Starting phenix.real_space_refine on Fri Jul 3 13:11:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g7t_29823/07_2026/8g7t_29823.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7t_29823/07_2026/8g7t_29823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8g7t_29823/07_2026/8g7t_29823.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g7t_29823/07_2026/8g7t_29823.cif" model { file = "/net/cci-nas-00/data/ceres_data/8g7t_29823/07_2026/8g7t_29823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7t_29823/07_2026/8g7t_29823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g7t_29823/07_2026/8g7t_29823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7t_29823/07_2026/8g7t_29823.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 52 5.49 5 S 77 5.16 5 C 8785 2.51 5 N 2400 2.21 5 O 2743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14059 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: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 5000 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 25, 'TRANS': 590} Chain breaks: 4 Chain: "D" 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: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "X" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 523 Unusual residues: {'GTP': 1} Classifications: {'RNA': 23, 'undetermined': 1} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 11} Link IDs: {'rna3p': 22, None: 1} Not linked: pdbres="GTP X 1 " pdbres=" G X 2 " Chain: "Y" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 516 Unusual residues: {'UTP': 1} Classifications: {'RNA': 23, 'undetermined': 1} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 12} Link IDs: {'rna3p': 22, None: 1} Not linked: pdbres="UTP Y 1 " pdbres=" C Y 2 " 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 4302 SG CYS A 810 95.220 82.980 65.658 1.00 24.09 S ATOM 4741 SG CYS A 864 97.097 86.788 66.632 1.00 35.22 S ATOM 4780 SG CYS A 869 93.983 86.644 64.616 1.00 40.34 S ATOM 11150 SG CYS C 864 39.821 27.357 65.024 1.00 81.69 S ATOM 11189 SG CYS C 869 39.334 31.210 66.004 1.00 85.78 S Time building chain proxies: 2.85, per 1000 atoms: 0.20 Number of scatterers: 14059 At special positions: 0 Unit cell: (120.816, 125.011, 136.757, 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 77 16.00 P 52 15.00 O 2743 8.00 N 2400 7.00 C 8785 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=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 518.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 864 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 869 " 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 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 36.9% alpha, 10.6% beta 13 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 245 through 250 removed outlier: 4.129A pdb=" N LEU A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 284 removed outlier: 3.642A pdb=" N LEU A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 312 removed outlier: 3.735A pdb=" N SER A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.726A pdb=" N ILE A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 333 through 339' Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.916A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 4.144A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.797A pdb=" N ASN A 376 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 395 removed outlier: 3.761A pdb=" N ILE A 386 " --> pdb=" O PRO A 382 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 434 removed outlier: 3.703A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 469 through 487 removed outlier: 3.896A pdb=" N TYR A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 4.008A pdb=" N SER A 497 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 520 removed outlier: 3.815A pdb=" N GLU A 510 " --> pdb=" O THR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 558 removed outlier: 3.753A pdb=" N LYS A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 545 " --> pdb=" O TYR A 541 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 552 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 578 removed outlier: 3.671A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 564 " --> pdb=" O MET A 560 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 567 " --> pdb=" O ALA A 563 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 578 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 592 removed outlier: 3.634A pdb=" N ASP A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 592 " --> pdb=" O GLN A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 601 removed outlier: 3.505A pdb=" N VAL A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 removed outlier: 3.552A pdb=" N ASP A 613 " --> pdb=" O PRO A 609 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS A 623 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 648 removed outlier: 3.763A pdb=" N ILE A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 654 removed outlier: 3.940A pdb=" N SER A 654 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 770 removed outlier: 3.894A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 780 removed outlier: 3.527A pdb=" N ARG A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 794 removed outlier: 3.576A pdb=" N THR A 785 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 840 removed outlier: 3.763A pdb=" N GLU A 840 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.713A pdb=" N LEU C 250 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA C 251 " --> pdb=" O