Starting phenix.real_space_refine on Thu Feb 5 19:56:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q9n_52965/02_2026/9q9n_52965.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q9n_52965/02_2026/9q9n_52965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q9n_52965/02_2026/9q9n_52965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q9n_52965/02_2026/9q9n_52965.map" model { file = "/net/cci-nas-00/data/ceres_data/9q9n_52965/02_2026/9q9n_52965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q9n_52965/02_2026/9q9n_52965.cif" } resolution = 3.0 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= 0.012 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 12183 2.51 5 N 3393 2.21 5 O 3681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 217 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19365 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5508 Classifications: {'peptide': 693} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 662} Chain breaks: 1 Chain: "B" Number of atoms: 5508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5508 Classifications: {'peptide': 693} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 662} Chain breaks: 1 Chain: "C" Number of atoms: 5508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5508 Classifications: {'peptide': 693} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 662} Chain breaks: 1 Chain: "d" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 835 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain breaks: 1 Chain: "e" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 835 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain breaks: 1 Chain: "f" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 835 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.39, per 1000 atoms: 0.23 Number of scatterers: 19365 At special positions: 0 Unit cell: (139.44, 144.42, 175.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 3681 8.00 N 3393 7.00 C 12183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.06 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.05 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.06 Simple disulfide: pdb=" SG CYS A 392 " - pdb=" SG CYS A 532 " distance=2.05 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.05 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.06 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.04 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.05 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.05 Simple disulfide: pdb=" SG CYS B 392 " - pdb=" SG CYS B 532 " distance=2.06 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.05 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.06 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.04 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.05 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.04 Simple disulfide: pdb=" SG CYS C 392 " - pdb=" SG CYS C 532 " distance=2.05 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.05 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 97 " distance=2.06 Simple disulfide: pdb=" SG CYS e 22 " - pdb=" SG CYS e 97 " distance=2.08 Simple disulfide: pdb=" SG CYS f 22 " - pdb=" SG CYS f 97 " distance=2.06 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG D 1 " - " ASN A 398 " " NAG E 1 " - " ASN C 398 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 141 " " NAG H 1 " - " ASN C 141 " " NAG I 1 " - " ASN C 430 " " NAG J 1 " - " ASN B 430 " " NAG K 1 " - " ASN A 430 " " NAG L 1 " - " ASN B 398 " " NAG M 1 " - " ASN A 674 " " NAG N 1 " - " ASN B 674 " " NAG O 1 " - " ASN C 674 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 654.9 milliseconds 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4470 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 39 sheets defined 34.1% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 91 through 107 removed outlier: 3.697A pdb=" N GLU A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 176 through 181 removed outlier: 4.345A pdb=" N GLN A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.558A pdb=" N ARG A 406 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 458 through 473 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 510 through 546 Proline residue: A 516 - end of helix removed outlier: 3.786A pdb=" N ARG A 523 " --> pdb=" O ASP A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 685 through 689 Processing helix chain 'A' and resid 701 through 725 removed outlier: 3.837A pdb=" N LEU A 714 " --> pdb=" O GLN A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 741 removed outlier: 3.908A pdb=" N GLY A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 773 removed outlier: 4.018A pdb=" N VAL A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY A 755 " --> pdb=" O LYS A 