_start: 0.8055 (ttm170) cc_final: 0.7680 (tpp80) REVERT: A 559 MET cc_start: 0.6707 (ppp) cc_final: 0.6336 (ppp) REVERT: A 560 PHE cc_start: 0.6823 (t80) cc_final: 0.6511 (t80) REVERT: A 574 GLU cc_start: 0.7425 (tp30) cc_final: 0.6918 (tp30) REVERT: A 619 MET cc_start: 0.7708 (tmm) cc_final: 0.7369 (tmm) REVERT: A 650 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7080 (tmt170) REVERT: A 652 GLU cc_start: 0.7945 (mp0) cc_final: 0.7121 (mp0) REVERT: A 657 PHE cc_start: 0.6416 (t80) cc_final: 0.6139 (t80) REVERT: A 673 ARG cc_start: 0.6831 (ptp90) cc_final: 0.5874 (ttp-170) REVERT: A 735 GLN cc_start: 0.8518 (mt0) cc_final: 0.8309 (mt0) REVERT: B 173 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6311 (tt) REVERT: B 179 GLU cc_start: 0.7804 (pt0) cc_final: 0.7050 (pt0) REVERT: B 197 ASP cc_start: 0.7301 (t0) cc_final: 0.7093 (t0) REVERT: B 223 MET cc_start: 0.7093 (tmm) cc_final: 0.6773 (tmm) REVERT: B 245 ILE cc_start: 0.8010 (mm) cc_final: 0.7757 (mm) REVERT: B 311 LYS cc_start: 0.8734 (tmmt) cc_final: 0.8271 (tmmt) REVERT: B 315 MET cc_start: 0.8311 (ptp) cc_final: 0.7908 (ptp) REVERT: B 345 ASN cc_start: 0.8624 (m-40) cc_final: 0.8408 (m110) REVERT: B 408 ASP cc_start: 0.7432 (t0) cc_final: 0.7049 (t0) REVERT: B 504 TYR cc_start: 0.8202 (t80) cc_final: 0.7496 (t80) REVERT: B 509 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7671 (mt-10) REVERT: B 511 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7797 (mm-40) REVERT: B 515 ARG cc_start: 0.8502 (ptp-110) cc_final: 0.8129 (ttm110) REVERT: B 532 HIS cc_start: 0.7489 (m-70) cc_final: 0.7139 (m-70) REVERT: B 547 ARG cc_start: 0.8446 (ptp-170) cc_final: 0.8170 (ptp-170) REVERT: B 613 LEU cc_start: 0.8446 (tt) cc_final: 0.8134 (tp) outliers start: 38 outliers final: 30 residues processed: 281 average time/residue: 0.2714 time to fit residues: 101.4301 Evaluate side-chains 296 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 263 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 THR 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 B residue 154 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 189 TRP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 658 GLU Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 689 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 113 optimal weight: 0.0970 chunk 69 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10422 Z= 0.188 Angle : 0.701 14.473 14132 Z= 0.340 Chirality : 0.044 0.237 1522 Planarity : 0.004 0.039 1784 Dihedral : 4.490 28.582 1356 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.28 % Allowed : 19.31 % Favored : 77.41 % 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: 0.41 (0.25), residues: 434 sheet: -1.27 (0.37), residues: 176 loop : -0.46 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 316 HIS 0.010 0.001 HIS A 494 PHE 0.021 0.001 PHE B 625 TYR 0.044 0.001 TYR B 693 ARG 0.006 0.000 ARG A 398 *********************** 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 309 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 273 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7085 (m-30) cc_final: 0.6664 (m-30) REVERT: A 260 LYS cc_start: 0.9191 (mmtm) cc_final: 0.8720 (mmtm) REVERT: A 261 PHE cc_start: 0.6830 (m-80) cc_final: 0.6029 (m-80) REVERT: A 356 TRP cc_start: 0.7755 (m100) cc_final: 0.7543 (m100) REVERT: A 397 PHE cc_start: 0.8392 (m-10) cc_final: 0.7905 (m-80) REVERT: A 399 ASN cc_start: 0.7731 (m-40) cc_final: 0.7384 (m-40) REVERT: A 428 GLU cc_start: 0.8169 (pm20) cc_final: 0.7210 (pm20) REVERT: A 432 LYS cc_start: 0.8555 (ptpp) cc_final: 0.8043 (ptpp) REVERT: A 450 ARG cc_start: 0.7382 (tmm-80) cc_final: 0.7061 (ttt180) REVERT: A 493 LYS cc_start: 0.8294 (ptpt) cc_final: 0.7888 (ptpt) REVERT: A 495 TRP cc_start: 0.5237 (OUTLIER) cc_final: 0.4791 (t60) REVERT: A 511 GLN cc_start: 0.7003 (mm-40) cc_final: 0.6737 (mm-40) REVERT: A 535 TYR cc_start: 0.8072 (m-10) cc_final: 0.6986 (m-10) REVERT: A 547 ARG cc_start: 0.8005 (ttm170) cc_final: 0.7631 (tpp80) REVERT: A 559 MET cc_start: 0.6764 (ppp) cc_final: 0.6394 (ppp) REVERT: A 560 PHE cc_start: 