GLN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 284 removed outlier: 3.590A pdb=" N THR C 271 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 276 " --> pdb=" O PHE C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 314 removed outlier: 3.565A pdb=" N SER C 308 " --> pdb=" O GLU C 304 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 341 removed outlier: 3.661A pdb=" N ILE C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 358 removed outlier: 3.501A pdb=" N LEU C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 357 " --> pdb=" O ASN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 366 removed outlier: 4.177A pdb=" N ILE C 365 " --> pdb=" O SER C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 377 Processing helix chain 'C' and resid 381 through 395 removed outlier: 3.622A pdb=" N ILE C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET C 387 " --> pdb=" O TYR C 383 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 388 " --> pdb=" O ASN C 384 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN C 389 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP C 392 " --> pdb=" O PHE C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 435 removed outlier: 3.847A pdb=" N ASP C 425 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR C 426 " --> pdb=" O GLU C 422 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 removed outlier: 4.005A pdb=" N LEU C 449 " --> pdb=" O ASN C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 487 removed outlier: 3.702A pdb=" N ILE C 474 " --> pdb=" O LYS C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 520 removed outlier: 3.779A pdb=" N GLU C 510 " --> pdb=" O THR C 506 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS C 520 " --> pdb=" O VAL C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 558 removed outlier: 3.582A pdb=" N LYS C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 553 " --> pdb=" O ASN C 549 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 554 " --> pdb=" O ASP C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 576 removed outlier: 3.822A pdb=" N LEU C 564 " --> pdb=" O MET C 560 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP C 565 " --> pdb=" O LYS C 561 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 570 " --> pdb=" O TYR C 566 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C 576 " --> pdb=" O SER C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 593 removed outlier: 3.520A pdb=" N ASP C 585 " --> pdb=" O GLU C 581 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 603 removed outlier: 3.538A pdb=" N VAL C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C 602 " --> pdb=" O GLU C 598 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP C 603 " --> pdb=" O SER C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 625 removed outlier: 3.617A pdb=" N ASP C 613 " --> pdb=" O PRO C 609 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN C 619 " --> pdb=" O CYS C 615 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 620 " --> pdb=" O PHE C 616 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 621 " --> pdb=" O ILE C 617 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 622 " --> pdb=" O LEU C 618 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS C 623 " --> pdb=" O GLN C 619 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 624 " --> pdb=" O GLU C 620 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN C 625 " --> pdb=" O GLU C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 648 removed outlier: 3.757A pdb=" N ASP C 641 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 642 " --> pdb=" O ALA C 638 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 644 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN C 645 " --> pdb=" O ASP C 641 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU C 648 " --> pdb=" O LYS C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 769 removed outlier: 3.567A pdb=" N ASN C 754 " --> pdb=" O LYS C 750 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C 756 " --> pdb=" O GLN C 752 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 766 " --> pdb=" O ASN C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 793 removed outlier: 3.650A pdb=" N HIS C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 783 " --> pdb=" O LYS C 779 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 789 " --> pdb=" O THR C 785 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 790 " --> pdb=" O HIS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 911 Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296 removed outlier: 6.509A pdb=" N VAL A 294 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 322 removed outlier: 3.717A pdb=" N THR A 322 " --> pdb=" O ILE A 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 462 removed outlier: 3.687A pdb=" N PHE A 459 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 740 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR A 742 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 631 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR A 715 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE A 633 " --> pdb=" O TYR A 715 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU A 632 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 7.384A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 831 through 833 removed outlier: 4.317A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 843 Processing sheet with id=AA7, first strand: chain 'A' and resid 858 through 860 removed outlier: 7.088A pdb=" N HIS A 876 " --> pdb=" O ARG A 859 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 282 Processing sheet with id=AA9, first strand: chain 'B' and resid 301 through 302 removed outlier: 4.087A pdb=" N TRP B 325 " --> pdb=" O TRP B 351 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 349 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 313 through 318 removed outlier: 3.784A pdb=" N HIS B 313 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP B 315 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 378 " --> pdb=" O TRP B 315 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 317 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 376 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 294 through 296 removed outlier: 6.558A pdb=" N VAL C 294 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASP C 372 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE C 296 " --> pdb=" O ASP C 372 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU C 408 " --> pdb=" O MET C 369 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N PHE C 371 " --> pdb=" O LEU C 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 460 through 462 removed outlier: 3.848A pdb=" N THR C 742 " --> pdb=" O ARG C 461 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL C 712 " --> pdb=" O PHE C 739 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU C 741 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C 714 " --> pdb=" O LEU C 741 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE C 631 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TYR C 715 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N PHE C 633 " --> pdb=" O TYR C 715 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 816 through 819 removed outlier: 3.770A pdb=" N CYS C 818 " --> pdb=" O LEU C 808 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 894 " --> pdb=" O THR C 903 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 842 through 846 removed outlier: 3.573A pdb=" N ALA C 860 " --> pdb=" O HIS C 876 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 862 " --> pdb=" O GLY C 874 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY C 874 " --> pdb=" O ILE C 862 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N CYS C 864 " --> pdb=" O ASP C 872 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ASP C 872 " --> pdb=" O CYS C 864 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 877 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL C 833 " --> pdb=" O PRO C 885 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR C 831 " --> pdb=" O ILE C 887 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE C 916 " --> pdb=" O VAL C 823 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 301 through 302 removed outlier: 3.580A pdb=" N VAL D 302 " --> pdb=" O PHE D 414 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA D 413 " --> pdb=" O GLY D 328 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY D 328 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TRP D 325 " --> pdb=" O TRP D 351 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 327 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS D 348 " --> pdb=" O TRP D 360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 386 through 389 removed outlier: 3.639A pdb=" N ALA D 388 " --> pdb=" O TRP D 379 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D 378 " --> pdb=" O TRP D 315 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP D 315 " --> pdb=" O ILE D 378 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS D 313 " --> pdb=" O LEU D 380 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE D 426 " --> pdb=" O ASP D 318 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2190 1.29 - 1.42: 4030 1.42 - 1.55: 8036 1.55 - 1.69: 107 1.69 - 1.82: 103 Bond restraints: 14466 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=" C3' UTP Y 1 " pdb=" C4' UTP Y 1 " ideal model delta sigma weight residual 1.527 1.300 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C1' GTP X 1 " pdb=" O4' GTP X 1 " ideal model delta sigma weight residual 1.410 1.617 -0.207 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C1' UTP Y 1 " pdb=" C2' UTP Y 1 " ideal model delta sigma weight residual 1.525 1.343 0.182 2.00e-02 2.50e+03 8.28e+01 bond pdb=" C5 GTP X 1 " pdb=" C6 GTP X 1 " ideal model delta sigma weight residual 1.390 1.550 -0.160 2.00e-02 2.50e+03 6.37e+01 ... (remaining 14461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 19541 2.40 - 4.80: 194 4.80 - 7.21: 32 7.21 - 9.61: 12 9.61 - 12.01: 4 Bond angle restraints: 19783 Sorted by residual: angle pdb=" O1A UTP Y 1 " pdb=" PA UTP Y 1 " pdb=" O2A UTP Y 1 " ideal model delta sigma weight residual 121.55 109.54 12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C ASN D 394 " pdb=" N GLN D 395 " pdb=" CA GLN D 395 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" O3A UTP Y 1 " pdb=" PB UTP Y 1 " pdb=" O3B UTP Y 1 " ideal model delta sigma weight residual 98.89 109.68 -10.79 3.00e+00 1.11e-01 1.29e+01 angle pdb=" O1B UTP Y 1 " pdb=" PB UTP Y 1 " pdb=" O2B UTP Y 1 " ideal model delta sigma weight residual 119.49 109.38 10.11 3.00e+00 1.11e-01 1.14e+01 angle pdb=" PA UTP Y 1 " pdb=" O3A UTP Y 1 " pdb=" PB UTP Y 1 " ideal model delta sigma weight residual 133.62 123.59 10.03 3.00e+00 1.11e-01 1.12e+01 ... (remaining 19778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.61: 8277 28.61 - 57.21: 317 57.21 - 85.82: 41 85.82 - 114.42: 9 114.42 - 143.03: 3 Dihedral angle restraints: 8647 sinusoidal: 3883 harmonic: 4764 Sorted by residual: dihedral