Starting phenix.real_space_refine on Thu Feb 15 02:43:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml7_23909/02_2024/7ml7_23909_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml7_23909/02_2024/7ml7_23909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml7_23909/02_2024/7ml7_23909.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml7_23909/02_2024/7ml7_23909.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml7_23909/02_2024/7ml7_23909_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ml7_23909/02_2024/7ml7_23909_neut.pdb" } resolution = 3.17 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= 0.000 sd= 1.000 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 Zn 1 6.06 5 S 38 5.16 5 C 6939 2.51 5 N 1756 2.21 5 O 2179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 44": "OE1" <-> "OE2" Residue "A ASP 61": "OD1" <-> "OD2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ASP 550": "OD1" <-> "OD2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ARG 643": "NH1" <-> "NH2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A GLU 823": "OE1" <-> "OE2" Residue "A ASP 833": "OD1" <-> "OD2" Residue "A GLU 858": "OE1" <-> "OE2" Residue "A GLU 1547": "OE1" <-> "OE2" Residue "A GLU 1559": "OE1" <-> "OE2" Residue "A GLU 1586": "OE1" <-> "OE2" Residue "A GLU 1642": "OE1" <-> "OE2" Residue "A GLU 1727": "OE1" <-> "OE2" Residue "A ASP 1773": "OD1" <-> "OD2" Residue "A ASP 1789": "OD1" <-> "OD2" Residue "A ASP 1840": "OD1" <-> "OD2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B ARG 505": "NH1" <-> "NH2" 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: 10913 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1216, 9834 Classifications: {'peptide': 1216} Link IDs: {'PTRANS': 30, 'TRANS': 1185} Chain breaks: 4 Chain: "B" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1078 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 13, 'TRANS': 124} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5665 SG CYS A 698 36.136 30.307 50.792 1.00 58.86 S Time building chain proxies: 6.04, per 1000 atoms: 0.55 Number of scatterers: 10913 At special positions: 0 Unit cell: (95.865, 112.05, 130.725, 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) Zn 1 29.99 S 38 16.00 O 2179 8.00 N 1756 7.00 C 6939 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 533 " 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: 4.26 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 757 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 698 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 653 " 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2594 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 17 sheets defined 40.3% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 41 through 63 Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.958A pdb=" N LYS A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.726A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 155 Processing helix chain 'A' and resid 167 through 197 removed outlier: 3.689A pdb=" N ARG A 173 " --> pdb=" O ASN A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 213 Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.608A pdb=" N ASN A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.699A pdb=" N TYR A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 280 removed outlier: 4.084A pdb=" N ILE A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.800A pdb=" N LEU A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU A 318 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.666A pdb=" N TYR A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 removed outlier: 3.576A pdb=" N MET A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.722A pdb=" N GLN A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.583A pdb=" N GLU A 358 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 409 removed outlier: 3.718A pdb=" N ASN A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 removed outlier: 3.675A pdb=" N ALA A 417 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU A 420 " --> pdb=" O PRO A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 434 Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 451 through 456 removed outlier: 5.529A pdb=" N LEU A 454 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG A 455 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 470 through 483 removed outlier: 3.672A pdb=" N TYR A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 523 through 539 removed outlier: 3.761A pdb=" N ALA