751 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 803 removed outlier: 3.929A pdb=" N SER A 803 " --> pdb=" O MET A 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 105 Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 176 through 181 removed outlier: 4.304A pdb=" N GLN B 181 " --> pdb=" O HIS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 458 through 474 Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 510 through 546 Proline residue: B 516 - end of helix removed outlier: 3.666A pdb=" N LYS B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 545 " --> pdb=" O GLU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 685 through 690 Processing helix chain 'B' and resid 701 through 725 removed outlier: 3.672A pdb=" N LEU B 714 " --> pdb=" O GLN B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 741 Processing helix chain 'B' and resid 742 through 773 removed outlier: 3.538A pdb=" N GLY B 746 " --> pdb=" O MET B 742 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL B 752 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B 755 " --> pdb=" O LYS B 751 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 803 removed outlier: 3.947A pdb=" N SER B 803 " --> pdb=" O MET B 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 106 Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 176 through 181 removed outlier: 4.371A pdb=" N GLN C 181 " --> pdb=" O HIS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 257 through 264 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 411 through 429 removed outlier: 3.671A pdb=" N ASP C 416 " --> pdb=" O CYS C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 473 removed outlier: 4.346A pdb=" N LEU C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 507 removed outlier: 3.771A pdb=" N LEU C 506 " --> pdb=" O GLU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 546 Proline residue: C 516 - end of helix removed outlier: 3.789A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 545 " --> pdb=" O GLU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 686 through 692 removed outlier: 4.035A pdb=" N THR C 690 " --> pdb=" O LEU C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 725 removed outlier: 3.699A pdb=" N LEU C 714 " --> pdb=" O GLN C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 743 removed outlier: 4.038A pdb=" N GLY C 741 " --> pdb=" O ALA C 737 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C 742 " --> pdb=" O PHE C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 772 removed outlier: 3.826A pdb=" N ALA C 748 " --> pdb=" O ASP C 744 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL C 749 " --> pdb=" O LEU C 745 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL C 752 " --> pdb=" O ALA C 748 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY C 755 " --> pdb=" O LYS C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 803 removed outlier: 4.174A pdb=" N SER C 803 " --> pdb=" O MET C 799 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 33 Processing helix chain 'd' and resid 88 through 92 removed outlier: 3.831A pdb=" N THR d 92 " --> pdb=" O PRO d 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 33 Processing helix chain 'e' and resid 88 through 92 removed outlier: 3.771A pdb=" N THR e 92 " --> pdb=" O PRO e 89 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 33 Processing helix chain 'f' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 6.586A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 563 removed outlier: 4.435A pdb=" N THR B 665 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 372 removed outlier: 6.782A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 14.306A pdb=" N TYR A 142 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 9.851A pdb=" N SER A 457 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 398 removed outlier: 6.814A pdb=" N ARG A 377 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR A 142 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 14.306A pdb=" N TYR A 142 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 9.851A pdb=" N SER A 457 " --> pdb=" O TYR A 142 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU A 144 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 186 through 191 Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.182A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N THR A 340 " --> pdb=" O GLY A 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 206 through 207 Processing sheet with id=AA8, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA9, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB1, first strand: chain 'A' and resid 638 through 642 removed outlier: 3.592A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 665 through 666 removed outlier: 6.646A pdb=" N THR A 