Starting phenix.real_space_refine on Fri May 16 09:03:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7v_29825/05_2025/8g7v_29825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7v_29825/05_2025/8g7v_29825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g7v_29825/05_2025/8g7v_29825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7v_29825/05_2025/8g7v_29825.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7v_29825/05_2025/8g7v_29825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7v_29825/05_2025/8g7v_29825.cif" } resolution = 3.9 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 48 5.49 5 S 78 5.16 5 C 8762 2.51 5 N 2393 2.21 5 O 2724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14007 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5234 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 619} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1392 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5005 Classifications: {'peptide': 618} Link IDs: {'PTRANS': 24, 'TRANS': 593} Chain breaks: 4 Chain: "D" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1386 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "X" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 501 Unusual residues: {'GTP': 1} Classifications: {'RNA': 22, 'undetermined': 1} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 11} Link IDs: {'rna3p': 21, None: 1} Not linked: pdbres="GTP X 1 " pdbres=" G X 2 " Chain: "Y" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 487 Classifications: {'RNA': 23} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 11} Link IDs: {'rna2p': 1, 'rna3p': 21} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" 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 4741 SG CYS A 864 96.663 76.558 85.552 1.00 44.09 S ATOM 4780 SG CYS A 869 93.580 76.262 83.569 1.00 47.18 S ATOM 10817 SG CYS C 810 84.696 25.785 72.262 1.00 61.51 S ATOM 10843 SG CYS C 813 88.128 24.213 72.341 1.00 69.91 S ATOM 11155 SG CYS C 864 88.208 27.375 74.808 1.00 60.77 S ATOM 11194 SG CYS C 869 87.723 27.618 71.176 1.00 66.05 S Time building chain proxies: 8.90, per 1000 atoms: 0.64 Number of scatterers: 14007 At special positions: 0 Unit cell: (119.138, 115.782, 153.537, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 78 16.00 P 48 15.00 O 2724 8.00 N 2393 7.00 C 8762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 402 " distance=2.04 Simple disulfide: pdb=" SG CYS D 347 " - pdb=" SG CYS D 402 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.54 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 810 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 864 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 813 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 869 " Number of angles added : 6 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3102 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 16 sheets defined 37.7% alpha, 10.1% beta 21 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 5.01 Creating SS restraints... Processing helix chain 'A' and resid 245 through 251 removed outlier: 3.790A pdb=" N ALA A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.814A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 283 removed outlier: 4.057A pdb=" N THR A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 347 through 358 removed outlier: 4.044A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.885A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 383 through 395 removed outlier: 3.924A pdb=" N ASN A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 469 through 488 removed outlier: 3.774A pdb=" N ARG A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 506 through 520 removed outlier: 4.002A pdb=" N GLU A 510 " --> pdb=" O THR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 558 removed outlier: 4.163A pdb=" N LYS A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 578 removed outlier: 4.302A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 564 " --> pdb=" O MET A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 602 removed outlier: 3.681A pdb=" N ASP A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 592 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 removed outlier: 3.615A pdb=" N PHE A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A 623 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 648 removed outlier: 3.615A pdb=" N GLU A 648 " --> pdb=" O LYS A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 769 removed outlier: 4.125A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 removed outlier: 3.695A pdb=" N ARG A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 781 " --> pdb=" O ARG A 777 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 783 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 794 " --> pdb=" O ILE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 840 removed outlier: 3.768A pdb=" N GLU A 840 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 250 through 255 removed outlier: 4.778A pdb=" N