A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 567 Processing helix chain 'A' and resid 587 through 599 removed outlier: 3.662A pdb=" N ALA A 599 " --> pdb=" O CYS A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 667 through 682 removed outlier: 3.527A pdb=" N LEU A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 727 removed outlier: 4.946A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER A 724 " --> pdb=" O LYS A 720 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU A 725 " --> pdb=" O ASP A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 774 Processing helix chain 'A' and resid 793 through 808 Processing helix chain 'A' and resid 814 through 833 Processing helix chain 'A' and resid 853 through 876 removed outlier: 4.319A pdb=" N GLN A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1572 removed outlier: 3.756A pdb=" N ILE A1565 " --> pdb=" O GLY A1561 " (cutoff:3.500A) Processing helix chain 'A' and resid 1582 through 1588 Processing helix chain 'A' and resid 1650 through 1652 No H-bonds generated for 'chain 'A' and resid 1650 through 1652' Processing helix chain 'A' and resid 1679 through 1682 removed outlier: 3.664A pdb=" N TYR A1682 " --> pdb=" O LYS A1679 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1679 through 1682' Processing helix chain 'A' and resid 1773 through 1779 Processing helix chain 'A' and resid 1792 through 1799 Processing helix chain 'A' and resid 1867 through 1871 removed outlier: 3.917A pdb=" N GLY A1871 " --> pdb=" O PRO A1868 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 495 through 501 removed outlier: 3.508A pdb=" N VAL B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 537 removed outlier: 3.719A pdb=" N ARG B 536 " --> pdb=" O SER B 532 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 239 removed outlier: 6.045A pdb=" N LEU A 98 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE A 130 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE A 100 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN A 97 " --> pdb=" O MET A 283 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU A 285 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS A 99 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY A 386 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.624A pdb=" N LEU A 290 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 628 through 629 removed outlier: 6.250A pdb=" N PHE A 650 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 628 through 629 removed outlier: 6.250A pdb=" N PHE A 650 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE A 691 " --> pdb=" O ILE A 736 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N SER A 738 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 693 " --> pdb=" O SER A 738 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 735 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N PHE A 780 " --> pdb=" O ILE A 735 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N TYR A 777 " --> pdb=" O LYS A 790 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 744 through 746 Processing sheet with id=AA7, first strand: chain 'A' and resid 1531 through 1532 removed outlier: 3.918A pdb=" N SER A1541 " --> pdb=" O SER A1554 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER A1554 " --> pdb=" O SER A1541 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL A1555 " --> pdb=" O SER A1613 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N THR A1615 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU A1557 " --> pdb=" O THR A1615 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLN A1620 " --> pdb=" O ILE A1636 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE A1636 " --> pdb=" O GLN A1620 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU A1622 " --> pdb=" O TYR A1634 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1673 through 1677 removed outlier: 5.888A pdb=" N ILE A1674 " --> pdb=" O ASN A1703 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N THR A1705 " --> pdb=" O ILE A1674 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE A1676 " --> pdb=" O THR A1705 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ILE A1729 " --> pdb=" O SER A1781 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN A1783 " --> pdb=" O ILE A1729 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL A1731 " --> pdb=" O ASN A1783 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1690 through 1693 Processing sheet with id=AB1, first strand: chain 'A' and resid 1814 through 1818 Processing sheet with id=AB2, first strand: chain 'A' and