665 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.625A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 559 through 563 removed outlier: 7.204A pdb=" N VAL B 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N VAL C 667 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLN B 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 366 through 372 removed outlier: 5.595A pdb=" N LYS B 368 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS B 151 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 14.260A pdb=" N TYR B 142 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N SER B 457 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 395 through 398 removed outlier: 6.806A pdb=" N ARG B 377 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR B 142 " --> pdb=" O ARG B 377 " (cutoff:3.500A) removed outlier: 14.260A pdb=" N TYR B 142 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N SER B 457 " --> pdb=" O TYR B 142 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU B 144 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 185 through 191 Processing sheet with id=AB8, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.209A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N THR B 340 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 206 through 207 Processing sheet with id=AC1, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AC2, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC3, first strand: chain 'B' and resid 638 through 642 removed outlier: 3.613A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.611A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 366 through 372 removed outlier: 5.627A pdb=" N LYS C 368 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LYS C 151 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 14.330A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 395 through 398 removed outlier: 6.820A pdb=" N ARG C 377 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR C 142 " --> pdb=" O ARG C 377 " (cutoff:3.500A) removed outlier: 14.330A pdb=" N TYR C 142 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 9.888A pdb=" N SER C 457 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU C 144 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 185 through 191 Processing sheet with id=AC8, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.208A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N THR C 340 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 206 through 207 Processing sheet with id=AD1, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AD2, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD3, first strand: chain 'C' and resid 638 through 642 removed outlier: 3.588A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'd' and resid 10 through 11 removed outlier: 6.762A pdb=" N GLY d 10 " --> pdb=" O THR d 114 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU d 36 " --> pdb=" O THR d 52 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR d 52 " --> pdb=" O LEU d 36 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TRP d 38 " --> pdb=" O VAL d 50 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER d 58 " --> pdb=" O THR d 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 10 through 11 removed outlier: 6.762A pdb=" N GLY d 10 " --> pdb=" O THR d 114 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'e' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'e' and resid 10 through 11 removed outlier: 6.736A pdb=" N GLY e 10 " --> pdb=" O THR e 114 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU e 36 " --> pdb=" O THR e 52 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR e 52 " --> pdb=" O LEU e 36 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TRP e 38 " --> pdb=" O VAL e 50 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER e 58 " --> pdb=" O THR e 54 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'e' and resid 10 through 11 removed outlier: 6.736A pdb=" N GLY e 10 " --> pdb=" O THR e 114 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'f' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'f' and resid 10 through 11 removed outlier: 6.746A pdb=" N GLY f 10 " --> pdb=" O THR f 114 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU f 36 " --> pdb=" O THR f 52 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR f 52 " --> pdb=" O LEU f 36 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TRP f 38 " --> pdb=" O VAL f 50 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE f 53 " --> pdb=" O ASN f 60 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN f 60 " --> pdb=" O ILE f 53 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP f 55 " --> pdb=" O SER f 58 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'f' and resid 10 through 11 removed outlier: 6.746A pdb=" N GLY f 10 " --> pdb=" O THR f 114 " (cutoff:3.500A) 1023 hydrogen bonds defined for protein. 