0.6798 (t80) cc_final: 0.6471 (t80) REVERT: A 578 LYS cc_start: 0.7269 (mmtt) cc_final: 0.7064 (mmtm) REVERT: A 619 MET cc_start: 0.7715 (tmm) cc_final: 0.7391 (tmm) REVERT: A 642 TRP cc_start: 0.8548 (t60) cc_final: 0.7655 (t60) REVERT: A 650 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7079 (tmt170) REVERT: A 652 GLU cc_start: 0.7917 (mp0) cc_final: 0.7068 (mp0) REVERT: A 673 ARG cc_start: 0.6806 (ptp90) cc_final: 0.5817 (ttp-110) REVERT: B 151 ARG cc_start: 0.8609 (ttm110) cc_final: 0.7875 (mtm110) REVERT: B 173 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6274 (tt) REVERT: B 179 GLU cc_start: 0.7802 (pt0) cc_final: 0.7034 (pt0) REVERT: B 197 ASP cc_start: 0.7267 (t0) cc_final: 0.7064 (t0) REVERT: B 223 MET cc_start: 0.7055 (tmm) cc_final: 0.6740 (tmm) REVERT: B 245 ILE cc_start: 0.7975 (mm) cc_final: 0.7767 (mm) REVERT: B 311 LYS cc_start: 0.8678 (tmmt) cc_final: 0.8240 (tmmt) REVERT: B 315 MET cc_start: 0.8321 (ptp) cc_final: 0.7906 (ptp) REVERT: B 345 ASN cc_start: 0.8466 (m-40) cc_final: 0.8261 (m-40) REVERT: B 346 PRO cc_start: 0.8628 (Cg_endo) cc_final: 0.8418 (Cg_exo) REVERT: B 347 PHE cc_start: 0.7696 (p90) cc_final: 0.7050 (p90) REVERT: B 349 VAL cc_start: 0.6339 (m) cc_final: 0.5925 (p) REVERT: B 408 ASP cc_start: 0.7380 (t0) cc_final: 0.7040 (t0) REVERT: B 414 ARG cc_start: 0.8255 (tpm170) cc_final: 0.7940 (tpm170) REVERT: B 504 TYR cc_start: 0.8171 (t80) cc_final: 0.7514 (t80) REVERT: B 509 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7597 (mt-10) REVERT: B 511 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7764 (mm-40) REVERT: B 569 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7485 (mtm) REVERT: B 613 LEU cc_start: 0.8379 (tt) cc_final: 0.8115 (tp) REVERT: B 703 MET cc_start: 0.4626 (mpp) cc_final: 0.4419 (mpp) REVERT: B 740 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.7196 (mtm-85) outliers start: 36 outliers final: 30 residues processed: 290 average time/residue: 0.2796 time to fit residues: 106.5170 Evaluate side-chains 300 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 266 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 THR 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 B residue 154 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 189 TRP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 658 GLU Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 689 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 0.0970 chunk 101 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10422 Z= 0.188 Angle : 0.708 14.378 14132 Z= 0.345 Chirality : 0.045 0.297 1522 Planarity : 0.004 0.039 1784 Dihedral : 4.461 28.595 1356 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.37 % Allowed : 19.67 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.24), residues: 1210 helix: 0.42 (0.25), residues: 434 sheet: -1.16 (0.38), residues: 174 loop : -0.43 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 316 HIS 0.010 0.001 HIS A 494 PHE 0.026 0.001 PHE A 657 TYR 0.025 0.001 TYR B 516 ARG 0.007 0.000 ARG B 626 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 266 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7097 (m-30) cc_final: 0.6670 (m-30) REVERT: A 260 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8721 (mmtm) REVERT: A 261 PHE cc_start: 0.6824 (m-80) cc_final: 0.6007 (m-80) REVERT: A 310 MET cc_start: 0.7325 (ppp) cc_final: 0.7019 (ppp) REVERT: A 356 TRP cc_start: 0.7783 (m100) cc_final: 0.7562 (m100) REVERT: A 397 PHE cc_start: 0.8378 (m-10) cc_final: 0.7869 (m-80) REVERT: A 399 ASN cc_start: 0.7757 (m-40) cc_final: 0.7407 (m-40) REVERT: A 428 GLU cc_start: 0.8095 (pm20) cc_final: 0.7086 (pm20) REVERT: A 432 LYS cc_start: 0.8552 (ptpp) cc_final: 0.7933 (ptpp) REVERT: A 450 ARG cc_start: 0.7395 (tmm-80) cc_final: 0.7088 (ttt180) REVERT: A 493 LYS cc_start: 0.8291 (ptpt) cc_final: 0.7877 (ptpt) REVERT: A 495 TRP cc_start: 0.5241 (OUTLIER) cc_final: 0.4869 (t60) REVERT: A 501 LEU cc_start: 0.7503 (mt) cc_final: 0.7194 (mt) REVERT: A 511 GLN cc_start: 0.6970 (mm-40) cc_final: 0.6732 (mm-40) REVERT: A 535 TYR cc_start: 0.8027 (m-10) cc_final: 