ALA C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 removed outlier: 4.270A pdb=" N LEU C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 315 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.664A pdb=" N ILE C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 removed outlier: 3.962A pdb=" N LEU C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.592A pdb=" N ILE C 365 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE C 366 " --> pdb=" O LEU C 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 362 through 366' Processing helix chain 'C' and resid 373 through 377 Processing helix chain 'C' and resid 381 through 395 Processing helix chain 'C' and resid 419 through 434 Processing helix chain 'C' and resid 445 through 451 Processing helix chain 'C' and resid 469 through 491 Processing helix chain 'C' and resid 492 through 497 removed outlier: 4.029A pdb=" N SER C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 521 removed outlier: 3.804A pdb=" N MET C 521 " --> pdb=" O GLN C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 558 removed outlier: 3.564A pdb=" N HIS C 557 " --> pdb=" O ILE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 576 removed outlier: 3.710A pdb=" N ALA C 563 " --> pdb=" O ARG C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 602 removed outlier: 3.910A pdb=" N LYS C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLN C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU C 596 " --> pdb=" O GLU C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 625 Processing helix chain 'C' and resid 636 through 649 Processing helix chain 'C' and resid 746 through 769 Processing helix chain 'C' and resid 773 through 792 Processing helix chain 'C' and resid 837 through 841 Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 295 removed outlier: 6.600A pdb=" N VAL A 294 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASP A 372 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 462 removed outlier: 3.837A pdb=" N PHE A 459 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 740 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 742 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 631 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR A 715 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 633 " --> pdb=" O TYR A 715 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819 removed outlier: 7.468A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 831 through 833 removed outlier: 4.512A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 843 Processing sheet with id=AA6, first strand: chain 'A' and resid 858 through 860 removed outlier: 6.248A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 280 through 282 removed outlier: 4.327A pdb=" N VAL B 317 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 376 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 301 through 302 removed outlier: 4.257A pdb=" N TRP B 325 " --> pdb=" O TRP B 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 260 through 263 removed outlier: 3.801A pdb=" N LEU C 408 " --> pdb=" O PHE C 371 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL C 294 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 457 through 462 removed outlier: 3.736A pdb=" N CYS C 738 " --> pdb=" O GLN C 457 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 816 through 819 removed outlier: 7.255A pdb=" N LEU C 816 " --> pdb=" O CYS C 810 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS C 810 " --> pdb=" O LEU C 816 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS C 818 " --> pdb=" O LEU C 808 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 823 through 824 Processing sheet with id=AB4, first strand: chain 'C' and resid 843 through 844 Processing sheet with id=AB5, first strand: chain 'C' and resid 874 through 876 Processing sheet with id=AB6, first strand: chain 'D' and resid 280 through 282 removed outlier: 3.564A pdb=" N LEU D 425 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D 426 " --> pdb=" O ASP D 318 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP D 315 " --> pdb=" O ILE D 378 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 301 through 303 removed outlier: 4.427A pdb=" N TRP D 325 " --> pdb=" O TRP D 351 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP D 351 " --> pdb=" O TRP D 325 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 327 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 349 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N CYS D 348 " --> pdb=" O TRP D 360 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 352 " --> pdb=" O GLN D 356 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN D 356 " --> pdb=" O LYS D 352 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2226 1.32 - 1.44: 4088 1.44 - 1.57: 7893 1.57 - 1.70: 96 1.70 - 1.82: 104 Bond restraints: 14407 Sorted by residual: bond pdb=" C1' GTP X 1 " pdb=" C2' GTP X 1 " ideal model delta sigma weight residual 1.524 1.292 0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C1' GTP