resid 1834 through 1837 Processing sheet with id=AB3, first strand: chain 'A' and resid 1856 through 1858 Processing sheet with id=AB4, first strand: chain 'A' and resid 1877 through 1880 Processing sheet with id=AB5, first strand: chain 'B' and resid 432 through 434 removed outlier: 4.119A pdb=" N GLN B 453 " --> pdb=" O THR B 433 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 437 through 440 removed outlier: 3.953A pdb=" N ASP B 516 " --> pdb=" O ILE B 544 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 437 through 440 removed outlier: 3.953A pdb=" N ASP B 516 " --> pdb=" O ILE B 544 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 474 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLU B 521 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL B 472 " --> pdb=" O GLU B 521 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 445 through 446 removed outlier: 3.505A pdb=" N ALA B 445 " --> pdb=" O PHE B 506 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1293 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: 4.63 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3566 1.34 - 1.46: 1781 1.46 - 1.57: 5695 1.57 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 11109 Sorted by residual: bond pdb=" C ILE B 485 " pdb=" N PRO B 486 " ideal model delta sigma weight residual 1.331 1.396 -0.064 1.21e-02 6.83e+03 2.83e+01 bond pdb=" C PRO A1847 " pdb=" N PRO A1848 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.82e+00 bond pdb=" N THR B 514 " pdb=" CA THR B 514 " ideal model delta sigma weight residual 1.460 1.485 -0.025 1.54e-02 4.22e+03 2.66e+00 bond pdb=" CA PHE B 494 " pdb=" CB PHE B 494 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.69e-02 3.50e+03 2.36e+00 bond pdb=" CG LEU A 285 " pdb=" CD2 LEU A 285 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.98e+00 ... (remaining 11104 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.36: 226 106.36 - 113.27: 5920 113.27 - 120.17: 4037 120.17 - 127.08: 4773 127.08 - 133.98: 71 Bond angle restraints: 15027 Sorted by residual: angle pdb=" C ASP B 484 " pdb=" N ILE B 485 " pdb=" CA ILE B 485 " ideal model delta sigma weight residual 120.33 125.51 -5.18 8.00e-01 1.56e+00 4.20e+01 angle pdb=" N LYS A 322 " pdb=" CA LYS A 322 " pdb=" C LYS A 322 " ideal model delta sigma weight residual 114.62 107.48 7.14 1.14e+00 7.69e-01 3.92e+01 angle pdb=" C ILE A 578 " pdb=" N HIS A 579 " pdb=" CA HIS A 579 " ideal model delta sigma weight residual 121.56 129.46 -7.90 1.56e+00 4.11e-01 2.56e+01 angle pdb=" C ASP B 513 " pdb=" N THR B 514 " pdb=" CA THR B 514 " ideal model delta sigma weight residual 122.46 128.21 -5.75 1.41e+00 5.03e-01 1.66e+01 angle pdb=" N SER A 300 " pdb=" CA SER A 300 " pdb=" C SER A 300 " ideal model delta sigma weight residual 114.09 108.15 5.94 1.55e+00 4.16e-01 1.47e+01 ... (remaining 15022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5944 17.93 - 35.87: 631 35.87 - 53.80: 147 53.80 - 71.73: 27 71.73 - 89.67: 20 Dihedral angle restraints: 6769 sinusoidal: 2759 harmonic: 4010 Sorted by residual: dihedral pdb=" CA TYR A 711 " pdb=" C TYR A 711 " pdb=" N PRO A 712 " pdb=" CA PRO A 712 " ideal model delta harmonic sigma weight residual 180.00 135.63 44.37 0 5.00e+00 4.00e-02 7.88e+01 dihedral pdb=" CB CYS B 415 " pdb=" SG CYS B 415 " pdb=" SG CYS B 533 " pdb=" CB CYS B 533 " ideal model delta sinusoidal sigma weight residual 93.00 40.19 52.81 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CA ARG B 474 " pdb=" C ARG B 474 " pdb=" N GLY B 475 " pdb=" CA GLY B 475 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 6766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1452 0.072 - 0.143: 219 0.143 - 0.215: 11 0.215 - 0.286: 2 0.286 - 0.358: 1 Chirality restraints: 1685 Sorted by residual: chirality pdb=" CA THR B 473 " pdb=" N THR B 473 " pdb=" C THR B 473 " pdb=" CB THR B 473 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CB ILE A1809 " pdb=" CA ILE A1809 " pdb=" CG1 ILE A1809 " pdb=" CG2 ILE A1809 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA PHE B 494 " pdb=" N PHE B 494 " pdb=" C PHE B 494 " pdb=" CB PHE B 494 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1682 not shown) Planarity restraints: 1952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 711 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 712 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 712 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 712 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 494 " -0.011 2.00e-02 2.50e+03 1.65e-02 4.79e+00 pdb=" CG