pdb=" O3A GTP X 1 " pdb=" O3B GTP X 1 " pdb=" PB GTP X 1 " pdb=" PG GTP X 1 " ideal model delta sinusoidal sigma weight residual 303.79 160.76 143.03 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" O5' GTP X 1 " pdb=" O3A GTP X 1 " pdb=" PA GTP X 1 " pdb=" PB GTP X 1 " ideal model delta sinusoidal sigma weight residual 274.12 155.49 118.63 1 2.00e+01 2.50e-03 3.55e+01 dihedral pdb=" CA VAL B 392 " pdb=" C VAL B 392 " pdb=" N ASP B 393 " pdb=" CA ASP B 393 " ideal model delta harmonic sigma weight residual 180.00 150.25 29.75 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 8644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1849 0.054 - 0.108: 286 0.108 - 0.162: 76 0.162 - 0.217: 8 0.217 - 0.271: 5 Chirality restraints: 2224 Sorted by residual: chirality pdb=" C3' UTP Y 1 " pdb=" C2' UTP Y 1 " pdb=" C4' UTP Y 1 " pdb=" O3' UTP Y 1 " both_signs ideal model delta sigma weight residual False -2.69 -2.42 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB ILE C 343 " pdb=" CA ILE C 343 " pdb=" CG1 ILE C 343 " pdb=" CG2 ILE C 343 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE A 343 " pdb=" CA ILE A 343 " pdb=" CG1 ILE A 343 " pdb=" CG2 ILE A 343 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2221 not shown) Planarity restraints: 2334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 261 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C ILE A 261 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 261 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 262 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 343 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C ILE A 343 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE A 343 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE A 344 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 261 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C ILE C 261 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE C 261 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE C 262 " 0.011 2.00e-02 2.50e+03 ... (remaining 2331 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1499 2.75 - 3.29: 12239 3.29 - 3.83: 22922 3.83 - 4.36: 26863 4.36 - 4.90: 44584 Nonbonded interactions: 108107 Sorted by model distance: nonbonded pdb=" O ASP C 469 " pdb=" OD1 ASP C 469 " model vdw 2.218 3.040 nonbonded pdb=" O SER D 407 " pdb=" OG SER D 407 " model vdw 2.322 3.040 nonbonded pdb=" O SER D 278 " pdb=" OG SER D 278 " model vdw 2.326 3.040 nonbonded pdb=" O SER B 278 " pdb=" OG SER B 278 " model vdw 2.330 3.040 nonbonded pdb=" OG SER D 335 " pdb=" OD1 ASP D 337 " model vdw 2.340 3.040 ... (remaining 108102 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 658 or resid 691 through 699 or resid 710 thro \ ugh 718 or resid 736 through 793 or resid 800 through 921 or resid 1001)) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 252 through 382 or (resid 383 through 384 and (name N or n \ ame CA or name C or name O or name CB )) or resid 385 through 430)) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.440 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.160 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 0.479 14475 Z= 0.354 Angle : 0.635 12.010 19787 Z= 0.330 Chirality : 0.045 0.271 2224 Planarity : 0.004 0.048 2334 Dihedral : 15.007 143.030 5539 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.29 % Allowed : 12.76 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.23 (0.15), residues: 1593 helix: -4.62 (0.06), residues: 536 sheet: -2.31 (0.33), residues: 250 loop : -2.99 (0.17), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 502 TYR 0.011 0.001 TYR C 879 PHE 0.014 0.001 PHE C 853 TRP 0.006 0.000 TRP D 379 HIS 0.002 0.000 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.29 (14466) covalent geometry : angle 0.63506 / 0.33 (19783) SS BOND : bond 0.00187 / 0.10 ( 2) SS BOND : angle 0.33865 / 0.21 ( 4) hydrogen bonds : bond 0.32916 / 21.08 ( 431) hydrogen bonds : angle 9.51812 / 6.54 ( 1213) metal coordination : bond 0.32655 / 16.11 ( 5) Misc. bond : bond 0.00023 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 272 time to evaluate : 0.530 Fit side-chains REVERT: A 272 PHE cc_start: 0.8137 (t80) cc_final: 0.7779 (t80) REVERT: A 405 VAL cc_start: 0.8804 (t) cc_final: 0.8567 (t) REVERT: A 579 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7644 (m-10) REVERT: B 348 CYS cc_start: 0.5952 (p) cc_final: 0.5745 (p) REVERT: B 402 CYS cc_start: 0.1746 (t) cc_final: 0.1269 (t) REVERT: C 579 PHE cc_start: 0.5205 (m-80) cc_final: 0.4612 (m-80) outliers start: 33 outliers final: 21 residues processed: 297 average time/residue: 0.1132 time to fit residues: 48.7419 Evaluate side-chains 196 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 408 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain D residue 392 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS A 380 GLN A 393 GLN A 445 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A 726 GLN A 762 ASN A 782 HIS A 805 ASN A 830 HIS A 876 HIS B 256 GLN B 313 HIS B 321 ASN C 299 GLN C 305 GLN C 317 HIS C 354 ASN C 380 GLN C 419 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 606 ASN ** C 623 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 HIS C 786 HIS D 313 HIS D 429 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.147162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106472 restraints weight = 22609.920| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.76 r_work: 0.3069 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14475 Z= 0.253 Angle : 0.630 9.749 19787 