X 1 " pdb=" O4' GTP X 1 " ideal model delta sigma weight residual 1.410 1.618 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C5 GTP X 1 " pdb=" C6 GTP X 1 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C4 GTP X 1 " pdb=" N3 GTP X 1 " ideal model delta sigma weight residual 1.355 1.493 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C2 GTP X 1 " pdb=" N2 GTP X 1 " ideal model delta sigma weight residual 1.330 1.453 -0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 14402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 19344 2.59 - 5.18: 305 5.18 - 7.77: 37 7.77 - 10.36: 1 10.36 - 12.95: 4 Bond angle restraints: 19691 Sorted by residual: angle pdb=" N VAL C 332 " pdb=" CA VAL C 332 " pdb=" C VAL C 332 " ideal model delta sigma weight residual 108.88 120.51 -11.63 2.16e+00 2.14e-01 2.90e+01 angle pdb=" N THR A 881 " pdb=" CA THR A 881 " pdb=" C THR A 881 " ideal model delta sigma weight residual 114.56 108.98 5.58 1.27e+00 6.20e-01 1.93e+01 angle pdb=" N THR B 299 " pdb=" CA THR B 299 " pdb=" C THR B 299 " ideal model delta sigma weight residual 110.80 101.71 9.09 2.13e+00 2.20e-01 1.82e+01 angle pdb=" CA VAL C 332 " pdb=" CB VAL C 332 " pdb=" CG1 VAL C 332 " ideal model delta sigma weight residual 110.40 117.18 -6.78 1.70e+00 3.46e-01 1.59e+01 angle pdb=" C ALA A 733 " pdb=" N ARG A 734 " pdb=" CA ARG A 734 " ideal model delta sigma weight residual 121.54 128.83 -7.29 1.91e+00 2.74e-01 1.46e+01 ... (remaining 19686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.36: 8210 26.36 - 52.72: 434 52.72 - 79.08: 104 79.08 - 105.44: 12 105.44 - 131.80: 2 Dihedral angle restraints: 8762 sinusoidal: 3996 harmonic: 4766 Sorted by residual: dihedral pdb=" C4' GTP X 1 " pdb=" C5' GTP X 1 " pdb=" O5' GTP X 1 " pdb=" PA GTP X 1 " ideal model delta sinusoidal sigma weight residual 260.87 129.08 131.80 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" O3B GTP X 1 " pdb=" O3A GTP X 1 " pdb=" PB GTP X 1 " pdb=" PA GTP X 1 " ideal model delta sinusoidal sigma weight residual 291.08 166.30 124.78 1 2.00e+01 2.50e-03 3.77e+01 dihedral pdb=" CA SER A 855 " pdb=" C SER A 855 " pdb=" N PHE A 856 " pdb=" CA PHE A 856 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 8759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1928 0.078 - 0.156: 268 0.156 - 0.234: 19 0.234 - 0.312: 1 0.312 - 0.390: 1 Chirality restraints: 2217 Sorted by residual: chirality pdb=" CA VAL C 332 " pdb=" N VAL C 332 " pdb=" C VAL C 332 " pdb=" CB VAL C 332 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB VAL A 877 " pdb=" CA VAL A 877 " pdb=" CG1 VAL A 877 " pdb=" CG2 VAL A 877 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE A 875 " pdb=" CA ILE A 875 " pdb=" CG1 ILE A 875 " pdb=" CG2 ILE A 875 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2214 not shown) Planarity restraints: 2330 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 332 " -0.100 5.00e-02 4.00e+02 1.51e-01 3.63e+01 pdb=" N PRO C 333 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 712 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C VAL C 712 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL C 712 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE C 713 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 381 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.72e+00 pdb=" N PRO A 382 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " 0.041 5.00e-02 4.00e+02 ... (remaining 2327 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2927 2.78 - 3.31: 12346 3.31 - 3.84: 23231 3.84 - 4.37: 25761 4.37 - 4.90: 43828 Nonbonded interactions: 108093 Sorted by model distance: nonbonded pdb=" CD LYS A 806 " pdb=" OD1 ASP A 896 " model vdw 2.246 3.440 nonbonded pdb=" O SER B 300 " pdb=" OG SER B 300 " model vdw 2.286 3.040 nonbonded pdb=" O LEU C 538 " pdb=" OG1 THR C 542 " model vdw 2.301 3.040 nonbonded pdb=" OG SER D 300 " pdb=" O LEU D 416 " model vdw 2.316 3.040 nonbonded pdb=" O LEU C 597 " pdb=" OG SER C 601 " model vdw 2.318 3.040 ... (remaining 108088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 241 through 661 or resid 690 through 699 or resid 709 thro \ ugh 718 or resid 734 through 845 or resid 858 through 921 or resid 1001)) selection = (chain 'C' and (resid 241 through 921 or resid 1001)) } ncs_group { reference = (chain 'B' and (resid 252 through 335 or (resid 336 and (name N or name CA or na \ me C or name O or name CB )) or resid 337 through 382 or (resid 383 through 384 \ and (name N or name CA or name C or name O or name CB )) or resid 385 through 43 \ 0)) selection = (chain 'D' and (resid 252 through 394 or (resid 395 through 399 and (name N or n \ ame CA or name C or name O or name CB )) or resid 400 through 430)) } 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.180 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.190 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.008 0.232 14416 Z= 0.354 Angle : 0.897 33.534 19701 Z= 0.461 Chirality : 0.053 0.390 2217 Planarity : 0.007 0.151 