Starting phenix.real_space_refine on Thu Aug 6 07:59:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g7t_29823/08_2026/8g7t_29823.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7t_29823/08_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_29823/08_2026/8g7t_29823.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g7t_29823/08_2026/8g7t_29823.cif" model { file = "/net/cci-nas-00/data/ceres_data/8g7t_29823/08_2026/8g7t_29823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7t_29823/08_2026/8g7t_29823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g7t_29823/08_2026/8g7t_29823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7t_29823/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: {'RNAv2': 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: {'RNAv2': 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: 2.66, per 1000 atoms: 0.19 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: 0.93 Conformation dependent library (CDL) restraints added in 569.5 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: 1.35 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: 1.95 Time building geometry restraints manager: 1.32 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: 19452 2.40 - 4.80: 283 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: 8230 28.61 - 57.21: 364 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: 1803 0.054 - 0.108: 286 0.108 - 0.162: 76 0.162 - 0.217: 9 0.217 - 0.271: 50 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=" P G Y 10 " pdb=" OP1 G Y 10 " pdb=" OP2 G Y 10 " pdb=" O5' G Y 10 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.45e+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: 1.200 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.390 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- 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= 0.355 Angle : 0.665 12.010 19787 Z= 0.337 Chirality : 0.057 0.271 2224 Planarity : 0.004 0.048 2334 Dihedral : 15.428 143.030 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 0.00579 / 0.29 (14466) covalent geometry : angle 0.66526 / 0.34 (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 : 0.499 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: 0.1143 time to fit residues: 49.2279 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 : 0.490 ------------------------------------------------------------------------------- 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 384 ASN 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 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 C 691 HIS C 769 GLN C 786 HIS D 313 HIS D 429 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.146536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107399 restraints weight = 22639.278| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.24 r_work: 0.3024 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 14475 Z= 0.269 Angle : 0.686 10.039 19787 Z= 0.336 Chirality : 0.048 0.246 2224 Planarity : 0.005 0.050 2334 Dihedral : 10.235 102.989 2360 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.88 % Allowed : 15.26 % 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: -3.40 (0.18), residues: 1593 helix: -1.75 (0.18), residues: 554 sheet: -2.35 (0.32), residues: 255 loop : -2.57 (0.19), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 589 TYR 0.018 0.002 TYR C 383 PHE 0.019 0.002 PHE A 388 TRP 0.009 0.001 TRP D 360 HIS 0.009 0.002 HIS A 782 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.27 (14466) covalent geometry : angle 0.68577 / 0.34 (19783) SS BOND : bond 0.00514 / 0.26 ( 2) SS BOND : angle 1.13780 / 0.81 ( 4) hydrogen bonds : bond 0.04652 / 3.00 ( 431) hydrogen bonds : angle 4.82856 / 3.32 ( 1213) metal coordination : bond 0.01046 / 0.51 ( 5) Misc. bond : bond 0.00075 / 0.04 ( 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 206 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 0.411 Fit side-chains REVERT: A 923 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.6617 (ppp) REVERT: C 479 MET cc_start: 0.9262 (mtm) cc_final: 0.9031 (mtp) REVERT: C 595 GLN cc_start: 0.8593 (pm20) cc_final: 0.8308 (pm20) REVERT: C 622 TYR cc_start: 0.7129 (m-80) cc_final: 0.6712 (m-10) REVERT: C 782 HIS cc_start: 0.7844 (m90) cc_final: 0.7431 (t70) REVERT: D 324 HIS cc_start: 0.7597 (m-70) cc_final: 0.7374 (m90) REVERT: D 411 TYR cc_start: 0.7247 (m-80) cc_final: 0.6979 (m-80) outliers start: 56 outliers final: 37 residues processed: 193 average time/residue: 0.0947 time to fit residues: 28.1444 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 : 0.462 ------------------------------------------------------------------------------- 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 A residue 923 MET 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 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: 0.7980 chunk 7 