Z= 0.323 Chirality : 0.044 0.254 2224 Planarity : 0.005 0.051 2334 Dihedral : 8.706 102.415 2360 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.61 % Allowed : 15.53 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.48 (0.18), residues: 1593 helix: -1.86 (0.18), residues: 550 sheet: -2.36 (0.32), residues: 255 loop : -2.60 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 811 TYR 0.017 0.002 TYR C 383 PHE 0.017 0.002 PHE A 388 TRP 0.008 0.001 TRP D 379 HIS 0.009 0.002 HIS C 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (14466) covalent geometry : angle 0.62976 / 0.32 (19783) SS BOND : bond 0.00493 / 0.25 ( 2) SS BOND : angle 1.13348 / 0.80 ( 4) hydrogen bonds : bond 0.05420 / 3.46 ( 431) hydrogen bonds : angle 4.89482 / 3.37 ( 1213) metal coordination : bond 0.00382 / 0.19 ( 5) Misc. bond : bond 0.00109 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 150 time to evaluate : 0.330 Fit side-chains REVERT: A 255 MET cc_start: 0.8856 (mtt) cc_final: 0.8597 (mtt) REVERT: C 579 PHE cc_start: 0.5684 (OUTLIER) cc_final: 0.4829 (m-10) REVERT: C 595 GLN cc_start: 0.8620 (pm20) cc_final: 0.8329 (pm20) REVERT: C 622 TYR cc_start: 0.7150 (m-80) cc_final: 0.6742 (m-10) REVERT: C 782 HIS cc_start: 0.7986 (m90) cc_final: 0.7454 (t70) REVERT: D 324 HIS cc_start: 0.7519 (m-70) cc_final: 0.7296 (m90) REVERT: D 411 TYR cc_start: 0.7206 (m-80) cc_final: 0.6982 (m-80) outliers start: 52 outliers final: 37 residues processed: 189 average time/residue: 0.0997 time to fit residues: 28.9099 Evaluate side-chains 175 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 691 HIS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 HIS A 794 GLN A 876 HIS C 691 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.153030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.109779 restraints weight = 22478.605| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.05 r_work: 0.3122 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14475 Z= 0.093 Angle : 0.470 8.266 19787 Z= 0.242 Chirality : 0.039 0.160 2224 Planarity : 0.003 0.039 2334 Dihedral : 7.628 97.624 2343 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.33 % Allowed : 15.67 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.20), residues: 1593 helix: -0.30 (0.22), residues: 548 sheet: -2.04 (0.34), residues: 233 loop : -2.28 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 316 TYR 0.020 0.001 TYR C 715 PHE 0.009 0.001 PHE A 471 TRP 0.023 0.001 TRP B 351 HIS 0.008 0.001 HIS A 782 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (14466) covalent geometry : angle 0.47026 / 0.24 (19783) SS BOND : bond 0.00305 / 0.16 ( 2) SS BOND : angle 0.93472 / 0.63 ( 4) hydrogen bonds : bond 0.03450 / 2.18 ( 431) hydrogen bonds : angle 4.21273 / 2.87 ( 1213) metal coordination : bond 0.00084 / 0.04 ( 5) Misc. bond : bond 0.00088 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.423 Fit side-chains REVERT: A 811 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8732 (ttt180) REVERT: A 923 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6498 (ppp) REVERT: B 334 MET cc_start: 0.5891 (tpp) cc_final: 0.5169 (mmt) REVERT: C 255 MET cc_start: 0.8335 (mmt) cc_final: 0.8099 (mmm) REVERT: C 579 PHE cc_start: 0.5776 (m-80) cc_final: 0.4923 (m-10) REVERT: C 595 GLN cc_start: 0.8653 (pm20) cc_final: 0.8333 (pm20) REVERT: C 622 TYR cc_start: 0.7065 (m-80) cc_final: 0.6642 (m-10) REVERT: C 782 HIS cc_start: 0.7883 (m90) cc_final: 0.7448 (t70) REVERT: C 895 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6846 (mt-10) REVERT: D 411 TYR cc_start: 0.7102 (m-80) cc_final: 0.6836 (m-80) outliers start: 48 outliers final: 32 residues processed: 188 average time/residue: 0.1012 time to fit residues: 28.7931 Evaluate side-chains 176 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 20.0000 chunk 78 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 83 optimal weight: 0.3980 chunk 152 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 132 optimal weight: 0.0370 chunk 103 optimal weight: 0.2980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.151886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.112599 restraints weight = 22596.761| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.80 r_work: 0.3107 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14475 Z= 0.088 Angle : 0.454 11.682 19787 Z= 0.231 Chirality : 0.039 0.146 2224 Planarity : 0.003 0.040 2334 Dihedral : 7.398 97.477 2343 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.26 % Allowed : 16.71 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.21), residues: 1593 helix: 0.51 (0.23), residues: 552 sheet: -1.84 (0.35), residues: 231 loop : -2.07 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.011 0.001 TYR D 390 PHE 0.009 0.001 PHE A 471 TRP 0.016 0.001 TRP B 351 HIS 0.018 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (14466) covalent geometry : angle 0.45381 / 0.23 (19783) SS BOND : bond 0.00256 / 0.13 ( 2) SS BOND : angle 1.73865 / 1.00 ( 4) hydrogen bonds : bond 0.02945 / 1.86 ( 431) hydrogen bonds : angle 3.88883 / 2.65 ( 1213) metal coordination : bond 0.00045 / 0.02 ( 5) Misc. bond : bond 0.00086 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 470 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8346 (mmmm) REVERT: A 811 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8668 (ttt180) REVERT: A 923 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6555 (ppp) REVERT: B 308 LEU cc_start: 0.2066 (OUTLIER) cc_final: 0.1760 (pp) REVERT: C 449 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7293 (tt) REVERT: C 579 PHE cc_start: 0.5788 (OUTLIER) cc_final: 0.4961 (m-10) REVERT: C 595 GLN cc_start: 0.8640 (pm20) cc_final: 0.8337 (pm20) REVERT: C 622 TYR cc_start: 0.7125 (m-80) cc_final: 0.6718 (m-10) REVERT: C 782 HIS cc_start: 0.7905 (m90) cc_final: 0.7496 (t70) REVERT: D 411 TYR cc_start: 0.6996 (m-80) cc_final: 0.6694 (m-80) outliers start: 47 outliers final: 32 residues processed: 190 average time/residue: 0.1059 time to fit residues: 30.3002 Evaluate side-chains 178 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 37 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 90 optimal weight: 0.0070 chunk 59 optimal weight: 0.