2760 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6423 1.34 - 1.46: 4846 1.46 - 1.58: 8357 1.58 - 1.69: 0 1.69 - 1.81: 174 Bond restraints: 19800 Sorted by residual: bond pdb=" C4 NAG O 1 " pdb=" O4 NAG O 1 " ideal model delta sigma weight residual 1.409 1.494 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C4 NAG J 1 " pdb=" O4 NAG J 1 " ideal model delta sigma weight residual 1.409 1.494 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C4 NAG F 1 " pdb=" O4 NAG F 1 " ideal model delta sigma weight residual 1.409 1.493 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C4 NAG H 1 " pdb=" O4 NAG H 1 " ideal model delta sigma weight residual 1.409 1.493 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C4 NAG I 1 " pdb=" O4 NAG I 1 " ideal model delta sigma weight residual 1.409 1.492 -0.083 2.00e-02 2.50e+03 1.72e+01 ... (remaining 19795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 19718 2.05 - 4.10: 6140 4.10 - 6.15: 914 6.15 - 8.20: 72 8.20 - 10.24: 12 Bond angle restraints: 26856 Sorted by residual: angle pdb=" N GLU B 682 " pdb=" CA GLU B 682 " pdb=" C GLU B 682 " ideal model delta sigma weight residual 111.28 121.15 -9.87 1.09e+00 8.42e-01 8.20e+01 angle pdb=" N GLU A 682 " pdb=" CA GLU A 682 " pdb=" C GLU A 682 " ideal model delta sigma weight residual 111.28 120.72 -9.44 1.09e+00 8.42e-01 7.50e+01 angle pdb=" CA PHE f 69 " pdb=" CB PHE f 69 " pdb=" CG PHE f 69 " ideal model delta sigma weight residual 113.80 121.34 -7.54 1.00e+00 1.00e+00 5.69e+01 angle pdb=" CA ASP B 672 " pdb=" CB ASP B 672 " pdb=" CG ASP B 672 " ideal model delta sigma weight residual 112.60 120.05 -7.45 1.00e+00 1.00e+00 5.54e+01 angle pdb=" N SER B 668 " pdb=" CA SER B 668 " pdb=" C SER B 668 " ideal model delta sigma weight residual 111.71 120.07 -8.36 1.15e+00 7.56e-01 5.29e+01 ... (remaining 26851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 11279 17.43 - 34.86: 616 34.86 - 52.29: 148 52.29 - 69.71: 34 69.71 - 87.14: 19 Dihedral angle restraints: 12096 sinusoidal: 5112 harmonic: 6984 Sorted by residual: dihedral pdb=" C LEU e 36 " pdb=" N LEU e 36 " pdb=" CA LEU e 36 " pdb=" CB LEU e 36 " ideal model delta harmonic sigma weight residual -122.60 -108.00 -14.60 0 2.50e+00 1.60e-01 3.41e+01 dihedral pdb=" C HIS A 692 " pdb=" N HIS A 692 " pdb=" CA HIS A 692 " pdb=" CB HIS A 692 " ideal model delta harmonic sigma weight residual -122.60 -137.10 14.50 0 2.50e+00 1.60e-01 3.37e+01 dihedral pdb=" C LEU d 36 " pdb=" N LEU d 36 " pdb=" CA LEU d 36 " pdb=" CB LEU d 36 " ideal model delta harmonic sigma weight residual -122.60 -108.47 -14.13 0 2.50e+00 1.60e-01 3.20e+01 ... (remaining 12093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2136 0.119 - 0.239: 707 0.239 - 0.358: 126 0.358 - 0.477: 20 0.477 - 0.596: 8 Chirality restraints: 2997 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.98e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.09e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.04e+01 ... (remaining 2994 not shown) Planarity restraints: 3483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 369 " -0.265 2.00e-02 2.50e+03 1.42e-01 5.03e+02 pdb=" CG TRP B 369 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP B 369 " 0.077 2.00e-02 2.50e+03 pdb=" CD2 TRP B 369 " 0.115 2.00e-02 2.50e+03 pdb=" NE1 TRP B 369 " 0.109 2.00e-02 2.50e+03 pdb=" CE2 TRP B 369 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 369 " 0.191 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 369 " -0.185 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 369 " 0.079 2.00e-02 2.50e+03 pdb=" CH2 TRP B 369 " -0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 369 " -0.188 2.00e-02 2.50e+03 9.83e-02 2.42e+02 pdb=" CG TRP A 369 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 369 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP A 369 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP A 369 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 TRP A 369 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 369 " 0.124 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 369 " -0.135 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 369 " 0.061 2.00e-02 2.50e+03 pdb=" CH2 TRP A 369 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 141 " -0.073 2.00e-02 2.50e+03 7.99e-02 7.99e+01 pdb=" CG ASN B 141 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 141 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN B 141 " 0.126 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.098 2.00e-02 2.50e+03 ... (remaining 3480 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 10112 3.02 - 3.49: 18247 3.49 - 3.96: 30414 3.96 - 4.43: 33743 4.43 - 4.90: 59029 Nonbonded interactions: 151545 Sorted by model distance: nonbonded pdb=" OE1 GLU A 187 " pdb=" OG1 THR B 690 " model vdw 2.545 3.040 nonbonded pdb=" N ASP d 55 " pdb=" O ASP d 55 " model vdw 2.562 2.496 nonbonded pdb=" N ASP e 55 " pdb=" O ASP e 55 " model vdw 2.566 2.496 nonbonded pdb=" OE2 GLU A 679 " pdb=" OG SER C 244 " model vdw 2.568 3.040 nonbonded pdb=" OG SER B 244 " pdb=" OE2 GLU C 679 " model vdw 2.571 3.040 ... (remaining 151540 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'd' selection = chain 'e' selection = chain 'f' } 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: 6.