2330 Dihedral : 16.749 131.797 5654 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.42 % Allowed : 9.09 % Favored : 90.49 % 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: -4.07 (0.16), residues: 1595 helix: -2.06 (0.17), residues: 569 sheet: -2.89 (0.28), residues: 253 loop : -3.13 (0.17), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 379 HIS 0.010 0.002 HIS C 691 PHE 0.024 0.002 PHE A 853 TYR 0.022 0.002 TYR C 879 ARG 0.004 0.001 ARG C 502 Details of bonding type rmsd hydrogen bonds : bond 0.16021 ( 536) hydrogen bonds : angle 6.57758 ( 1501) metal coordination : bond 0.13347 ( 6) metal coordination : angle 16.68953 ( 6) SS BOND : bond 0.00362 ( 2) SS BOND : angle 0.38745 ( 4) covalent geometry : bond 0.00719 (14407) covalent geometry : angle 0.84908 (19691) Misc. bond : bond 0.09817 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 199 time to evaluate : 1.535 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: A 385 MET cc_start: 0.8800 (mmm) cc_final: 0.8510 (mtp) REVERT: A 387 MET cc_start: 0.8649 (mmm) cc_final: 0.8386 (mmp) REVERT: A 573 ASN cc_start: 0.8260 (t0) cc_final: 0.8022 (t0) REVERT: A 828 GLU cc_start: 0.7165 (mp0) cc_final: 0.6905 (mp0) REVERT: A 890 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7497 (tm-30) REVERT: B 266 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7758 (mttm) REVERT: B 400 TYR cc_start: 0.6077 (t80) cc_final: 0.5526 (t80) REVERT: C 300 ILE cc_start: 0.9142 (mm) cc_final: 0.8901 (mt) REVERT: C 419 ASN cc_start: 0.8873 (p0) cc_final: 0.8617 (p0) REVERT: C 598 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8103 (mt-10) REVERT: C 624 LEU cc_start: 0.8703 (tt) cc_final: 0.8358 (mp) REVERT: D 357 LEU cc_start: 0.5726 (tp) cc_final: 0.5306 (pp) outliers start: 6 outliers final: 5 residues processed: 204 average time/residue: 0.3007 time to fit residues: 86.5925 Evaluate side-chains 138 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 133 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain D residue 282 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 40.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS A 336 GLN A 353 ASN A 375 HIS A 393 GLN A 404 GLN A 445 ASN A 595 GLN A 623 HIS A 625 ASN A 645 ASN A 805 ASN B 301 GLN B 338 GLN B 394 ASN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN C 349 GLN C 354 ASN C 595 GLN C 692 ASN C 830 HIS D 381 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.120059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.093243 restraints weight = 36205.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.093786 restraints weight = 25998.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.094373 restraints weight = 19913.482| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14416 Z= 0.191 Angle : 0.639 13.389 19701 Z= 0.326 Chirality : 0.043 0.225 2217 Planarity : 0.005 0.103 2330 Dihedral : 13.643 103.291 2449 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.22 % Allowed : 13.74 % Favored : 84.04 % 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: -2.72 (0.19), residues: 1595 helix: -0.34 (0.20), residues: 585 sheet: -2.52 (0.30), residues: 248 loop : -2.77 (0.19), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 379 HIS 0.006 0.001 HIS A 623 PHE 0.022 0.002 PHE A 853 TYR 0.016 0.002 TYR C 541 ARG 0.004 0.000 ARG C 533 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 536) hydrogen bonds : angle 5.00783 ( 1501) metal coordination : bond 0.01010 ( 6) metal coordination : angle 3.27216 ( 6) SS BOND : bond 0.00886 ( 2) SS BOND : angle 0.61935 ( 4) covalent geometry : bond 0.00427 (14407) covalent geometry : angle 0.63698 (19691) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8902 (mmm) cc_final: 0.8561 (mtp) REVERT: A 387 MET cc_start: 0.8894 (mmm) cc_final: 0.8682 (mmp) REVERT: A 573 ASN cc_start: 0.8463 (t0) cc_final: 0.8242 (t0) REVERT: A 828 GLU cc_start: 0.7400 (mp0) cc_final: 0.7063 (mp0) REVERT: B 257 TRP cc_start: 0.6544 (m100) cc_final: 0.6290 (m100) REVERT: B 337 ASP cc_start: 0.8203 (m-30) cc_final: 0.7957 (m-30) REVERT: B 379 TRP cc_start: 0.7236 (t-100) cc_final: 0.6877 (t-100) REVERT: C 300 ILE cc_start: 0.9200 (mm) cc_final: 0.8735 (mt) REVERT: C 419 ASN cc_start: 0.8882 (p0) cc_final: 0.8410 (p0) REVERT: C 479 MET cc_start: 0.8853 (mtm) cc_final: 0.8333 (mtm) REVERT: C 560 MET cc_start: 0.8132 (mmt) cc_final: 0.7841 (mmt) REVERT: C 598 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8221 (mp0) REVERT: C 624 LEU cc_start: 0.8694 (tt) cc_final: 0.8339 (mp) outliers start: 32 outliers final: 22 residues processed: 174 average time/residue: 0.2443 time to fit residues: 63.0581 Evaluate side-chains 146 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN B 321 ASN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.119827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.096363 restraints weight = 36303.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.095524 restraints weight = 36503.