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 67 optimal weight: 0.0870 chunk 54 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 26 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 HIS 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 = 0.3981 r_free = 0.3981 target = 0.151706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.112865 restraints weight = 22412.990| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.09 r_work: 0.3066 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14475 Z= 0.109 Angle : 0.510 8.432 19787 Z= 0.252 Chirality : 0.043 0.177 2224 Planarity : 0.004 0.039 2334 Dihedral : 9.637 100.130 2343 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.19 % Allowed : 16.44 % Favored : 80.37 % 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: -2.27 (0.20), residues: 1593 helix: -0.25 (0.22), residues: 550 sheet: -2.10 (0.33), residues: 247 loop : -2.24 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 316 TYR 0.020 0.001 TYR C 715 PHE 0.010 0.001 PHE A 471 TRP 0.020 0.001 TRP B 351 HIS 0.008 0.001 HIS A 782 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (14466) covalent geometry : angle 0.50966 / 0.25 (19783) SS BOND : bond 0.00306 / 0.15 ( 2) SS BOND : angle 0.92160 / 0.66 ( 4) hydrogen bonds : bond 0.03503 / 2.21 ( 431) hydrogen bonds : angle 4.23311 / 2.88 ( 1213) metal coordination : bond 0.00153 / 0.08 ( 5) Misc. bond : bond 0.00075 / 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 196 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 811 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8712 (ttt180) REVERT: B 321 ASN cc_start: 0.7185 (m-40) cc_final: 0.6674 (t0) REVERT: B 334 MET cc_start: 0.5991 (tpp) cc_final: 0.5247 (mmt) REVERT: B 400 TYR cc_start: 0.6840 (t80) cc_final: 0.6585 (t80) REVERT: C 579 PHE cc_start: 0.5456 (m-80) cc_final: 0.5063 (m-80) REVERT: C 595 GLN cc_start: 0.8638 (pm20) cc_final: 0.8329 (pm20) REVERT: C 622 TYR cc_start: 0.7127 (m-80) cc_final: 0.6758 (m-10) REVERT: C 623 HIS cc_start: 0.7486 (t-170) cc_final: 0.7250 (t-170) REVERT: C 782 HIS cc_start: 0.7913 (m90) cc_final: 0.7501 (t70) REVERT: C 895 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6841 (mt-10) outliers start: 46 outliers final: 34 residues processed: 184 average time/residue: 0.0937 time to fit residues: 26.6317 Evaluate side-chains 173 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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 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 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 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: 6.9990 chunk 78 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 0.0870 chunk 152 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 overall best weight: 2.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS A 375 HIS ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 HIS D 285 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.147932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107326 restraints weight = 22514.498| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.77 r_work: 0.3037 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14475 Z= 0.169 Angle : 0.540 9.490 19787 Z= 0.265 Chirality : 0.044 0.198 2224 Planarity : 0.004 0.044 2334 Dihedral : 9.603 102.796 2341 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.23 % Allowed : 16.85 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.73 (0.21), residues: 1593 helix: 0.38 (0.23), residues: 556 sheet: -1.82 (0.32), residues: 269 loop : -2.08 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 811 TYR 0.012 0.001 TYR C 715 PHE 0.010 0.001 PHE A 471 TRP 0.014 0.001 TRP B 351 HIS 0.019 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (14466) covalent geometry : angle 0.54014 / 0.26 (19783) SS BOND : bond 0.00942 / 0.49 ( 2) SS BOND : angle 1.22788 / 0.87 ( 4) hydrogen bonds : bond 0.03473 / 2.19 ( 431) hydrogen bonds : angle 4.06873 / 2.77 ( 1213) metal coordination : bond 0.00200 / 0.10 ( 5) Misc. bond : bond 0.00053 / 0.03 ( 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 206 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 145 time to evaluate : 0.481 Fit side-chains REVERT: A 470 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8366 (mmmm) REVERT: A 811 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8753 (ttt180) REVERT: A 923 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.6576 (ppp) REVERT: B 308 LEU cc_start: 0.2523 (OUTLIER) cc_final: 0.2200 (pp) REVERT: C 255 MET cc_start: 0.8333 (mmt) cc_final: 0.8075 (mmm) REVERT: C 449 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7536 (tt) REVERT: C 452 VAL cc_start: 0.6613 (OUTLIER) cc_final: 0.6341 (p) REVERT: C 595 GLN cc_start: 0.8642 (pm20) cc_final: 0.8357 (pm20) REVERT: C 622 TYR cc_start: 0.7149 (m-80) cc_final: 0.6714 (m-10) REVERT: C 623 HIS cc_start: 0.7537 (t-170) cc_final: 0.7324 (t-170) REVERT: C 647 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.7835 (tt) REVERT: C 782 HIS cc_start: 0.7955 (m90) cc_final: 0.7547 (t70) REVERT: C 895 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6822 (mt-10) REVERT: D 411 TYR cc_start: 0.6996 (m-80) cc_final: 0.6693 (m-80) outliers start: 61 outliers final: 39 residues processed: 191 average time/residue: 0.1002 time to fit residues: 29.1666 Evaluate side-chains 180 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 317 HIS 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 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 765 ILE 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 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 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 641 ASP Chi-restraints excluded: chain C residue 647 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 37 optimal weight: 2.9990 chunk 76 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 153 optimal weight: 40.0000 chunk 51 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 HIS A 317 HIS A 500 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.147278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.107062 restraints weight = 22456.510| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.79 r_work: 0.3027 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14475 Z= 0.167 Angle : 0.543 8.774 19787 Z= 0.267 Chirality : 0.044 0.192 2224 Planarity : 0.004 0.069 2334 Dihedral : 9.583 101.884 2341 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.09 % Allowed : 18.10 % 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: -1.50 (0.22), residues: 1593 helix: 0.70 (0.23), residues: 560 sheet: -1.97 (0.31), residues: 292 loop : -1.93 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 336 TYR 0.013 0.001 TYR B 400 PHE 0.010 0.001 PHE A 471 TRP 0.017 0.001 TRP B 351 HIS 0.009 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (14466) covalent geometry : angle 0.54313 / 0.27 (19783) SS BOND : bond 0.00228 / 0.12 ( 2) SS BOND : angle 1.08198 / 0.79 ( 4) hydrogen bonds : bond 0.03338 / 2.11 ( 431) hydrogen bonds : angle 3.99431 / 2.72 ( 1213) metal coordination : bond 0.00186 / 0.09 ( 5) Misc. bond : bond 0.00048 / 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 198 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 139 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 470 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8356 (mmmm) REVERT: A 811 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8759 (ttt180) REVERT: A 890 GLU cc_start: 0.8469 (tt0) cc_final: 0.8236 (tt0) REVERT: A 923 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6534 (ppp) REVERT: B 308 LEU cc_start: 0.2685 (OUTLIER) cc_final: 0.2336 (pp) REVERT: C 449 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7694 (tt) REVERT: C 452 VAL cc_start: 0.6727 (OUTLIER) cc_final: 0.6446 (p) REVERT: C 622 TYR cc_start: 0.7198 (m-80) cc_final: 0.6814 (m-10) REVERT: C 782 HIS cc_start: 0.7981 (m90) cc_final: 0.7571 (t70) REVERT: C 895 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6853 (mt-10) outliers start: 59 outliers final: 41 residues processed: 185 average time/residue: 0.0976 time to fit residues: 27.5676 Evaluate side-chains 177 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 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 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 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 515 THR 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 691 HIS 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: 10.0000 chunk 131 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 137 optimal weight: 0.2980 chunk 108 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 156 optimal weight: 20.0000 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS A 384 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN A 782 HIS A 876 HIS ** 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 = 0.3907 r_free = 0.3907 target = 0.145213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104706 restraints weight = 22471.869| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.77 r_work: 0.2991 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14475 Z= 0.239 Angle : 0.604 9.490 19787 Z= 0.294 Chirality : 0.046 0.219 2224 Planarity : 0.004 0.062 2334 Dihedral : 9.691 104.181 2341 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 4.51 % Allowed : 18.24 % Favored : 77.25 % 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: 0.70 (0.23), residues: 564 sheet: -1.92 (0.31), residues: 298 loop : -1.82 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 811 TYR 0.012 0.002 TYR A 566 PHE 0.011 0.001 PHE A 776 TRP 0.018 0.001 TRP B 351 HIS 0.015 0.002 HIS C 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.24 (14466) covalent geometry : angle 0.60341 / 0.29 (19783) SS BOND : bond 0.00885 / 0.46 ( 2) SS BOND : angle 1.34979 / 0.97 ( 4) hydrogen bonds : bond 0.03752 / 2.38 ( 431) hydrogen bonds : angle 4.10106 / 2.79 ( 1213) metal coordination : bond 0.00329 / 0.17 ( 5) Misc. bond : bond 0.00100 / 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 201 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 136 time to evaluate : 0.504 Fit side-chains REVERT: A 470 LYS cc_start: 0.8592 (mmmt) cc_final: 0.8359 (mmmm) REVERT: A 811 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.8808 (ttt180) REVERT: A 890 GLU cc_start: 0.8502 (tt0) cc_final: 0.8271 (tt0) REVERT: A 923 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.6551 (ppp) REVERT: B 308 LEU cc_start: 0.3313 (OUTLIER) cc_final: 0.2939 (pp) REVERT: B 371 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6922 (p0) REVERT: C 449 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7731 (tt) REVERT: C 452 VAL cc_start: 0.6878 (OUTLIER) cc_final: 0.6547 (p) REVERT: C 622 TYR cc_start: 0.7168 (m-80) cc_final: 0.6846 (m-10) REVERT: C 657 LYS cc_start: 0.7161 (mttt) cc_final: 0.6539 (ttmt) REVERT: C 691 HIS cc_start: 0.5546 (m-70) cc_final: 0.5300 (m-70) REVERT: C 782 HIS cc_start: 0.8070 (m90) cc_final: 0.7612 (t70) outliers start: 65 outliers final: 48 residues processed: 187 average time/residue: 0.0960 time to fit residues: 27.4104 Evaluate side-chains 183 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 129 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 317 HIS 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 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 694 LEU 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 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 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 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 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 515 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 26 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 78 optimal weight: 0.0870 chunk 18 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS A 384 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.149221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106990 restraints weight = 22340.186| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.73 r_work: 0.3090 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14475 Z= 0.091 Angle : 0.510 12.095 19787 Z= 0.249 Chirality : 0.043 0.175 2224 Planarity : 0.003 0.053 2334 Dihedral : 9.499 96.539 2341 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.47 % Allowed : 19.42 % Favored : 77.12 % 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: -1.06 (0.22), residues: 1593 helix: 1.09 (0.23), residues: 562 sheet: -1.58 (0.33), residues: 263 loop : -1.78 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.012 0.001 TYR C 303 PHE 0.022 0.001 PHE D 389 TRP 0.021 0.001 TRP B 351 HIS 0.009 0.001 HIS C 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (14466) covalent geometry : angle 0.51018 / 0.25 (19783) SS BOND : bond 0.00201 / 0.10 ( 2) SS BOND : angle 0.86929 / 0.56 ( 4) hydrogen bonds : bond 0.02766 / 1.75 ( 431) hydrogen bonds : angle 3.80073 / 2.59 ( 1213) metal coordination : bond 0.00034 / 0.02 ( 5) Misc. bond : bond 0.00110 / 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 193 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 143 time to evaluate : 0.509 Fit side-chains REVERT: A 470 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8460 (mmmm) REVERT: A 923 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.6437 (ppp) REVERT: B 308 LEU cc_start: 0.3269 (OUTLIER) cc_final: 0.2954 (pp) REVERT: B 352 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7621 (ptpt) REVERT: B 371 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6966 (p0) REVERT: C 449 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7400 (tt) REVERT: C 452 VAL cc_start: 0.6899 (OUTLIER) cc_final: 0.6573 (p) REVERT: C 622 TYR cc_start: 0.7227 (m-80) cc_final: 0.6856 (m-10) REVERT: C 657 LYS cc_start: 0.6858 (mttt) cc_final: 0.6246 (ttmt) REVERT: C 782 HIS cc_start: 0.8165 (m90) cc_final: 0.7611 (t70) REVERT: D 411 TYR cc_start: 0.7021 (m-80) cc_final: 0.6484 (m-80) outliers start: 50 outliers final: 38 residues processed: 182 average time/residue: 0.0984 time to fit residues: 27.0669 Evaluate side-chains 174 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 317 HIS Chi-restraints excluded: chain A residue 344 ILE 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 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 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 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 308 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 352 LYS 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 242 LYS 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 452 VAL 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 641 ASP 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 262 THR 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: 9.9990 chunk 134 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 120 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS A 384 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS A 769 GLN A 876 HIS ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS C 786 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.141751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099245 restraints weight = 22638.880| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.89 r_work: 0.2939 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.087 14475 Z= 0.427 Angle : 0.805 12.322 19787 Z= 0.385 Chirality : 0.053 0.266 2224 Planarity : 0.005 0.061 2334 Dihedral : 10.183 107.066 2341 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 4.23 % Allowed : 19.14 % Favored : 76.63 % 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: -1.71 (0.22), residues: 1593 helix: 0.33 (0.22), residues: 576 sheet: -1.98 (0.31), residues: 298 loop : -1.94 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 811 TYR 0.016 0.002 TYR A 541 PHE 0.022 0.002 PHE D 389 TRP 0.011 0.002 TRP D 292 HIS 0.012 0.002 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.01002 / 0.43 (14466) covalent geometry : angle 0.80496 / 0.39 (19783) SS BOND : bond 0.00957 / 0.49 ( 2) SS BOND : angle 1.93343 / 1.54 ( 4) hydrogen bonds : bond 0.04953 / 3.20 ( 431) hydrogen bonds : angle 4.47560 / 3.06 ( 1213) metal coordination : bond 0.00651 / 0.33 ( 5) Misc. bond : bond 0.00255 / 0.13 ( 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 182 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 121 time to evaluate : 0.502 Fit side-chains REVERT: A 470 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8356 (mmmm) REVERT: A 811 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.8891 (ttt180) REVERT: A 923 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.6605 (ppp) REVERT: B 308 LEU cc_start: 0.3853 (OUTLIER) cc_final: 0.3450 (pp) REVERT: B 410 LEU cc_start: 0.6849 (mt) cc_final: 0.6601 (mt) REVERT: C 622 TYR cc_start: 0.7111 (m-80) cc_final: 0.6656 (m-10) REVERT: C 657 LYS cc_start: 0.7022 (mttt) cc_final: 0.6529 (ttmt) REVERT: C 753 ILE cc_start: 0.8775 (pt) cc_final: 0.8524 (mt) REVERT: C 782 HIS cc_start: 0.8181 (m90) cc_final: 0.7732 (t70) REVERT: D 420 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6460 (t-90) outliers start: 61 outliers final: 45 residues processed: 172 average time/residue: 0.1063 time to fit residues: 27.8496 Evaluate side-chains 166 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 117 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 317 HIS 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 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 811 ARG Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 876 HIS 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 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 375 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 452 VAL Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 515 THR 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 262 THR Chi-restraints excluded: chain D residue 354 THR 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: 0.9990 chunk 117 optimal weight: 0.0770 chunk 99 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 28 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 GLN A 876 HIS ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.147705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106846 restraints weight = 22401.425| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.70 r_work: 0.3077 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14475 Z= 0.101 Angle : 0.544 12.151 19787 Z= 0.266 Chirality : 0.044 0.193 2224 Planarity : 0.004 0.052 2334 Dihedral : 9.609 98.330 2341 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.77 % Allowed : 20.39 % Favored : 76.84 % 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: -1.12 (0.22), residues: 1593 helix: 0.93 (0.23), residues: 563 sheet: -1.63 (0.33), residues: 271 loop : -1.70 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 336 TYR 0.014 0.001 TYR C 509 PHE 0.023 0.001 PHE D 389 TRP 0.021 0.001 TRP B 351 HIS 0.014 0.001 HIS C 557 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (14466) covalent geometry : angle 0.54346 / 0.27 (19783) SS BOND : bond 0.00214 / 0.11 ( 2) SS BOND : angle 0.75834 / 0.50 ( 4) hydrogen bonds : bond 0.02863 / 1.80 ( 431) hydrogen bonds : angle 3.95174 / 2.70 ( 1213) metal coordination : bond 0.00062 / 0.03 ( 5) Misc. bond : bond 0.00110 / 0.05 ( 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 170 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.514 Fit side-chains REVERT: A 923 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.6602 (ppp) REVERT: C 622 TYR cc_start: 0.7213 (m-80) cc_final: 0.6740 (m-10) REVERT: C 657 LYS cc_start: 0.7083 (mttt) cc_final: 0.6424 (ttmt) REVERT: C 782 HIS cc_start: 0.8228 (m90) cc_final: 0.7681 (t70) REVERT: D 420 HIS cc_start: 0.7098 (OUTLIER) cc_final: 0.6533 (t-90) outliers start: 40 outliers final: 32 residues processed: 161 average time/residue: 0.1077 time to fit residues: 26.6156 Evaluate side-chains 158 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 574 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 725 ILE 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 923 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 281 VAL 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 452 VAL 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 852 GLN Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 262 THR 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: 0.8980 chunk 154 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.144579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.104397 restraints weight = 22410.757| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.68 r_work: 0.2981 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14475 Z= 0.231 Angle : 0.624 12.035 19787 Z= 0.301 Chirality : 0.046 0.219 2224 Planarity : 0.004 0.056 2334 Dihedral : 9.676 104.636 2341 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.98 % Allowed : 20.46 % Favored : 76.56 % 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: -1.22 (0.22), residues: 1593 helix: 0.87 (0.23), residues: 567 sheet: -1.89 (0.31), residues: 297 loop : -1.66 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 811 TYR 0.019 0.002 TYR C 548 PHE 0.009 0.001 PHE A 776 TRP 0.014 0.001 TRP B 351 HIS 0.006 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (14466) covalent geometry : angle 0.62396 / 0.30 (19783) SS BOND : bond 0.00550 / 0.28 ( 2) SS BOND : angle 1.25744 / 0.96 ( 4) hydrogen bonds : bond 0.03644 / 2.32 ( 431) hydrogen bonds : angle 4.06183 / 2.78 ( 1213) metal coordination : bond 0.00348 / 0.17 ( 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 167 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 0.521 Fit side-chains REVERT: A 470 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8289 (mmmm) REVERT: A 923 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6585 (ppp) REVERT: B 295 GLU cc_start: 0.6862 (mp0) cc_final: 0.6587 (pm20) REVERT: C 622 TYR cc_start: 0.7183 (m-80) cc_final: 0.6690 (m-10) REVERT: C 657 LYS cc_start: 0.7072 (mttt) cc_final: 0.6588 (ttmt) REVERT: C 782 HIS cc_start: 0.8118 (m90) cc_final: 0.7714 (t70) REVERT: D 420 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6502 (t-90) outliers start: 43 outliers final: 38 residues processed: 158 average time/residue: 0.1082 time to fit residues: 26.2279 Evaluate side-chains 160 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 574 VAL 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 876 HIS 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 281 VAL 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 242 LYS 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 452 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 693 ILE Chi-restraints excluded: chain C residue 852 GLN Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 262 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: 2.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 HIS ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 HIS ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.146218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106657 restraints weight = 22351.135| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.91 r_work: 0.3016 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.4508 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= 0.144 Angle : 0.567 11.837 19787 Z= 0.275 Chirality : 0.044 0.194 2224 Planarity : 0.004 0.052 2334 Dihedral : 9.580 101.273 2341 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.64 % Allowed : 20.60 % Favored : 76.77 % 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: -1.04 (0.22), residues: 1593 helix: 0.99 (0.23), residues: 565 sheet: -1.61 (0.33), residues: 265 loop : -1.65 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 336 TYR 0.019 0.001 TYR C 548 PHE 0.012 0.001 PHE C 504 TRP 0.017 0.001 TRP B 351 HIS 0.006 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (14466) covalent geometry : angle 0.56735 / 0.28 (19783) SS BOND : bond 0.00380 / 0.19 ( 2) SS BOND : angle 1.01632 / 0.74 ( 4) hydrogen bonds : bond 0.03168 / 2.00 ( 431) hydrogen bonds : angle 3.95851 / 2.70 ( 1213) metal coordination : bond 0.00143 / 0.07 ( 5) Misc. bond : bond 0.00050 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3834.17 seconds wall clock time: 66 minutes 22.79 seconds (3982.79 seconds total)