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.980 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.011 0.085 19845 Z= 0.622 Angle : 1.925 10.940 26970 Z= 1.269 Chirality : 0.121 0.596 2997 Planarity : 0.016 0.206 3471 Dihedral : 12.027 87.143 7563 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 0.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.89 % Favored : 97.99 % Rotamer: Outliers : 0.69 % Allowed : 2.83 % Favored : 96.48 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 3.12 % 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: -1.08 (0.15), residues: 2385 helix: -0.28 (0.18), residues: 666 sheet: -0.77 (0.19), residues: 594 loop : -0.82 (0.16), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 318 TYR 0.112 0.016 TYR B 254 PHE 0.080 0.012 PHE C 287 TRP 0.265 0.023 TRP B 369 HIS 0.011 0.004 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.01096 (19800) covalent geometry : angle 1.90457 (26856) SS BOND : bond 0.02424 ( 21) SS BOND : angle 2.58250 ( 42) hydrogen bonds : bond 0.17539 ( 948) hydrogen bonds : angle 7.54587 ( 2760) link_BETA1-4 : bond 0.04001 ( 12) link_BETA1-4 : angle 5.91340 ( 36) link_NAG-ASN : bond 0.01848 ( 12) link_NAG-ASN : angle 5.30953 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 313 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 806 MET cc_start: 0.1807 (mtt) cc_final: 0.0024 (ttt) REVERT: C 620 ASN cc_start: 0.8909 (t0) cc_final: 0.8651 (t0) REVERT: C 795 PHE cc_start: 0.9029 (t80) cc_final: 0.8788 (t80) REVERT: C 806 MET cc_start: 0.1261 (ptp) cc_final: -0.0290 (ttt) REVERT: e 74 ASP cc_start: 0.7714 (t0) cc_final: 0.6945 (t0) outliers start: 14 outliers final: 8 residues processed: 326 average time/residue: 0.7523 time to fit residues: 268.2092 Evaluate side-chains 205 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain d residue 74 ASP Chi-restraints excluded: chain f residue 69 PHE Chi-restraints excluded: chain f residue 74 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 HIS A 724 HIS B 681 HIS C 370 GLN C 472 GLN C 724 HIS e 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.097964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.063404 restraints weight = 46832.441| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.55 r_work: 0.2889 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19845 Z= 0.151 Angle : 0.665 8.443 26970 Z= 0.354 Chirality : 0.045 0.269 2997 Planarity : 0.004 0.032 3471 Dihedral : 6.032 117.124 3221 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.54 % Allowed : 9.82 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.16), residues: 2385 helix: 2.06 (0.20), residues: 651 sheet: -0.30 (0.19), residues: 639 loop : -0.25 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG f 112 TYR 0.025 0.001 TYR C 179 PHE 0.031 0.002 PHE A 770 TRP 0.021 0.002 TRP A 369 HIS 0.006 0.001 HIS A 681 Details of bonding type rmsd covalent geometry : bond 0.00315 (19800) covalent geometry : angle 0.65292 (26856) SS BOND : bond 0.00622 ( 21) SS BOND : angle 1.56835 ( 42) hydrogen bonds : bond 0.04693 ( 948) hydrogen bonds : angle 5.46187 ( 2760) link_BETA1-4 : bond 0.00349 ( 12) link_BETA1-4 : angle 2.41255 ( 36) link_NAG-ASN : bond 0.00648 ( 12) link_NAG-ASN : angle 2.08482 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 754 MET cc_start: 0.9304 (tpp) cc_final: 0.8535 (tpp) REVERT: A 806 MET cc_start: 0.2808 (mtt) cc_final: -0.0024 (ttt) REVERT: B 182 PHE cc_start: 0.8704 (m-80) cc_final: 0.8377 (m-80) REVERT: C 182 PHE cc_start: 0.9158 (m-80) cc_final: 0.8687 (m-80) REVERT: C 620 ASN cc_start: 0.9050 (t0) cc_final: 0.8671 (t0) REVERT: C 806 MET cc_start: 0.1983 (ptp) cc_final: -0.0045 (ttt) REVERT: d 91 ASP cc_start: 0.9093 (m-30) cc_final: 0.8745 (m-30) REVERT: e 88 LYS cc_start: 0.9272 (mttp) cc_final: 0.8962 (mttp) REVERT: e 91 ASP cc_start: 0.9070 (m-30) cc_final: 0.8701 (m-30) REVERT: e 112 ARG cc_start: 0.9098 (mmm-85) cc_final: 0.8862 (tpp80) REVERT: f 6 GLU cc_start: 0.7791 (tt0) cc_final: 0.7584 (tt0) REVERT: f 74 ASP cc_start: 0.7877 (t0) cc_final: 0.7477 (t0) outliers start: 31 outliers final: 14 residues processed: 230 average time/residue: 0.5885 time to fit residues: 151.0393 Evaluate side-chains 198 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain d residue 84 MET Chi-restraints excluded: chain e residue 84 MET Chi-restraints excluded: chain f residue 3 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 71 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 75 optimal weight: 0.0970 chunk 190 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS B 724 HIS C 534 HIS C 657 HIS f 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.097179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.062544 restraints weight = 46891.699| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.56 r_work: 0.2885 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19845 Z= 0.166 Angle : 0.605 11.115 26970 Z= 0.318 Chirality : 0.043 0.229 2997 Planarity : 0.004 0.036 3471 Dihedral : 5.126 58.360 3212 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.54 % Allowed : 11.31 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.17), residues: 2385 helix: 2.48 (0.21), residues: 651 sheet: -0.11 (0.19), residues: 639 loop : -0.20 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG f 112 TYR 0.024 0.001 TYR C 179 PHE 0.031 0.002 PHE A 770 TRP 0.016 0.002 TRP d 101 HIS 0.004 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00378 (19800) covalent geometry : angle 0.59656 (26856) SS BOND : bond 0.00802 ( 21) SS BOND : angle 1.10805 ( 42) hydrogen bonds : bond 0.04020 ( 948) hydrogen bonds : angle 5.14465 ( 2760) link_BETA1-4 : bond 0.00416 ( 12) link_BETA1-4 : angle 2.15035 ( 36) link_NAG-ASN : bond 0.00434 ( 12) link_NAG-ASN : angle 1.51665 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 HIS cc_start: 0.8606 (m90) cc_final: 0.8217 (m90) REVERT: A 179 TYR cc_start: 0.8834 (m-80) cc_final: 0.8620 (m-10) REVERT: A 806 MET cc_start: 0.2810 (mtt) cc_final: 0.0001 (ttt) REVERT: B 177 HIS cc_start: 0.8752 (m90) cc_final: 0.8289 (m90) REVERT: B 182 PHE cc_start: 0.8677 (m-80) cc_final: 0.8318 (m-80) REVERT: B 535 GLU cc_start: 0.8742 (mp0) cc_final: 0.8529 (mp0) REVERT: C 620 ASN cc_start: 0.9109 (t0) cc_final: 0.8699 (t0) REVERT: C 754 MET cc_start: 0.9356 (tpp) cc_final: 0.8593 (tpp) REVERT: C 806 MET cc_start: 0.2054 (ptp) cc_final: 0.0043 (ttt) REVERT: d 74 ASP cc_start: 0.8012 (t0) cc_final: 0.7584 (t0) REVERT: d 91 ASP cc_start: 0.9050 (m-30) cc_final: 0.8644 (m-30) REVERT: d 98 ASN cc_start: 0.9278 (OUTLIER) cc_final: 0.9072 (t0) REVERT: e 40 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8106 (ttp-170) REVERT: e 77 GLU cc_start: 0.8500 (mp0) cc_final: 0.8263 (mp0) REVERT: e 88 LYS cc_start: 0.9227 (mttp) cc_final: 0.8859 (mttp) REVERT: e 91 ASP cc_start: 0.9027 (m-30) cc_final: 0.8542 (m-30) REVERT: f 74 ASP cc_start: 0.7970 (t0) cc_final: 0.7622 (t0) REVERT: f 91 ASP cc_start: 0.9037 (m-30) cc_final: 0.8668 (m-30) outliers start: 31 outliers final: 19 residues processed: 221 average time/residue: 0.6132 time to fit residues: 151.5362 Evaluate side-chains 204 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain d residue 3 GLN Chi-restraints excluded: chain d residue 84 MET Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain d residue 98 ASN Chi-restraints excluded: chain e residue 40 ARG Chi-restraints excluded: chain e residue 84 MET Chi-restraints excluded: chain f residue 3 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 153 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 657 HIS C 181 GLN e 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.094810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063421 restraints weight = 45014.493| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 3.26 r_work: 0.2867 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19845 Z= 0.177 Angle : 0.585 12.624 26970 Z= 0.306 Chirality : 0.043 0.213 2997 Planarity : 0.003 0.031 3471 Dihedral : 5.016 59.985 3212 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.33 % Allowed : 11.21 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2385 helix: 2.60 (0.20), residues: 651 sheet: 0.07 (0.19), residues: 627 loop : -0.18 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG f 112 TYR 0.016 0.001 TYR C 179 PHE 0.029 0.001 PHE B 770 TRP 0.019 0.002 TRP A 174 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00407 (19800) covalent geometry : angle 0.57814 (26856) SS BOND : bond 0.00739 ( 21) SS BOND : angle 1.04874 ( 42) hydrogen bonds : bond 0.03697 ( 948) hydrogen bonds : angle 5.02314 ( 2760) link_BETA1-4 : bond 0.00380 ( 12) link_BETA1-4 : angle 1.93198 ( 36) link_NAG-ASN : bond 0.00343 ( 12) link_NAG-ASN : angle 1.35454 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 202 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 HIS cc_start: 0.8435 (m90) cc_final: 0.8163 (m90) REVERT: A 535 GLU cc_start: 0.8689 (mp0) cc_final: 0.8391 (mp0) REVERT: A 731 