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 782 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.149725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.107196 restraints weight = 22468.376| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.65 r_work: 0.3091 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14475 Z= 0.128 Angle : 0.479 9.973 19787 Z= 0.243 Chirality : 0.040 0.177 2224 Planarity : 0.003 0.040 2334 Dihedral : 7.521 99.689 2340 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.68 % Allowed : 17.61 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.21), residues: 1593 helix: 0.87 (0.23), residues: 555 sheet: -1.87 (0.33), residues: 252 loop : -1.96 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.010 0.001 TYR D 390 PHE 0.009 0.001 PHE A 471 TRP 0.013 0.001 TRP B 332 HIS 0.007 0.001 HIS A 782 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (14466) covalent geometry : angle 0.47865 / 0.24 (19783) SS BOND : bond 0.00376 / 0.20 ( 2) SS BOND : angle 1.08610 / 0.72 ( 4) hydrogen bonds : bond 0.03053 / 1.93 ( 431) hydrogen bonds : angle 3.81352 / 2.59 ( 1213) metal coordination : bond 0.00123 / 0.06 ( 5) Misc. bond : bond 0.00041 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 0.521 Fit side-chains REVERT: A 470 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8522 (mmmm) REVERT: A 811 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8795 (ttt180) REVERT: A 923 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.6622 (ppp) REVERT: B 308 LEU cc_start: 0.2383 (OUTLIER) cc_final: 0.2051 (pp) REVERT: B 348 CYS cc_start: 0.6773 (p) cc_final: 0.6472 (p) REVERT: C 255 MET cc_start: 0.8378 (mmt) cc_final: 0.8099 (mmm) REVERT: C 449 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7423 (tt) REVERT: C 452 VAL cc_start: 0.6687 (OUTLIER) cc_final: 0.6440 (p) REVERT: C 579 PHE cc_start: 0.5749 (OUTLIER) cc_final: 0.5543 (m-80) REVERT: C 595 GLN cc_start: 0.8676 (pm20) cc_final: 0.8375 (pm20) REVERT: C 622 TYR cc_start: 0.7201 (m-80) cc_final: 0.6791 (m-10) REVERT: C 647 ILE cc_start: 0.8383 (mm) cc_final: 0.8169 (tp) REVERT: C 782 HIS cc_start: 0.8078 (m90) cc_final: 0.7589 (t70) REVERT: D 411 TYR cc_start: 0.7085 (m-80) cc_final: 0.6767 (m-80) outliers start: 53 outliers final: 38 residues processed: 182 average time/residue: 0.1039 time to fit residues: 28.6108 Evaluate side-chains 185 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 852 GLN Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 107 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 chunk 137 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 375 HIS A 384 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN A 769 GLN A 782 HIS A 876 HIS ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.145302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104693 restraints weight = 22528.141| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.99 r_work: 0.2982 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 14475 Z= 0.271 Angle : 0.596 9.743 19787 Z= 0.303 Chirality : 0.044 0.212 2224 Planarity : 0.004 0.038 2334 Dihedral : 8.314 104.395 2340 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.30 % Allowed : 17.82 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.22), residues: 1593 helix: 0.63 (0.23), residues: 567 sheet: -1.75 (0.31), residues: 297 loop : -1.85 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 342 TYR 0.013 0.002 TYR A 566 PHE 0.017 0.002 PHE D 389 TRP 0.013 0.001 TRP B 332 HIS 0.008 0.001 HIS A 782 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.27 (14466) covalent geometry : angle 0.59573 / 0.30 (19783) SS BOND : bond 0.00952 / 0.49 ( 2) SS BOND : angle 1.58504 / 1.12 ( 4) hydrogen bonds : bond 0.04034 / 2.58 ( 431) hydrogen bonds : angle 4.14477 / 2.82 ( 1213) metal coordination : bond 0.00407 / 0.21 ( 5) Misc. bond : bond 0.00093 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 136 time to evaluate : 0.500 Fit side-chains REVERT: A 255 MET cc_start: 0.8812 (mtt) cc_final: 0.8509 (mtt) REVERT: A 470 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8375 (mmmm) REVERT: A 811 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.8839 (ttt180) REVERT: A 923 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.6633 (ppp) REVERT: B 308 LEU cc_start: 0.3178 (OUTLIER) cc_final: 0.2810 (pp) REVERT: B 371 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7058 (p0) REVERT: C 255 MET cc_start: 0.8426 (mmt) cc_final: 0.8017 (mmm) REVERT: C 449 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7467 (tt) REVERT: C 622 TYR cc_start: 0.7219 (m-80) cc_final: 0.6856 (m-10) REVERT: C 782 HIS cc_start: 0.8054 (m90) cc_final: 0.7615 (t70) REVERT: D 411 TYR cc_start: 0.7058 (m-80) cc_final: 0.6670 (m-80) outliers start: 62 outliers final: 43 residues processed: 183 average time/residue: 0.1011 time to fit residues: 28.1739 Evaluate side-chains 175 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 852 GLN Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 26 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 92 optimal weight: 0.0020 chunk 116 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 chunk 124 optimal weight: 0.0770 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 GLN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS C 691 HIS D 301 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.150395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108604 restraints weight = 22356.541| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.70 r_work: 0.3097 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14475 Z= 0.088 Angle : 0.482 8.838 19787 Z= 0.245 Chirality : 0.040 0.195 2224 Planarity : 0.004 0.074 2334 Dihedral : 7.432 93.575 2340 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.47 % Allowed : 18.79 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.22), residues: 1593 helix: 1.15 (0.23), residues: 560 sheet: -1.54 (0.32), residues: 276 loop : -1.78 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 320 TYR 0.011 0.001 TYR C 303 PHE 0.025 0.001 PHE D 389 TRP 0.019 0.001 TRP B 351 HIS 0.005 0.001 HIS C 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (14466) covalent geometry : angle 0.48186 / 0.24 (19783) SS BOND : bond 0.00644 / 0.34 ( 2) SS BOND : angle 0.88833 / 0.53 ( 4) hydrogen bonds : bond 0.02658 / 1.68 ( 431) hydrogen bonds : angle 3.74124 / 2.54 ( 1213) metal coordination : bond 0.00081 / 0.04 ( 5) Misc. bond : bond 0.00097 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 470 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8319 (mmmm) REVERT: A 923 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6460 (ppp) REVERT: B 295 GLU cc_start: 0.7146 (pm20) cc_final: 0.6821 (pm20) REVERT: B 308 LEU cc_start: 0.3136 (OUTLIER) cc_final: 0.2827 (pp) REVERT: B 352 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7580 (ptpt) REVERT: C 255 MET cc_start: 0.8369 (mmt) cc_final: 0.7954 (mmm) REVERT: C 449 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7418 (tt) REVERT: C 622 TYR cc_start: 0.7155 (m-80) cc_final: 0.6844 (m-10) REVERT: C 782 HIS cc_start: 0.8029 (m90) cc_final: 0.7571 (t70) REVERT: D 411 TYR cc_start: 0.6899 (m-80) cc_final: 0.6585 (m-80) outliers start: 50 outliers final: 39 residues processed: 175 average time/residue: 0.0964 time to fit residues: 26.2014 Evaluate side-chains 174 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 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 408 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 CYS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 691 HIS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 852 GLN Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 124 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 109 optimal weight: 0.0970 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 34 optimal weight: 0.0170 overall best weight: 2.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN C 557 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.147171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.104881 restraints weight = 22452.280| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.85 r_work: 0.3037 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14475 Z= 0.167 Angle : 0.530 13.624 19787 Z= 0.266 Chirality : 0.041 0.203 2224 Planarity : 0.004 0.068 2334 Dihedral : 7.739 102.221 2340 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.74 % Allowed : 18.93 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.22), residues: 1593 helix: 1.09 (0.23), residues: 566 sheet: -1.67 (0.31), residues: 300 loop : -1.68 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 811 TYR 0.012 0.001 TYR C 548 PHE 0.010 0.001 PHE A 471 TRP 0.019 0.001 TRP B 332 HIS 0.005 0.001 HIS C 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (14466) covalent geometry : angle 0.52942 / 0.27 (19783) SS BOND : bond 0.00431 / 0.22 ( 2) SS BOND : angle 0.96844 / 0.71 ( 4) hydrogen bonds : bond 0.03179 / 2.01 ( 431) hydrogen bonds : angle 3.82150 / 2.60 ( 1213) metal coordination : bond 0.00210 / 0.11 ( 5) Misc. bond : bond 0.00034 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 470 LYS cc_start: 0.8547 (mmmt) cc_final: 0.8333 (mmmm) REVERT: A 923 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.6456 (ppp) REVERT: B 308 LEU cc_start: 0.3269 (OUTLIER) cc_final: 0.2962 (pp) REVERT: C 449 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7453 (tt) REVERT: C 556 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8238 (tm-30) REVERT: C 622 TYR cc_start: 0.7203 (m-80) cc_final: 0.6900 (m-10) REVERT: C 782 HIS cc_start: 0.8060 (m90) cc_final: 0.7615 (t70) REVERT: D 411 TYR cc_start: 0.6931 (m-80) cc_final: 0.6604 (m-80) outliers start: 54 outliers final: 40 residues processed: 179 average time/residue: 0.0970 time to fit residues: 26.6451 Evaluate side-chains 174 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 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 408 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 852 GLN Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 122 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 63 optimal weight: 0.0570 chunk 126 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.148813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106353 restraints weight = 22454.151| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.72 r_work: 0.3080 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14475 Z= 0.108 Angle : 0.497 12.904 19787 Z= 0.250 Chirality : 0.040 0.213 2224 Planarity : 0.003 0.063 2334 Dihedral : 7.493 97.256 2340 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.40 % Allowed : 18.79 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.22), residues: 1593 helix: 1.26 (0.23), residues: 564 sheet: -1.50 (0.32), residues: 285 loop : -1.65 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 559 TYR 0.014 0.001 TYR D 400 PHE 0.009 0.001 PHE A 471 TRP 0.020 0.001 TRP B 332 HIS 0.009 0.001 HIS C 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (14466) covalent geometry : angle 0.49680 / 0.25 (19783) SS BOND : bond 0.00309 / 0.16 ( 2) SS BOND : angle 0.87195 / 0.60 ( 4) hydrogen bonds : bond 0.02804 / 1.77 ( 431) hydrogen bonds : angle 3.73230 / 2.54 ( 1213) metal coordination : bond 0.00094 / 0.05 ( 5) Misc. bond : bond 0.00059 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 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: 49 poor density : 131 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 923 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.6503 (ppp) REVERT: B 308 LEU cc_start: 0.3516 (OUTLIER) cc_final: 0.3225 (pp) REVERT: C 449 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7420 (tt) REVERT: C 622 TYR cc_start: 0.7201 (m-80) cc_final: 0.6902 (m-10) REVERT: C 782 HIS cc_start: 0.8205 (m90) cc_final: 0.7665 (t70) REVERT: D 411 TYR cc_start: 0.6933 (m-80) cc_final: 0.6650 (m-80) outliers start: 49 outliers final: 42 residues processed: 171 average time/residue: 0.0958 time to fit residues: 25.2967 Evaluate side-chains 175 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 130 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 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 408 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 449 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 852 GLN Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 91 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 72 optimal weight: 0.5980 chunk 76 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 ASN A 384 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS A 769 GLN A 876 HIS ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.145064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.104962 restraints weight = 22463.927| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.82 r_work: 0.2981 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14475 Z= 0.251 Angle : 0.612 11.945 19787 Z= 0.308 Chirality : 0.044 0.214 2224 Planarity : 0.004 0.067 2334 Dihedral : 8.183 105.034 2340 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.54 % Allowed : 18.59 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.22), residues: 1593 helix: 0.95 (0.23), residues: 569 sheet: -1.51 (0.32), residues: 281 loop : -1.71 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 811 TYR 0.018 0.002 TYR C 548 PHE 0.012 0.002 PHE A 776 TRP 0.022 0.001 TRP B 332 HIS 0.006 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.25 (14466) covalent geometry : angle 0.61172 / 0.31 (19783) SS BOND : bond 0.00635 / 0.32 ( 2) SS BOND : angle 1.41197 / 1.08 ( 4) hydrogen bonds : bond 0.03810 / 2.42 ( 431) hydrogen bonds : angle 4.02248 / 2.74 ( 1213) metal coordination : bond 0.00390 / 0.20 ( 5) Misc. bond : bond 0.00078 / 0.04 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 0.429 Fit side-chains REVERT: A 255 MET cc_start: 0.8828 (mtt) cc_final: 0.8501 (mtt) REVERT: A 923 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.6543 (ppp) REVERT: B 308 LEU cc_start: 0.3801 (OUTLIER) cc_final: 0.3479 (pp) REVERT: C 255 MET cc_start: 0.8422 (mmt) cc_final: 0.7919 (mmm) REVERT: C 622 TYR cc_start: 0.7179 (m-80) cc_final: 0.6827 (m-10) REVERT: C 782 HIS cc_start: 0.8127 (m90) cc_final: 0.7690 (t70) REVERT: D 411 TYR cc_start: 0.6884 (m-80) cc_final: 0.6589 (m-80) outliers start: 51 outliers final: 42 residues processed: 162 average time/residue: 0.0967 time to fit residues: 24.0634 Evaluate side-chains 159 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 852 GLN Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 136 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 11 optimal weight: 0.0870 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 384 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS B 260 HIS ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.146645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106969 restraints weight = 22417.423| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.98 r_work: 0.2999 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14475 Z= 0.168 Angle : 0.545 11.593 19787 Z= 0.275 Chirality : 0.042 0.201 2224 Planarity : 0.004 0.064 2334 Dihedral : 7.760 100.839 2338 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.19 % Allowed : 19.00 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.22), residues: 1593 helix: 1.05 (0.23), residues: 566 sheet: -1.59 (0.32), residues: 291 loop : -1.64 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 811 TYR 0.018 0.001 TYR C 548 PHE 0.008 0.001 PHE A 863 TRP 0.021 0.001 TRP B 332 HIS 0.005 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (14466) covalent geometry : angle 0.54507 / 0.28 (19783) SS BOND : bond 0.00444 / 0.23 ( 2) SS BOND : angle 1.09879 / 0.81 ( 4) hydrogen bonds : bond 0.03247 / 2.05 ( 431) hydrogen bonds : angle 3.91961 / 2.67 ( 1213) metal coordination : bond 0.00213 / 0.11 ( 5) Misc. bond : bond 0.00030 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3796.71 seconds wall clock time: 65 minutes 41.79 seconds (3941.79 seconds total)