0.6942 (m-10) REVERT: A 547 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7629 (tpp80) REVERT: A 559 MET cc_start: 0.6750 (ppp) cc_final: 0.6372 (ppp) REVERT: A 560 PHE cc_start: 0.6765 (t80) cc_final: 0.6460 (t80) REVERT: A 578 LYS cc_start: 0.7248 (mmtt) cc_final: 0.7023 (mmtm) REVERT: A 619 MET cc_start: 0.7735 (tmm) cc_final: 0.7405 (tmm) REVERT: A 642 TRP cc_start: 0.8515 (t60) cc_final: 0.7568 (t60) REVERT: A 650 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7103 (tmt170) REVERT: A 652 GLU cc_start: 0.7918 (mp0) cc_final: 0.7164 (mp0) REVERT: A 673 ARG cc_start: 0.6845 (ptp90) cc_final: 0.5887 (ttp-110) REVERT: A 731 LYS cc_start: 0.8464 (tttt) cc_final: 0.8222 (tttt) REVERT: B 173 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6240 (tt) REVERT: B 179 GLU cc_start: 0.7794 (pt0) cc_final: 0.7031 (pt0) REVERT: B 223 MET cc_start: 0.7034 (tmm) cc_final: 0.6730 (tmm) REVERT: B 273 GLN cc_start: 0.7333 (mm-40) cc_final: 0.7024 (mp10) REVERT: B 311 LYS cc_start: 0.8685 (tmmt) cc_final: 0.8234 (tmmt) REVERT: B 315 MET cc_start: 0.8360 (ptp) cc_final: 0.7998 (ptp) REVERT: B 345 ASN cc_start: 0.8402 (m-40) cc_final: 0.8102 (m-40) REVERT: B 347 PHE cc_start: 0.7657 (p90) cc_final: 0.6898 (p90) REVERT: B 349 VAL cc_start: 0.6364 (m) cc_final: 0.5952 (p) REVERT: B 408 ASP cc_start: 0.7384 (t0) cc_final: 0.7065 (t0) REVERT: B 504 TYR cc_start: 0.8175 (t80) cc_final: 0.7485 (t80) REVERT: B 509 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7628 (mt-10) REVERT: B 532 HIS cc_start: 0.7513 (m-70) cc_final: 0.7171 (m-70) REVERT: B 539 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7529 (mm-40) REVERT: B 547 ARG cc_start: 0.8357 (ptp-170) cc_final: 0.7949 (ptp-170) REVERT: B 569 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7502 (mtm) REVERT: B 613 LEU cc_start: 0.8384 (tt) cc_final: 0.8132 (tp) REVERT: B 703 MET cc_start: 0.4440 (mpp) cc_final: 0.4238 (mpp) outliers start: 37 outliers final: 30 residues processed: 283 average time/residue: 0.2633 time to fit residues: 98.9304 Evaluate side-chains 297 residues out of total 1098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 263 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 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 244 ASP Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 PHE Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 588 THR 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 B residue 154 VAL Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 189 TRP Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 637 THR Chi-restraints excluded: chain B residue 658 GLU Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 687 GLU Chi-restraints excluded: chain B residue 689 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 4.9990 chunk 14 optimal weight: 50.0000 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 chunk 83 optimal weight: 6.9990 chunk 5 optimal weight: 0.0060 chunk 68 optimal weight: 0.9980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.204879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.167386 restraints weight = 17499.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.173314 restraints weight = 10192.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.177418 restraints weight = 6894.450| |-----------------------------------------------------------------------------| r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10422 Z= 0.177 Angle : 0.697 13.962 14132 Z= 0.343 Chirality : 0.044 0.301 1522 Planarity : 0.004 0.038 1784 Dihedral : 4.398 29.913 1356 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.91 % Allowed : 20.13 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.24), residues: 1210 helix: 0.38 (0.25), residues: 434 sheet: -1.07 (0.38), residues: 176 loop : -0.44 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 316 HIS 0.009 0.001 HIS A 494 PHE 0.028 0.001 PHE A 657 TYR 0.036 0.001 TYR B 693 ARG 0.011 0.000 ARG B 740 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2726.00 seconds wall clock time: 49 minutes 55.68 seconds (2995.68 seconds total)