PHE B 494 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 494 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 494 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE B 494 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 494 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 494 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1846 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A1847 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A1847 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1847 " 0.029 5.00e-02 4.00e+02 ... (remaining 1949 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 249 2.67 - 3.23: 10220 3.23 - 3.79: 16770 3.79 - 4.34: 23138 4.34 - 4.90: 38427 Nonbonded interactions: 88804 Sorted by model distance: nonbonded pdb=" OD2 ASP A 546 " pdb="ZN ZN A2001 " model vdw 2.116 2.230 nonbonded pdb=" O GLU A1794 " pdb=" OG SER A1798 " model vdw 2.239 2.440 nonbonded pdb=" O ILE A1550 " pdb=" NZ LYS A1603 " model vdw 2.248 2.520 nonbonded pdb=" O SER A 2 " pdb=" OG SER A 2 " model vdw 2.284 2.440 nonbonded pdb=" OD1 ASN A 185 " pdb=" OH TYR A 209 " model vdw 2.289 2.440 ... (remaining 88799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.190 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 35.150 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.004 0.064 11109 Z= 0.271 Angle : 0.748 12.939 15027 Z= 0.419 Chirality : 0.050 0.358 1685 Planarity : 0.005 0.102 1952 Dihedral : 16.192 89.667 4172 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.82 % Favored : 92.10 % Rotamer: Outliers : 0.48 % Allowed : 17.90 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -3.39 (0.19), residues: 1342 helix: -1.40 (0.20), residues: 497 sheet: -2.90 (0.32), residues: 210 loop : -2.67 (0.21), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 449 HIS 0.007 0.001 HIS A 579 PHE 0.037 0.002 PHE B 494 TYR 0.016 0.002 TYR A1645 ARG 0.009 0.001 ARG B 477 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 184 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.7685 (ttt) cc_final: 0.7271 (ttm) REVERT: A 176 MET cc_start: 0.8532 (tpt) cc_final: 0.8152 (tpt) REVERT: A 347 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7722 (tt0) REVERT: A 385 GLN cc_start: 0.7916 (mt0) cc_final: 0.7399 (mt0) REVERT: A 448 MET cc_start: 0.7438 (mmt) cc_final: 0.6842 (mmt) REVERT: A 692 GLU cc_start: 0.7678 (tt0) cc_final: 0.7366 (tm-30) REVERT: A 700 MET cc_start: 0.8903 (mmm) cc_final: 0.8671 (mmp) REVERT: A 818 LYS cc_start: 0.8247 (ttpp) cc_final: 0.7954 (ptmt) REVERT: A 1572 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7265 (mptt) REVERT: A 1624 ILE cc_start: 0.6987 (tt) cc_final: 0.6672 (tp) REVERT: A 1632 GLN cc_start: 0.7692 (tt0) cc_final: 0.7117 (tt0) REVERT: B 457 ASP cc_start: 0.8752 (p0) cc_final: 0.8321 (p0) REVERT: B 460 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8273 (tm-30) REVERT: B 467 GLN cc_start: 0.8174 (mt0) cc_final: 0.7929 (mt0) REVERT: B 535 ARG cc_start: 0.7768 (mmm-85) cc_final: 0.7515 (mtt180) outliers start: 6 outliers final: 3 residues processed: 188 average time/residue: 0.2393 time to fit residues: 61.7705 Evaluate side-chains 140 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 757 HIS Chi-restraints excluded: chain B residue 430 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 183 GLN A 385 GLN A 402 GLN A 405 ASN A 479 GLN A 699 ASN A 732 GLN A 741 GLN A1570 ASN A1601 ASN A1675 ASN A1689 ASN A1712 ASN A1732 ASN ** A1895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN B 489 GLN B 501 ASN B 508 HIS B 538 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11109 Z= 0.199 Angle : 0.537 9.926 15027 Z= 0.285 Chirality : 0.043 0.166 1685 Planarity : 0.004 0.094 1952 Dihedral : 5.208 42.049 1461 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.23 % Favored : 92.70 % Rotamer: Outliers : 2.50 % Allowed : 19.76 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -2.19 (0.21), residues: 1342 helix: -0.01 (0.23), residues: 503 sheet: -2.32 (0.32), residues: 217 loop : -2.36 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 449 HIS 0.002 0.001 HIS A 35 PHE 0.025 0.001 PHE B 494 TYR 0.013 0.001 TYR A1645 ARG 0.003 0.000 ARG B 527 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.7802 (ttt) cc_final: 0.7295 (mtp) REVERT: A 176 MET cc_start: 0.8535 (tpt) cc_final: 0.8202 (tpt) REVERT: A 250 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6376 (mt-10) REVERT: A 346 PHE cc_start: 0.8281 (m-10) cc_final: 0.8020 (m-10) REVERT: A 347 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7759 (tt0) REVERT: A 385 GLN cc_start: 0.8068 (mt0) cc_final: 0.7636 (mt0) REVERT: A 700 MET cc_start: 0.8870 (mmm) cc_final: 0.8650 (mmp) REVERT: A 818 LYS cc_start: 0.8303 (ttpp) cc_final: 0.8002 (ptmt) REVERT: A 1582 MET cc_start: 0.7017 (tpp) cc_final: 0.6382 (mmm) REVERT: A 1607 ASP cc_start: 0.6237 (OUTLIER) cc_final: 0.5780 (t70) REVERT: A 1632 GLN cc_start: 0.7651 (tt0) cc_final: 0.7202 (tt0) REVERT: B 448 GLU cc_start: 0.8156 (pt0) cc_final: 0.7945 (pt0) REVERT: B 457 ASP cc_start: 0.8706 (p0) cc_final: 0.8451 (p0) REVERT: B 462 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8000 (mm-30) REVERT: B 467 GLN cc_start: 0.8188 (mt0) cc_final: 0.7847 (mt0) REVERT: B 535 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7428 (mtt180) outliers start: 31 outliers final: 20 residues processed: 166 average time/residue: 0.2325 time to fit residues: 54.9778 Evaluate side-chains 154 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 1588 MET Chi-restraints excluded: chain A residue 1607 ASP Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1658 GLU Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1856 PHE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 525 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1601 ASN ** A1895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11109 Z= 0.316 Angle : 0.592 10.909 15027 Z= 0.310 Chirality : 0.045 0.187 1685 Planarity : 0.004 0.100 1952 Dihedral : 5.151 41.186 1456 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.42 % Favored : 91.51 % Rotamer: Outliers : 4.27 % Allowed : 20.81 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -1.78 (0.22), residues: 1342 helix: 0.50 (0.23), residues: 502 sheet: -2.25 (0.33), residues: 231 loop : -2.20 (0.22), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 449 HIS 0.003 0.001 HIS A 579 PHE 0.027 0.002 PHE B 494 TYR 0.018 0.001 TYR A1645 ARG 0.002 0.000 ARG A1571 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 133 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.7765 (ttt) cc_final: 0.7293 (mtp) REVERT: A 176 MET cc_start: 0.8619 (tpt) cc_final: 0.8269 (tpt) REVERT: A 347 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7722 (tt0) REVERT: A 385 GLN cc_start: 0.7903 (mt0) cc_final: 0.7554 (mt0) REVERT: A 435 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8498 (tt) REVERT: A 696 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8738 (mp) REVERT: A 700 MET cc_start: 0.8884 (mmm) cc_final: 0.8643 (mmp) REVERT: A 874 GLN cc_start: 0.6282 (tt0) cc_final: 0.6053 (tt0) REVERT: A 1607 ASP cc_start: 0.6273 (OUTLIER) cc_final: 0.5821 (t70) REVERT: A 1653 GLN cc_start: 0.7458 (mt0) cc_final: 0.7172 (mm110) REVERT: A 1887 TYR cc_start: 0.6787 (t80) cc_final: 0.6579 (t80) REVERT: B 457 ASP cc_start: 0.8783 (p0) cc_final: 0.8259 (p0) REVERT: B 460 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8106 (tm-30) REVERT: B 462 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8028 (mm-30) outliers start: 53 outliers final: 32 residues processed: 178 average time/residue: 0.2186 time to fit residues: 56.5947 Evaluate side-chains 162 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 127 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 1555 VAL Chi-restraints excluded: chain A residue 1588 MET Chi-restraints excluded: chain A residue 1607 ASP Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1631 ILE Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1658 GLU Chi-restraints excluded: chain A residue 1754 THR Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1856 PHE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1888 PHE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 525 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 0.0370 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A1601 ASN ** A1895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11109 Z= 0.210 Angle : 0.537 10.713 15027 Z= 0.283 Chirality : 0.043 0.208 1685 Planarity : 0.004 0.095 1952 Dihedral : 4.925 40.996 1456 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.23 % Favored : 92.70 % Rotamer: Outliers : 3.55 % Allowed : 22.58 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -1.40 (0.23), residues: 1342 helix: 0.86 (0.24), residues: 502 sheet: -2.03 (0.33), residues: 227 loop : -2.03 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 449 HIS 0.003 0.001 HIS A 757 PHE 0.027 0.001 PHE B 494 TYR 0.013 0.001 TYR A1645 ARG 0.003 0.000 ARG B 535 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.7784 (ttt) cc_final: 0.7286 (mtp) REVERT: A 176 MET cc_start: 0.8544 (tpt) cc_final: 0.8201 (tpt) REVERT: A 347 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7695 (tt0) REVERT: A 483 MET cc_start: 0.7854 (mmt) cc_final: 0.7516 (mmm) REVERT: A 548 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7501 (p0) REVERT: A 696 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8700 (mp) REVERT: A 700 MET cc_start: 0.8904 (mmm) cc_final: 0.8681 (mmp) REVERT: A 874 GLN cc_start: 0.6327 (tt0) cc_final: 0.6085 (tt0) REVERT: A 1607 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.6100 (t70) REVERT: A 1632 GLN cc_start: 0.7692 (tt0) cc_final: 0.7352 (tt0) REVERT: A 1653 GLN cc_start: 0.7406 (mt0) cc_final: 0.7155 (mm110) REVERT: A 1887 TYR cc_start: 0.6764 (t80) cc_final: 0.6554 (t80) REVERT: B 457 ASP cc_start: 0.8683 (p0) cc_final: 0.8258 (p0) REVERT: B 460 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8132 (tm-30) REVERT: B 462 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7962 (mm-30) outliers start: 44 outliers final: 29 residues processed: 174 average time/residue: 0.1853 time to fit residues: 47.1807 Evaluate side-chains 157 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1607 ASP Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1658 GLU Chi-restraints excluded: chain A residue 1699 THR Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1856 PHE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1888 PHE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 522 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 110 optimal weight: 0.0770 chunk 89 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1601 ASN ** A1895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11109 Z= 0.264 Angle : 0.558 11.977 15027 Z= 0.293 Chirality : 0.044 0.178 1685 Planarity : 0.004 0.097 1952 Dihedral : 4.979 41.235 1456 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.35 % Favored : 91.58 % Rotamer: Outliers : 4.35 % Allowed : 22.50 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -1.27 (0.23), residues: 1342 helix: 0.95 (0.24), residues: 502 sheet: -1.98 (0.34), residues: 229 loop : -1.93 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 449 HIS 0.002 0.001 HIS A 579 PHE 0.027 0.001 PHE B 494 TYR 0.015 0.001 TYR A1645 ARG 0.003 0.000 ARG B 527 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 131 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.7787 (ttt) cc_final: 0.7285 (mtp) REVERT: A 347 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7704 (tt0) REVERT: A 483 MET cc_start: 0.7900 (mmt) cc_final: 0.7530 (mmm) REVERT: A 548 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7594 (p0) REVERT: A 656 ASP cc_start: 0.6711 (m-30) cc_final: 0.6451 (t0) REVERT: A 696 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8717 (mp) REVERT: A 700 MET cc_start: 0.8932 (mmm) cc_final: 0.8689 (mmp) REVERT: A 741 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8856 (tt0) REVERT: A 1607 ASP cc_start: 0.6503 (OUTLIER) cc_final: 0.5909 (t70) REVERT: A 1632 GLN cc_start: 0.7796 (tt0) cc_final: 0.7521 (tt0) REVERT: A 1653 GLN cc_start: 0.7491 (mt0) cc_final: 0.7169 (mm110) REVERT: B 457 ASP cc_start: 0.8710 (p0) cc_final: 0.8260 (p0) REVERT: B 460 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8117 (tm-30) REVERT: B 462 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7954 (mm-30) REVERT: B 541 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.7828 (tt) outliers start: 54 outliers final: 38 residues processed: 178 average time/residue: 0.1812 time to fit residues: 47.7518 Evaluate side-chains 168 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1555 VAL Chi-restraints excluded: chain A residue 1588 MET Chi-restraints excluded: chain A residue 1607 ASP Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1658 GLU Chi-restraints excluded: chain A residue 1699 THR Chi-restraints excluded: chain A residue 1754 THR Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1856 PHE Chi-restraints excluded: chain A residue 1857 VAL Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1888 PHE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 513 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 541 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 874 GLN ** A1570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1601 ASN ** A1895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11109 Z= 0.208 Angle : 0.527 12.499 15027 Z= 0.278 Chirality : 0.043 0.155 1685 Planarity : 0.004 0.094 1952 Dihedral : 4.818 41.058 1456 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.53 % Favored : 92.40 % Rotamer: Outliers : 4.27 % Allowed : 23.31 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -1.09 (0.23), residues: 1342 helix: 1.04 (0.24), residues: 507 sheet: -1.86 (0.34), residues: 229 loop : -1.79 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 449 HIS 0.002 0.001 HIS A 579 PHE 0.026 0.001 PHE B 494 TYR 0.021 0.001 TYR A1887 ARG 0.003 0.000 ARG B 527 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 135 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.7730 (ttt) cc_final: 0.7317 (mtp) REVERT: A 176 MET cc_start: 0.8488 (tpt) cc_final: 0.8125 (tpt) REVERT: A 346 PHE cc_start: 0.8452 (m-10) cc_final: 0.8197 (m-10) REVERT: A 347 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7774 (tt0) REVERT: A 483 MET cc_start: 0.7830 (mmt) cc_final: 0.7501 (mmm) REVERT: A 656 ASP cc_start: 0.6768 (m-30) cc_final: 0.6540 (t0) REVERT: A 696 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8685 (mp) REVERT: A 700 MET cc_start: 0.8956 (mmm) cc_final: 0.8744 (mmp) REVERT: A 1540 LEU cc_start: 0.4491 (OUTLIER) cc_final: 0.4177 (tt) REVERT: A 1607 ASP cc_start: 0.6575 (OUTLIER) cc_final: 0.5978 (t70) REVERT: A 1622 GLU cc_start: 0.6732 (mp0) cc_final: 0.6307 (mp0) REVERT: A 1632 GLN cc_start: 0.7778 (tt0) cc_final: 0.7463 (tt0) REVERT: A 1653 GLN cc_start: 0.7501 (mt0) cc_final: 0.7269 (mm-40) REVERT: B 457 ASP cc_start: 0.8685 (p0) cc_final: 0.8228 (p0) REVERT: B 460 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8127 (tm-30) REVERT: B 462 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7926 (mm-30) REVERT: B 541 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.7813 (tt) outliers start: 53 outliers final: 39 residues processed: 178 average time/residue: 0.1988 time to fit residues: 51.8237 Evaluate side-chains 171 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 128 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1555 VAL Chi-restraints excluded: chain A residue 1558 ASP Chi-restraints excluded: chain A residue 1588 MET Chi-restraints excluded: chain A residue 1601 ASN Chi-restraints excluded: chain A residue 1604 PHE Chi-restraints excluded: chain A residue 1607 ASP Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1658 GLU Chi-restraints excluded: chain A residue 1699 THR Chi-restraints excluded: chain A residue 1760 VAL Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1856 PHE Chi-restraints excluded: chain A residue 1857 VAL Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1888 PHE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 541 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 385 GLN A 554 ASN ** A1570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1601 ASN ** A1895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11109 Z= 0.136 Angle : 0.501 12.350 15027 Z= 0.264 Chirality : 0.042 0.145 1685 Planarity : 0.004 0.089 1952 Dihedral : 4.570 40.991 1456 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.08 % Favored : 92.85 % Rotamer: Outliers : 3.71 % Allowed : 24.03 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.85 (0.23), residues: 1342 helix: 1.26 (0.24), residues: 507 sheet: -1.74 (0.34), residues: 227 loop : -1.68 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 449 HIS 0.002 0.001 HIS A 579 PHE 0.023 0.001 PHE B 494 TYR 0.011 0.001 TYR A1645 ARG 0.004 0.000 ARG B 527 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 146 time to evaluate : 1.460 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.7707 (ttt) cc_final: 0.7293 (mtp) REVERT: A 176 MET cc_start: 0.8458 (tpt) cc_final: 0.8091 (tpt) REVERT: A 346 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.8134 (m-10) REVERT: A 347 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7738 (tt0) REVERT: A 483 MET cc_start: 0.7889 (mmt) cc_final: 0.7589 (mmm) REVERT: A 699 ASN cc_start: 0.8813 (m110) cc_final: 0.8586 (m-40) REVERT: A 700 MET cc_start: 0.8925 (mmm) cc_final: 0.8713 (mmp) REVERT: A 741 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8784 (tt0) REVERT: A 1591 LYS cc_start: 0.6684 (pttp) cc_final: 0.6423 (mtpt) REVERT: A 1607 ASP cc_start: 0.6477 (OUTLIER) cc_final: 0.5751 (t70) REVERT: A 1622 GLU cc_start: 0.6623 (mp0) cc_final: 0.6253 (mp0) REVERT: A 1632 GLN cc_start: 0.7733 (tt0) cc_final: 0.7388 (tt0) REVERT: A 1653 GLN cc_start: 0.7475 (mt0) cc_final: 0.7259 (mm-40) REVERT: B 457 ASP cc_start: 0.8608 (p0) cc_final: 0.8154 (p0) REVERT: B 460 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8143 (tm-30) REVERT: B 462 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7842 (mm-30) outliers start: 46 outliers final: 35 residues processed: 180 average time/residue: 0.2026 time to fit residues: 53.5184 Evaluate side-chains 174 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1555 VAL Chi-restraints excluded: chain A residue 1558 ASP Chi-restraints excluded: chain A residue 1604 PHE Chi-restraints excluded: chain A residue 1607 ASP Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1658 GLU Chi-restraints excluded: chain A residue 1699 THR Chi-restraints excluded: chain A residue 1760 VAL Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1856 PHE Chi-restraints excluded: chain A residue 1857 VAL Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1888 PHE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 474 ARG Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 525 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 ASN ** A1570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1601 ASN ** A1895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11109 Z= 0.211 Angle : 0.539 12.353 15027 Z= 0.282 Chirality : 0.043 0.187 1685 Planarity : 0.004 0.092 1952 Dihedral : 4.661 41.443 1456 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.60 % Favored : 92.32 % Rotamer: Outliers : 4.60 % Allowed : 23.79 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.33 % 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: -0.80 (0.23), residues: 1342 helix: 1.27 (0.24), residues: 507 sheet: -1.72 (0.33), residues: 232 loop : -1.62 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 449 HIS 0.003 0.001 HIS B 451 PHE 0.065 0.001 PHE B 494 TYR 0.012 0.001 TYR A1645 ARG 0.004 0.000 ARG B 527 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 133 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 12 MET cc_start: 0.7746 (ttt) cc_final: 0.7289 (mtp) REVERT: A 176 MET cc_start: 0.8518 (tpt) cc_final: 0.8152 (tpt) REVERT: A 346 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8179 (m-10) REVERT: A 347 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7764 (tt0) REVERT: A 483 MET cc_start: 0.7862 (mmt) cc_final: 0.7546 (mmm) REVERT: A 699 ASN cc_start: 0.8941 (m110) cc_final: 0.8649 (m-40) REVERT: A 700 MET cc_start: 0.8930 (mmm) cc_final: 0.8709 (mmp) REVERT: A 741 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8811 (tt0) REVERT: A 790 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8574 (mmtt) REVERT: A 833 ASP cc_start: 0.7718 (t0) cc_final: 0.7440 (t0) REVERT: A 1591 LYS cc_start: 0.6670 (pttp) cc_final: 0.6409 (mtpt) REVERT: A 1603 LYS cc_start: 0.3810 (OUTLIER) cc_final: 0.3247 (ptmm) REVERT: A 1607 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.5922 (t70) REVERT: A 1622 GLU cc_start: 0.6654 (mp0) cc_final: 0.6280 (mp0) REVERT: A 1632 GLN cc_start: 0.7719 (tt0) cc_final: 0.7437 (tt0) REVERT: A 1653 GLN cc_start: 0.7513 (mt0) cc_final: 0.7293 (mm-40) REVERT: B 432 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8400 (mt) REVERT: B 457 ASP cc_start: 0.8652 (p0) cc_final: 0.8188 (p0) REVERT: B 460 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8143 (tm-30) REVERT: B 462 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7898 (mm-30) REVERT: B 541 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.7829 (tt) outliers start: 57 outliers final: 42 residues processed: 179 average time/residue: 0.1745 time to fit residues: 46.4870 Evaluate side-chains 179 residues out of total 1240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 131 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 588 LYS Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1555 VAL Chi-restraints excluded: chain A residue 1558 ASP Chi-restraints excluded: chain A residue 1588 MET Chi-restraints excluded: chain A residue 1603 LYS Chi-restraints excluded: chain A residue 1604 PHE Chi-restraints excluded: chain A residue 1607 ASP Chi-restraints excluded: chain A residue 1616 THR Chi-restraints excluded: chain A residue 1640 THR Chi-restraints excluded: chain A residue 1658 GLU Chi-restraints excluded: chain A residue 1699 THR Chi-restraints excluded: chain A residue 1754 THR Chi-restraints excluded: chain A residue 1760 VAL Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1856 PHE Chi-restraints excluded: chain A residue 1857 VAL Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1888 PHE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 474 ARG Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 498 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 541 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: