Starting phenix.real_space_refine on Mon Dec 30 23:25:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7v_29825/12_2024/8g7v_29825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7v_29825/12_2024/8g7v_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_29825/12_2024/8g7v_29825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7v_29825/12_2024/8g7v_29825.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7v_29825/12_2024/8g7v_29825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7v_29825/12_2024/8g7v_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-5532/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: 8.89, per 1000 atoms: 0.63 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: 3.62 Conformation dependent library (CDL) restraints added in 1.6 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: 4.95 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: 4.97 Time building geometry restraints manager: 4.10 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: 0.860 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: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.750 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.030 ------------------------------------------------------------------------------- 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 : 0.007 0.232 14407 Z= 0.460 Angle : 0.849 12.952 19691 Z= 0.458 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 *********************** 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 : 1.647 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: 0.3132 time to fit residues: 90.6020 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 : 1.778 ------------------------------------------------------------------------------- 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: 3.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 40.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14407 Z= 0.266 Angle : 0.630 12.951 19691 Z= 0.323 Chirality : 0.042 0.220 2217 Planarity : 0.005 0.102 2330 Dihedral : 13.626 102.676 2449 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.22 % Allowed : 13.25 % Favored : 84.52 % 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: -0.35 (0.20), residues: 585 sheet: -2.51 (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 *********************** 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 : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8854 (mmm) cc_final: 0.8464 (mtp) REVERT: A 387 MET cc_start: 0.8697 (mmm) cc_final: 0.8494 (mmp) REVERT: A 573 ASN cc_start: 0.8245 (t0) cc_final: 0.8010 (t0) REVERT: A 828 GLU cc_start: 0.7306 (mp0) cc_final: 0.7007 (mp0) REVERT: B 337 ASP cc_start: 0.8007 (m-30) cc_final: 0.7763 (m-30) REVERT: B 379 TRP cc_start: 0.6789 (t-100) cc_final: 0.6562 (t-100) REVERT: C 300 ILE cc_start: 0.9199 (mm) cc_final: 0.8759 (mt) REVERT: C 419 ASN cc_start: 0.8884 (p0) cc_final: 0.8404 (p0) REVERT: C 598 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8101 (mp0) REVERT: C 624 LEU cc_start: 0.8699 (tt) cc_final: 0.8422 (mp) outliers start: 32 outliers final: 23 residues processed: 174 average time/residue: 0.2703 time to fit residues: 70.4293 Evaluate side-chains 149 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 412 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 82 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 148 optimal weight: 40.0000 chunk 160 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14407 Z= 0.308 Angle : 0.636 14.620 19691 Z= 0.322 Chirality : 0.043 0.249 2217 Planarity : 0.005 0.095 2330 Dihedral : 13.362 89.194 2447 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.12 % Allowed : 15.34 % Favored : 81.54 % 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: -2.20 (0.20), residues: 1595 helix: 0.29 (0.21), residues: 586 sheet: -2.33 (0.32), residues: 247 loop : -2.62 (0.20), residues: 762 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 0.028 0.002 PHE C 471 TYR 0.018 0.002 TYR C 313 ARG 0.003 0.000 ARG A 811 *********************** 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 181 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8646 (mtt) cc_final: 0.8394 (mtt) REVERT: A 385 MET cc_start: 0.8874 (mmm) cc_final: 0.8507 (mtp) REVERT: A 573 ASN cc_start: 0.8240 (t0) cc_final: 0.7990 (t0) REVERT: A 828 GLU cc_start: 0.7389 (mp0) cc_final: 0.7076 (mp0) REVERT: B 312 LYS cc_start: 0.7270 (mmtm) cc_final: 0.6982 (ptpp) REVERT: B 337 ASP cc_start: 0.8028 (m-30) cc_final: 0.7774 (m-30) REVERT: C 300 ILE cc_start: 0.9188 (mm) cc_final: 0.8778 (mt) REVERT: C 419 ASN cc_start: 0.8820 (p0) cc_final: 0.8337 (p0) REVERT: C 598 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8029 (mt-10) REVERT: C 716 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7122 (tm-30) outliers start: 45 outliers final: 34 residues processed: 173 average time/residue: 0.2467 time to fit residues: 65.0458 Evaluate side-chains 156 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 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 475 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 834 LEU 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 146 optimal weight: 30.0000 chunk 111 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 148 optimal weight: 50.0000 chunk 157 optimal weight: 30.0000 chunk 77 optimal weight: 1.9990 chunk 141 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 321 ASN B 420 HIS ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14407 Z= 0.136 Angle : 0.530 10.507 19691 Z= 0.270 Chirality : 0.040 0.252 2217 Planarity : 0.004 0.079 2330 Dihedral : 13.141 90.880 2446 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.85 % Allowed : 17.07 % Favored : 80.08 % 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: -1.63 (0.21), residues: 1595 helix: 0.87 (0.22), residues: 586 sheet: -1.98 (0.33), residues: 247 loop : -2.41 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 315 HIS 0.003 0.000 HIS B 313 PHE 0.026 0.001 PHE C 471 TYR 0.015 0.001 TYR C 313 ARG 0.002 0.000 ARG C 502 *********************** 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 192 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8884 (mmm) cc_final: 0.8654 (mmm) REVERT: A 434 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8972 (tt) REVERT: A 525 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.7077 (tmm) REVERT: A 573 ASN cc_start: 0.8252 (t0) cc_final: 0.8050 (t0) REVERT: A 828 GLU cc_start: 0.7271 (mp0) cc_final: 0.7016 (mp0) REVERT: B 257 TRP cc_start: 0.5477 (m100) cc_final: 0.5199 (m100) REVERT: B 337 ASP cc_start: 0.7996 (m-30) cc_final: 0.7738 (m-30) REVERT: C 385 MET cc_start: 0.8535 (mmm) cc_final: 0.8273 (mmp) REVERT: C 419 ASN cc_start: 0.8807 (p0) cc_final: 0.8387 (p0) REVERT: C 598 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8119 (mt-10) REVERT: C 624 LEU cc_start: 0.8605 (tt) cc_final: 0.8345 (mp) REVERT: C 716 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7100 (tm-30) outliers start: 41 outliers final: 32 residues processed: 182 average time/residue: 0.2395 time to fit residues: 67.4643 Evaluate side-chains 163 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.632 ------------------------------------------------------------------------------- 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 525 MET 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 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 826 ILE 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 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 131 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN B 420 HIS ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 GLN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14407 Z= 0.337 Angle : 0.656 14.596 19691 Z= 0.327 Chirality : 0.044 0.251 2217 Planarity : 0.004 0.085 2330 Dihedral : 13.157 89.412 2445 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 3.61 % Allowed : 18.32 % Favored : 78.07 % 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: -1.65 (0.21), residues: 1595 helix: 0.84 (0.22), residues: 588 sheet: -2.02 (0.31), residues: 279 loop : -2.39 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 315 HIS 0.005 0.001 HIS A 281 PHE 0.029 0.002 PHE C 471 TYR 0.022 0.002 TYR C 313 ARG 0.005 0.000 ARG C 824 *********************** 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: 52 poor density : 131 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8717 (mtt) cc_final: 0.8505 (mtt) REVERT: A 385 MET cc_start: 0.8860 (mmm) cc_final: 0.8446 (mtp) REVERT: A 525 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7215 (tmm) REVERT: A 573 ASN cc_start: 0.8235 (t0) cc_final: 0.7996 (t0) REVERT: A 828 GLU cc_start: 0.7419 (mp0) cc_final: 0.7095 (mp0) REVERT: B 337 ASP cc_start: 0.8112 (m-30) cc_final: 0.7834 (m-30) REVERT: C 419 ASN cc_start: 0.8845 (p0) cc_final: 0.8442 (p0) REVERT: C 560 MET cc_start: 0.8465 (mmt) cc_final: 0.8234 (mmt) REVERT: C 598 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8109 (mt-10) REVERT: C 716 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7041 (tm-30) outliers start: 52 outliers final: 43 residues processed: 175 average time/residue: 0.2375 time to fit residues: 64.8220 Evaluate side-chains 165 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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 441 THR Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain A residue 525 MET 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 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 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 53 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 157 optimal weight: 30.0000 chunk 130 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14407 Z= 0.158 Angle : 0.552 11.137 19691 Z= 0.277 Chirality : 0.041 0.259 2217 Planarity : 0.004 0.075 2330 Dihedral : 13.050 89.596 2445 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.12 % Allowed : 19.64 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1595 helix: 1.07 (0.22), residues: 591 sheet: -1.88 (0.34), residues: 249 loop : -2.24 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 315 HIS 0.002 0.001 HIS C 281 PHE 0.029 0.001 PHE C 471 TYR 0.018 0.001 TYR C 313 ARG 0.002 0.000 ARG C 559 *********************** 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 185 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8674 (mtt) cc_final: 0.8435 (mtt) REVERT: A 385 MET cc_start: 0.8863 (mmm) cc_final: 0.8656 (mmm) REVERT: A 828 GLU cc_start: 0.7389 (mp0) cc_final: 0.7089 (mp0) REVERT: B 337 ASP cc_start: 0.8095 (m-30) cc_final: 0.7795 (m-30) REVERT: B 414 PHE cc_start: 0.8147 (m-80) cc_final: 0.7878 (m-80) REVERT: C 385 MET cc_start: 0.8536 (mmm) cc_final: 0.8286 (mmp) REVERT: C 598 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8147 (mt-10) REVERT: C 716 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7032 (tm-30) outliers start: 45 outliers final: 39 residues processed: 176 average time/residue: 0.2472 time to fit residues: 66.6314 Evaluate side-chains 164 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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 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 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 452 VAL 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 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 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 152 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 98 optimal weight: 0.0770 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14407 Z= 0.263 Angle : 0.625 13.023 19691 Z= 0.307 Chirality : 0.043 0.254 2217 Planarity : 0.004 0.078 2330 Dihedral : 13.049 88.169 2445 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 3.68 % Allowed : 19.78 % 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: -1.40 (0.21), residues: 1595 helix: 0.99 (0.22), residues: 592 sheet: -1.86 (0.33), residues: 272 loop : -2.23 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 315 HIS 0.004 0.001 HIS A 281 PHE 0.033 0.001 PHE C 471 TYR 0.027 0.002 TYR C 313 ARG 0.003 0.000 ARG C 559 *********************** 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 187 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 134 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8709 (mtt) cc_final: 0.8484 (mtt) REVERT: A 525 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7122 (tmm) REVERT: A 828 GLU cc_start: 0.7417 (mp0) cc_final: 0.7093 (mp0) REVERT: B 337 ASP cc_start: 0.8162 (m-30) cc_final: 0.7868 (m-30) REVERT: B 414 PHE cc_start: 0.8181 (m-80) cc_final: 0.7932 (m-80) REVERT: C 247 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8521 (mt0) REVERT: C 598 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8167 (mt-10) REVERT: C 716 GLU cc_start: 0.7625 (tm-30) cc_final: 0.6891 (tm-30) outliers start: 53 outliers final: 47 residues processed: 178 average time/residue: 0.2379 time to fit residues: 64.6426 Evaluate side-chains 170 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 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 525 MET 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 718 VAL Chi-restraints excluded: chain A residue 884 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 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 247 GLN 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 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 825 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 14 optimal weight: 0.4980 chunk 123 optimal weight: 9.9990 chunk 142 optimal weight: 30.0000 chunk 150 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN A 794 GLN B 420 HIS B 423 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14407 Z= 0.149 Angle : 0.565 13.013 19691 Z= 0.281 Chirality : 0.041 0.244 2217 Planarity : 0.004 0.069 2330 Dihedral : 12.935 90.860 2445 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.12 % Allowed : 20.82 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.22), residues: 1595 helix: 1.24 (0.22), residues: 591 sheet: -1.65 (0.35), residues: 254 loop : -2.13 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 315 HIS 0.002 0.000 HIS B 324 PHE 0.023 0.001 PHE C 471 TYR 0.027 0.001 TYR B 400 ARG 0.003 0.000 ARG B 342 *********************** 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 183 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 MET cc_start: 0.8644 (mtt) cc_final: 0.8430 (mtt) REVERT: A 525 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7101 (tmm) REVERT: A 828 GLU cc_start: 0.7394 (mp0) cc_final: 0.7095 (mp0) REVERT: B 417 TYR cc_start: 0.8224 (t80) cc_final: 0.7920 (t80) REVERT: C 385 MET cc_start: 0.8473 (mmm) cc_final: 0.8252 (mmp) REVERT: C 598 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8197 (mt-10) REVERT: C 716 GLU cc_start: 0.7591 (tm-30) cc_final: 0.6913 (tm-30) outliers start: 45 outliers final: 34 residues processed: 174 average time/residue: 0.2454 time to fit residues: 65.5114 Evaluate side-chains 162 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR 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 441 THR 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 894 VAL Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 366 THR 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 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 903 THR 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 416 LEU 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 137 optimal weight: 8.9990 chunk 146 optimal weight: 30.0000 chunk 150 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 114 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 145 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 GLN C 247 GLN C 619 GLN C 784 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14407 Z= 0.324 Angle : 0.664 14.166 19691 Z= 0.328 Chirality : 0.044 0.263 2217 Planarity : 0.004 0.074 2330 Dihedral : 12.993 89.916 2445 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.54 % Allowed : 20.40 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1595 helix: 1.05 (0.21), residues: 590 sheet: -1.85 (0.33), residues: 265 loop : -2.21 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 315 HIS 0.004 0.001 HIS A 281 PHE 0.020 0.002 PHE C 471 TYR 0.028 0.002 TYR C 313 ARG 0.003 0.000 ARG C 559 *********************** 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 178 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8777 (mmm) cc_final: 0.8348 (mtp) REVERT: A 521 MET cc_start: 0.8400 (ttm) cc_final: 0.8069 (ttm) REVERT: A 525 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.7038 (tmm) REVERT: A 828 GLU cc_start: 0.7459 (mp0) cc_final: 0.7127 (mp0) REVERT: B 417 TYR cc_start: 0.8242 (t80) cc_final: 0.7894 (t80) REVERT: C 385 MET cc_start: 0.8521 (mmm) cc_final: 0.8289 (mmp) REVERT: C 598 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8186 (mt-10) REVERT: C 716 GLU cc_start: 0.7669 (tm-30) cc_final: 0.6913 (tm-30) outliers start: 51 outliers final: 43 residues processed: 168 average time/residue: 0.2505 time to fit residues: 65.0639 Evaluate side-chains 166 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 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 300 ILE 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 479 MET 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 884 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 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 425 ASP Chi-restraints excluded: chain C residue 452 VAL 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 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 416 LEU 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 154 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 149 optimal weight: 50.0000 chunk 129 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14407 Z= 0.185 Angle : 0.596 12.203 19691 Z= 0.297 Chirality : 0.042 0.251 2217 Planarity : 0.004 0.070 2330 Dihedral : 12.901 89.028 2445 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.78 % Allowed : 21.30 % Favored : 75.92 % 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: 1.30 (0.22), residues: 586 sheet: -1.62 (0.34), residues: 261 loop : -2.11 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 646 HIS 0.002 0.001 HIS C 876 PHE 0.020 0.001 PHE C 471 TYR 0.025 0.001 TYR B 400 ARG 0.002 0.000 ARG A 811 ********************** 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 169 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 525 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7028 (tmm) REVERT: A 755 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7742 (pmm) REVERT: A 828 GLU cc_start: 0.7458 (mp0) cc_final: 0.7129 (mp0) REVERT: B 316 GLU cc_start: 0.5073 (tp30) cc_final: 0.4317 (tp30) REVERT: B 417 TYR cc_start: 0.8166 (t80) cc_final: 0.7790 (t80) REVERT: C 385 MET cc_start: 0.8528 (mmm) cc_final: 0.8284 (mmp) REVERT: C 598 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8181 (mt-10) REVERT: C 716 GLU cc_start: 0.7658 (tm-30) cc_final: 0.6865 (tm-30) outliers start: 40 outliers final: 38 residues processed: 161 average time/residue: 0.2461 time to fit residues: 61.1999 Evaluate side-chains 166 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 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 755 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 903 THR 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 425 ASP Chi-restraints excluded: chain C residue 452 VAL 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 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 416 LEU 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 137 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.119911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.097292 restraints weight = 36505.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.096233 restraints weight = 38177.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097416 restraints weight = 32566.338| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14407 Z= 0.305 Angle : 0.658 13.606 19691 Z= 0.326 Chirality : 0.044 0.260 2217 Planarity : 0.004 0.073 2330 Dihedral : 12.933 88.893 2445 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 3.05 % Allowed : 21.37 % Favored : 75.57 % 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: -1.24 (0.22), residues: 1595 helix: 1.17 (0.21), residues: 585 sheet: -1.71 (0.34), residues: 269 loop : -2.17 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 646 HIS 0.004 0.001 HIS C 876 PHE 0.019 0.002 PHE C 471 TYR 0.029 0.002 TYR B 400 ARG 0.003 0.000 ARG C 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2441.66 seconds wall clock time: 46 minutes 57.94 seconds (2817.94 seconds total)