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8156 (tpt) REVERT: A 739 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.9169 (m-10) REVERT: A 806 MET cc_start: 0.2737 (mtt) cc_final: 0.0049 (ttt) REVERT: B 177 HIS cc_start: 0.8562 (m90) cc_final: 0.8209 (m90) REVERT: B 535 GLU cc_start: 0.8762 (mp0) cc_final: 0.8493 (mp0) REVERT: C 754 MET cc_start: 0.9384 (tpp) cc_final: 0.8574 (tpp) REVERT: C 792 PHE cc_start: 0.9252 (m-10) cc_final: 0.8925 (m-80) REVERT: C 799 MET cc_start: 0.9142 (mmp) cc_final: 0.8781 (ptm) REVERT: C 806 MET cc_start: 0.2155 (ptp) cc_final: 0.0139 (ttt) REVERT: d 74 ASP cc_start: 0.8158 (t0) cc_final: 0.7855 (t0) REVERT: d 88 LYS cc_start: 0.9250 (mttp) cc_final: 0.8982 (mttp) REVERT: d 91 ASP cc_start: 0.9033 (m-30) cc_final: 0.8656 (m-30) REVERT: e 40 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8137 (ttp-170) REVERT: e 88 LYS cc_start: 0.9217 (mttp) cc_final: 0.8854 (mttp) REVERT: e 91 ASP cc_start: 0.9113 (m-30) cc_final: 0.8705 (m-30) REVERT: f 74 ASP cc_start: 0.8124 (t0) cc_final: 0.7899 (t0) REVERT: f 91 ASP cc_start: 0.9039 (m-30) cc_final: 0.8649 (m-30) outliers start: 47 outliers final: 20 residues processed: 225 average time/residue: 0.6379 time to fit residues: 160.5648 Evaluate side-chains 207 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 373 ASP Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain d residue 3 GLN Chi-restraints excluded: chain d residue 84 MET Chi-restraints excluded: chain d residue 94 VAL Chi-restraints excluded: chain e residue 40 ARG Chi-restraints excluded: chain e residue 84 MET Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 94 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 24 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 4 optimal weight: 0.0020 chunk 177 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 chunk 56 optimal weight: 0.4980 chunk 176 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.095129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.064003 restraints weight = 44434.401| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.26 r_work: 0.2853 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19845 Z= 0.116 Angle : 0.569 16.904 26970 Z= 0.297 Chirality : 0.042 0.199 2997 Planarity : 0.003 0.039 3471 Dihedral : 4.825 59.307 3212 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.49 % Allowed : 12.70 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.11 (0.17), residues: 2385 helix: 2.60 (0.20), residues: 654 sheet: 0.25 (0.19), residues: 642 loop : -0.05 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG f 112 TYR 0.024 0.001 TYR A 179 PHE 0.031 0.001 PHE A 770 TRP 0.021 0.001 TRP A 174 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00257 (19800) covalent geometry : angle 0.56361 (26856) SS BOND : bond 0.00463 ( 21) SS BOND : angle 0.88795 ( 42) hydrogen bonds : bond 0.03291 ( 948) hydrogen bonds : angle 4.89325 ( 2760) link_BETA1-4 : bond 0.00363 ( 12) link_BETA1-4 : angle 1.79700 ( 36) link_NAG-ASN : bond 0.00387 ( 12) link_NAG-ASN : angle 1.34543 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 HIS cc_start: 0.8478 (m90) cc_final: 0.8245 (m90) REVERT: A 806 MET cc_start: 0.2875 (mtt) cc_final: 0.0119 (ttt) REVERT: B 177 HIS cc_start: 0.8588 (m90) cc_final: 0.8328 (m90) REVERT: B 535 GLU cc_start: 0.8792 (mp0) cc_final: 0.8450 (mp0) REVERT: C 535 GLU cc_start: 0.8829 (mp0) cc_final: 0.8618 (mp0) REVERT: C 792 PHE cc_start: 0.9256 (m-10) cc_final: 0.8931 (m-80) REVERT: C 806 MET cc_start: 0.2033 (ptp) cc_final: 0.0126 (ttt) REVERT: d 74 ASP cc_start: 0.8097 (t0) cc_final: 0.7827 (t0) REVERT: d 88 LYS cc_start: 0.9224 (mttp) cc_final: 0.8883 (mttp) REVERT: d 91 ASP cc_start: 0.9038 (m-30) cc_final: 0.8569 (m-30) REVERT: e 88 LYS cc_start: 0.9194 (mttp) cc_final: 0.8727 (mttp) REVERT: e 91 ASP cc_start: 0.9109 (m-30) cc_final: 0.8548 (m-30) REVERT: f 74 ASP cc_start: 0.8068 (t0) cc_final: 0.7790 (t0) REVERT: f 91 ASP cc_start: 0.9062 (m-30) cc_final: 0.8781 (m-30) outliers start: 30 outliers final: 14 residues processed: 226 average time/residue: 0.6097 time to fit residues: 154.1499 Evaluate side-chains 197 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain d residue 3 GLN Chi-restraints excluded: chain d residue 84 MET Chi-restraints excluded: chain f residue 84 MET Chi-restraints excluded: chain f residue 94 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 87 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 657 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.096894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.066243 restraints weight = 44794.860| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.20 r_work: 0.2911 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19845 Z= 0.135 Angle : 0.578 15.189 26970 Z= 0.299 Chirality : 0.042 0.189 