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097174 restraints weight = 30692.315| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14416 Z= 0.222 Angle : 0.647 15.033 19701 Z= 0.327 Chirality : 0.043 0.249 2217 Planarity : 0.005 0.096 2330 Dihedral : 13.370 89.646 2446 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.12 % Allowed : 15.61 % Favored : 81.26 % 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: -2.22 (0.20), residues: 1595 helix: 0.27 (0.21), residues: 586 sheet: -2.33 (0.31), residues: 261 loop : -2.63 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 315 HIS 0.005 0.001 HIS A 281 PHE 0.020 0.002 PHE C 471 TYR 0.018 0.002 TYR C 313 ARG 0.003 0.000 ARG C 559 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 536) hydrogen bonds : angle 4.86759 ( 1501) metal coordination : bond 0.01025 ( 6) metal coordination : angle 2.92497 ( 6) SS BOND : bond 0.00238 ( 2) SS BOND : angle 0.29737 ( 4) covalent geometry : bond 0.00499 (14407) covalent geometry : angle 0.64543 (19691) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8675 (mtt) cc_final: 0.8431 (mtt) REVERT: A 385 MET cc_start: 0.8951 (mmm) cc_final: 0.8605 (mtp) REVERT: A 434 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9078 (tt) REVERT: A 573 ASN cc_start: 0.8324 (t0) cc_final: 0.8070 (t0) REVERT: A 828 GLU cc_start: 0.7423 (mp0) cc_final: 0.7099 (mp0) REVERT: B 337 ASP cc_start: 0.8091 (m-30) cc_final: 0.7831 (m-30) REVERT: B 379 TRP cc_start: 0.6751 (t-100) cc_final: 0.6274 (t-100) REVERT: C 300 ILE cc_start: 0.9194 (mm) cc_final: 0.8785 (mt) REVERT: C 419 ASN cc_start: 0.8803 (p0) cc_final: 0.8326 (p0) REVERT: C 598 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8030 (mt-10) REVERT: C 716 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7071 (tm-30) outliers start: 45 outliers final: 34 residues processed: 177 average time/residue: 0.2347 time to fit residues: 62.9101 Evaluate side-chains 158 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 616 PHE Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 161 optimal weight: 10.0000 chunk 21 optimal weight: 0.4980 chunk 130 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 517 GLN ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.122834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.098330 restraints weight = 36097.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.099049 restraints weight = 33468.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.100155 restraints weight = 21853.093| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14416 Z= 0.102 Angle : 0.537 10.856 19701 Z= 0.272 Chirality : 0.040 0.256 2217 Planarity : 0.004 0.080 2330 Dihedral : 13.145 90.614 2446 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.91 % Allowed : 16.72 % Favored : 80.36 % 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: -1.67 (0.21), residues: 1595 helix: 0.83 (0.22), residues: 586 sheet: -2.02 (0.33), residues: 247 loop : -2.42 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 379 HIS 0.002 0.001 HIS C 281 PHE 0.020 0.001 PHE C 471 TYR 0.014 0.001 TYR C 313 ARG 0.003 0.000 ARG C 502 Details of bonding type rmsd hydrogen bonds : bond 0.03406 ( 536) hydrogen bonds : angle 4.39117 ( 1501) metal coordination : bond 0.00455 ( 6) metal coordination : angle 2.31346 ( 6) SS BOND : bond 0.00448 ( 2) SS BOND : angle 0.40955 ( 4) covalent geometry : bond 0.00224 (14407) covalent geometry : angle 0.53587 (19691) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8907 (mmm) cc_final: 0.8697 (mmm) REVERT: A 434 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9027 (tt) REVERT: A 573 ASN cc_start: 0.8336 (t0) cc_final: 0.8128 (t0) REVERT: A 828 GLU cc_start: 0.7365 (mp0) cc_final: 0.7052 (mp0) REVERT: B 277 ASP cc_start: 0.7872 (p0) cc_final: 0.7604 (p0) REVERT: B 337 ASP cc_start: 0.8002 (m-30) cc_final: 0.7734 (m-30) REVERT: C 385 MET cc_start: 0.8583 (mmm) cc_final: 0.8333 (mmp) REVERT: C 419 ASN cc_start: 0.8805 (p0) cc_final: 0.8393 (p0) REVERT: C 598 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8102 (mt-10) REVERT: C 716 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7075 (tm-30) outliers start: 42 outliers final: 36 residues processed: 182 average time/residue: 0.2385 time to fit residues: 67.0112 Evaluate side-chains 165 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 826 ILE Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 416 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 145 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 129 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN B 321 ASN B 420 HIS ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.120648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.095707 restraints weight = 36508.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.095323 restraints weight = 27111.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.096100 restraints weight = 23675.073| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14416 Z= 0.176 Angle : 0.614 13.104 19701 Z= 0.305 Chirality : 0.042 0.252 2217 Planarity : 0.004 0.081 2330 Dihedral : 13.119 88.118 2445 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.47 % Allowed : 18.39 % Favored : 78.14 % 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: -1.58 (0.21), residues: 1595 helix: 0.91 (0.22), residues: 591 sheet: -1.99 (0.33), residues: 250 loop : -2.38 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 315 HIS 0.004 0.001 HIS B 313 PHE 0.030 0.001 PHE C 471 TYR 0.021 0.001 TYR C 313 ARG 0.004 0.000 ARG C 559 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 536) hydrogen bonds : angle 4.52874 ( 1501) metal coordination : bond 0.00922 ( 6) metal coordination : angle 1.94815 ( 6) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.21788 ( 4) covalent geometry : bond 0.00398 (14407) covalent geometry : angle 0.61282 (19691) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8703 (mtt) cc_final: 0.8448 (mtt) REVERT: A 385 MET cc_start: 0.8917 (mmm) cc_final: 0.8711 (mmm) REVERT: A 573 ASN cc_start: 0.8387 (t0) cc_final: 0.8162 (t0) REVERT: A 828 GLU cc_start: 0.7434 (mp0) cc_final: 0.7116 (mp0) REVERT: B 337 ASP cc_start: 0.8198 (m-30) cc_final: 0.7910 (m-30) REVERT: C 419 ASN cc_start: 0.8833 (p0) cc_final: 0.8441 (p0) REVERT: C 598 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8212 (mt-10) REVERT: C 716 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7056 (tm-30) outliers start: 50 outliers final: 41 residues processed: 175 average time/residue: 0.2261 time to fit residues: 61.1338 Evaluate side-chains 166 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 471 PHE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 616 PHE Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 0.0670 chunk 138 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 68 optimal weight: 0.0050 overall best weight: 2.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 ASN B 420 HIS ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.121941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.096987 restraints weight = 36697.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.096833 restraints weight = 29677.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.097611 restraints weight = 23647.867| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14416 Z= 0.129 Angle : 0.570 11.714 19701 Z= 0.283 Chirality : 0.041 0.256 2217 Planarity : 0.004 0.076 2330 Dihedral : 13.046 89.002 2445 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.61 % Allowed : 19.29 % Favored : 77.10 % 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: -1.37 (0.21), residues: 1595 helix: 1.05 (0.22), residues: 591 sheet: -1.83 (0.35), residues: 234 loop : -2.24 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 315 HIS 0.003 0.001 HIS B 313 PHE 0.033 0.001 PHE C 471 TYR 0.019 0.001 TYR C 313 ARG 0.004 0.000 ARG C 559 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 536) hydrogen bonds : angle 4.35010 ( 1501) metal coordination : bond 0.00647 ( 6) metal coordination : angle 1.91017 ( 6) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.21544 ( 4) covalent geometry : bond 0.00292 (14407) covalent geometry : angle 0.56888 (19691) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8691 (mtt) cc_final: 0.8482 (mtt) REVERT: A 385 MET cc_start: 0.8890 (mmm) cc_final: 0.8689 (mmm) REVERT: A 434 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9043 (tt) REVERT: A 828 GLU cc_start: 0.7429 (mp0) cc_final: 0.7115 (mp0) REVERT: B 257 TRP cc_start: 0.5734 (m100) cc_final: 0.5445 (m100) REVERT: B 312 LYS cc_start: 0.7383 (mmtm) cc_final: 0.7059 (ptpp) REVERT: B 337 ASP cc_start: 0.8176 (m-30) cc_final: 0.7872 (m-30) REVERT: B 414 PHE cc_start: 0.8225 (m-80) cc_final: 0.7933 (m-80) REVERT: C 385 MET cc_start: 0.8546 (mmm) cc_final: 0.8263 (mmp) REVERT: C 479 MET cc_start: 0.9133 (mmm) cc_final: 0.8908 (mmt) REVERT: C 598 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8211 (mt-10) REVERT: C 716 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7071 (tm-30) REVERT: C 883 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6853 (tm-30) outliers start: 52 outliers final: 44 residues processed: 178 average time/residue: 0.2271 time to fit residues: 62.6247 Evaluate side-chains 172 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 127 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 634 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 111 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 78 optimal weight: 0.0980 chunk 35 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN B 321 ASN B 420 HIS B 423 ASN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.123544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.099740 restraints weight = 36335.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.100849 restraints weight = 35319.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.101673 restraints weight = 22630.485| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14416 Z= 0.093 Angle : 0.546 10.764 19701 Z= 0.270 Chirality : 0.041 0.249 2217 Planarity : 0.004 0.067 2330 Dihedral : 12.919 91.982 2445 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.05 % Allowed : 20.40 % Favored : 76.54 % 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: -1.10 (0.22), residues: 1595 helix: 1.29 (0.22), residues: 591 sheet: -1.67 (0.35), residues: 244 loop : -2.12 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 315 HIS 0.002 0.000 HIS A 375 PHE 0.032 0.001 PHE C 471 TYR 0.018 0.001 TYR C 541 ARG 0.002 0.000 ARG B 342 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 536) hydrogen bonds : angle 4.10770 ( 1501) metal coordination : bond 0.00399 ( 6) metal coordination : angle 2.07094 ( 6) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.22781 ( 4) covalent geometry : bond 0.00204 (14407) covalent geometry : angle 0.54505 (19691) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8663 (mtt) cc_final: 0.8447 (mtt) REVERT: A 385 MET cc_start: 0.8874 (mmm) cc_final: 0.8669 (mmm) REVERT: A 434 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9027 (tt) REVERT: A 828 GLU cc_start: 0.7379 (mp0) cc_final: 0.7086 (mp0) REVERT: B 316 GLU cc_start: 0.4627 (tp30) cc_final: 0.4197 (tp30) REVERT: C 385 MET cc_start: 0.8540 (mmm) cc_final: 0.8239 (mmp) REVERT: C 479 MET cc_start: 0.8901 (mmm) cc_final: 0.8660 (mmt) REVERT: C 560 MET cc_start: 0.8346 (tpp) cc_final: 0.7679 (mmt) REVERT: C 716 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7005 (tm-30) outliers start: 44 outliers final: 32 residues processed: 181 average time/residue: 0.2306 time to fit residues: 65.6399 Evaluate side-chains 164 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 74 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 152 optimal weight: 0.3980 chunk 157 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.122947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099476 restraints weight = 36216.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.099907 restraints weight = 32398.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.101068 restraints weight = 23280.942| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14416 Z= 0.099 Angle : 0.549 11.101 19701 Z= 0.272 Chirality : 0.041 0.269 2217 Planarity : 0.004 0.063 2330 Dihedral : 12.803 91.662 2445 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.12 % Allowed : 20.40 % Favored : 76.47 % 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: -0.95 (0.22), residues: 1595 helix: 1.38 (0.22), residues: 593 sheet: -1.49 (0.36), residues: 245 loop : -2.04 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 315 HIS 0.002 0.000 HIS C 876 PHE 0.020 0.001 PHE C 471 TYR 0.018 0.001 TYR C 541 ARG 0.002 0.000 ARG B 342 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 536) hydrogen bonds : angle 4.03377 ( 1501) metal coordination : bond 0.00459 ( 6) metal coordination : angle 1.47629 ( 6) SS BOND : bond 0.00116 ( 2) SS BOND : angle 0.21225 ( 4) covalent geometry : bond 0.00219 (14407) covalent geometry : angle 0.54871 (19691) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9048 (tt) REVERT: A 525 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.7006 (tmm) REVERT: A 828 GLU cc_start: 0.7332 (mp0) cc_final: 0.7047 (mp0) REVERT: B 417 TYR cc_start: 0.8190 (t80) cc_final: 0.7898 (t80) REVERT: C 319 TYR cc_start: 0.7652 (m-80) cc_final: 0.7230 (m-80) REVERT: C 385 MET cc_start: 0.8539 (mmm) cc_final: 0.8248 (mmp) REVERT: C 479 MET cc_start: 0.8905 (mmm) cc_final: 0.8624 (mmt) REVERT: C 560 MET cc_start: 0.8195 (tpp) cc_final: 0.7735 (mmt) REVERT: C 716 GLU cc_start: 0.7616 (tm-30) cc_final: 0.6963 (tm-30) outliers start: 45 outliers final: 38 residues processed: 175 average time/residue: 0.2208 time to fit residues: 59.9506 Evaluate side-chains 169 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 106 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 151 optimal weight: 30.0000 chunk 115 optimal weight: 0.9990 chunk 7 optimal weight: 0.0050 chunk 62 optimal weight: 4.9990 chunk 131 optimal weight: 0.0970 chunk 85 optimal weight: 0.0970 chunk 83 optimal weight: 10.0000 chunk 158 optimal weight: 0.0370 overall best weight: 0.2470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 GLN C 259 ASN D 324 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.126017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.101557 restraints weight = 35979.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.102272 restraints weight = 30434.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.103160 restraints weight = 21893.163| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14416 Z= 0.091 Angle : 0.550 13.485 19701 Z= 0.273 Chirality : 0.040 0.262 2217 Planarity : 0.003 0.056 2330 Dihedral : 12.635 92.664 2445 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.57 % Allowed : 21.24 % Favored : 76.20 % 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: -0.71 (0.22), residues: 1595 helix: 1.62 (0.22), residues: 587 sheet: -1.37 (0.35), residues: 252 loop : -1.91 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 315 HIS 0.003 0.000 HIS B 313 PHE 0.023 0.001 PHE C 471 TYR 0.021 0.001 TYR B 400 ARG 0.006 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.02790 ( 536) hydrogen bonds : angle 3.92118 ( 1501) metal coordination : bond 0.00266 ( 6) metal coordination : angle 2.20132 ( 6) SS BOND : bond 0.00037 ( 2) SS BOND : angle 0.22392 ( 4) covalent geometry : bond 0.00195 (14407) covalent geometry : angle 0.54852 (19691) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9103 (tt) REVERT: A 755 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7697 (pmm) REVERT: A 828 GLU cc_start: 0.7292 (mp0) cc_final: 0.7070 (mp0) REVERT: B 417 TYR cc_start: 0.8087 (t80) cc_final: 0.7782 (t80) REVERT: C 319 TYR cc_start: 0.7514 (m-80) cc_final: 0.7151 (m-80) REVERT: C 385 MET cc_start: 0.8442 (mmm) cc_final: 0.8110 (mmp) REVERT: C 560 MET cc_start: 0.8054 (tpp) cc_final: 0.7611 (mmt) REVERT: C 716 GLU cc_start: 0.7596 (tm-30) cc_final: 0.6943 (tm-30) outliers start: 37 outliers final: 30 residues processed: 171 average time/residue: 0.2290 time to fit residues: 60.2759 Evaluate side-chains 169 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 25 optimal weight: 0.0270 chunk 41 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 784 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.125140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.101129 restraints weight = 36271.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.102144 restraints weight = 31866.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.103229 restraints weight = 21240.191| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14416 Z= 0.096 Angle : 0.560 14.262 19701 Z= 0.275 Chirality : 0.041 0.263 2217 Planarity : 0.003 0.054 2330 Dihedral : 12.554 91.611 2445 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.43 % Allowed : 21.17 % Favored : 76.41 % 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: -0.63 (0.22), residues: 1595 helix: 1.60 (0.22), residues: 587 sheet: -1.16 (0.36), residues: 249 loop : -1.85 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 315 HIS 0.002 0.000 HIS A 280 PHE 0.022 0.001 PHE C 471 TYR 0.023 0.001 TYR A 303 ARG 0.005 0.000 ARG C 533 Details of bonding type rmsd hydrogen bonds : bond 0.02930 ( 536) hydrogen bonds : angle 3.91751 ( 1501) metal coordination : bond 0.00348 ( 6) metal coordination : angle 1.85177 ( 6) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.18772 ( 4) covalent geometry : bond 0.00212 (14407) covalent geometry : angle 0.55954 (19691) Misc. bond : bond 0.00008 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 755 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7732 (pmm) REVERT: A 828 GLU cc_start: 0.7309 (mp0) cc_final: 0.7064 (mp0) REVERT: B 417 TYR cc_start: 0.8048 (t80) cc_final: 0.7778 (t80) REVERT: C 319 TYR cc_start: 0.7540 (m-80) cc_final: 0.7161 (m-80) REVERT: C 385 MET cc_start: 0.8440 (mmm) cc_final: 0.8116 (mmp) REVERT: C 560 MET cc_start: 0.8071 (tpp) cc_final: 0.7598 (mmt) REVERT: C 716 GLU cc_start: 0.7586 (tm-30) cc_final: 0.6933 (tm-30) outliers start: 35 outliers final: 32 residues processed: 162 average time/residue: 0.2143 time to fit residues: 54.4440 Evaluate side-chains 163 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 820 THR Chi-restraints excluded: chain C residue 834 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain C residue 916 ILE Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain D residue 349 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 158 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 150 optimal weight: 50.0000 chunk 107 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 97 optimal weight: 0.0870 chunk 149 optimal weight: 8.9990 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.099242 restraints weight = 36536.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.099124 restraints weight = 30100.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.100048 restraints weight = 23018.862| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14416 Z= 0.110 Angle : 0.582 13.817 19701 Z= 0.284 Chirality : 0.041 0.252 2217 Planarity : 0.004 0.053 2330 Dihedral : 12.546 89.030 2445 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.43 % Allowed : 21.58 % Favored : 75.99 % 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: -0.65 (0.22), residues: 1595 helix: 1.57 (0.22), residues: 589 sheet: -1.21 (0.35), residues: 263 loop : -1.85 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 315 HIS 0.002 0.001 HIS C 876 PHE 0.021 0.001 PHE C 471 TYR 0.022 0.001 TYR C 541 ARG 0.005 0.000 ARG C 533 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 536) hydrogen bonds : angle 3.96305 ( 1501) metal coordination : bond 0.00480 ( 6) metal coordination : angle 1.92983 ( 6) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.17978 ( 4) covalent geometry : bond 0.00249 (14407) covalent geometry : angle 0.58069 (19691) Misc. bond : bond 0.00002 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3771.24 seconds wall clock time: 67 minutes 19.57 seconds (4039.57 seconds total)