2997 Planarity : 0.003 0.044 3471 Dihedral : 4.731 59.757 3212 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.93 % Allowed : 12.85 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.20 (0.17), residues: 2385 helix: 2.68 (0.20), residues: 651 sheet: 0.35 (0.20), residues: 612 loop : -0.02 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG f 112 TYR 0.023 0.001 TYR A 179 PHE 0.034 0.001 PHE C 795 TRP 0.015 0.001 TRP f 101 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00308 (19800) covalent geometry : angle 0.57260 (26856) SS BOND : bond 0.00470 ( 21) SS BOND : angle 0.80166 ( 42) hydrogen bonds : bond 0.03259 ( 948) hydrogen bonds : angle 4.85699 ( 2760) link_BETA1-4 : bond 0.00354 ( 12) link_BETA1-4 : angle 1.70156 ( 36) link_NAG-ASN : bond 0.00313 ( 12) link_NAG-ASN : angle 1.28710 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 421 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7742 (mpp) REVERT: A 806 MET cc_start: 0.2959 (mtt) cc_final: 0.0219 (ttt) REVERT: B 177 HIS cc_start: 0.8490 (m90) cc_final: 0.8242 (m90) REVERT: B 535 GLU cc_start: 0.8792 (mp0) cc_final: 0.8553 (mp0) REVERT: B 754 MET cc_start: 0.9255 (tpp) cc_final: 0.8722 (tpp) REVERT: C 182 PHE cc_start: 0.9033 (m-80) cc_final: 0.8770 (m-80) REVERT: C 754 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8708 (tpp) REVERT: C 792 PHE cc_start: 0.9253 (m-10) cc_final: 0.8926 (m-80) REVERT: C 806 MET cc_start: 0.2438 (ptp) cc_final: 0.0458 (ttt) REVERT: d 88 LYS cc_start: 0.9152 (mttp) cc_final: 0.8749 (mttp) REVERT: d 91 ASP cc_start: 0.9024 (m-30) cc_final: 0.8506 (m-30) REVERT: e 88 LYS cc_start: 0.9179 (mttp) cc_final: 0.8814 (mttp) REVERT: e 91 ASP cc_start: 0.9147 (m-30) cc_final: 0.8763 (m-30) REVERT: f 91 ASP cc_start: 0.9106 (m-30) cc_final: 0.8784 (m-30) outliers start: 39 outliers final: 24 residues processed: 224 average time/residue: 0.5805 time to fit residues: 146.4869 Evaluate side-chains 204 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain d residue 3 GLN Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain e residue 84 MET Chi-restraints excluded: chain f residue 84 MET Chi-restraints excluded: chain f residue 94 VAL Chi-restraints excluded: chain f residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 182 optimal weight: 3.9990 chunk 195 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 152 optimal weight: 0.0980 chunk 79 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.094138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.062818 restraints weight = 44130.101| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.48 r_work: 0.2812 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19845 Z= 0.118 Angle : 0.593 16.382 26970 Z= 0.303 Chirality : 0.042 0.201 2997 Planarity : 0.003 0.037 3471 Dihedral : 4.608 59.457 3212 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.08 % Allowed : 13.89 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.21 (0.17), residues: 2385 helix: 2.59 (0.20), residues: 654 sheet: 0.47 (0.20), residues: 630 loop : -0.04 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 178 TYR 0.022 0.001 TYR A 179 PHE 0.032 0.001 PHE C 770 TRP 0.016 0.001 TRP d 101 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00266 (19800) covalent geometry : angle 0.58844 (26856) SS BOND : bond 0.00573 ( 21) SS BOND : angle 0.72388 ( 42) hydrogen bonds : bond 0.03100 ( 948) hydrogen bonds : angle 4.80426 ( 2760) link_BETA1-4 : bond 0.00336 ( 12) link_BETA1-4 : angle 1.62337 ( 36) link_NAG-ASN : bond 0.00343 ( 12) link_NAG-ASN : angle 1.24205 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 201 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 754 MET cc_start: 0.8986 (tpp) cc_final: 0.8703 (tpp) REVERT: A 792 PHE cc_start: 0.9145 (m-10) cc_final: 0.8803 (m-80) REVERT: A 806 MET cc_start: 0.2820 (mtt) cc_final: 0.0445 (ttt) REVERT: B 163 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8436 (ptm) REVERT: B 177 HIS cc_start: 0.8574 (m90) cc_final: 0.8330 (m90) REVERT: B 535 GLU cc_start: 0.8850 (mp0) cc_final: 0.8391 (mp0) REVERT: B 754 MET cc_start: 0.9193 (tpp) cc_final: 0.8668 (tpp) REVERT: C 182 PHE cc_start: 0.8859 (m-80) cc_final: 0.8610 (m-80) REVERT: C 754 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8620 (tpp) REVERT: C 792 PHE cc_start: 0.9260 (m-10) cc_final: 0.8936 (m-80) REVERT: C 806 MET cc_start: 0.1993 (ptp) cc_final: 0.0263 (ttt) REVERT: d 5 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8849 (m) REVERT: d 88 LYS cc_start: 0.9055 (mttp) cc_final: 0.8654 (mttp) REVERT: d 91 ASP cc_start: 0.8974 (m-30) cc_final: 0.8520 (m-30) REVERT: e 66 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8397 (mtmm) REVERT: e 74 ASP cc_start: 0.8172 (t0) cc_final: 0.7664 (t0) REVERT: e 88 LYS cc_start: 0.9100 (mttp) cc_final: 0.8725 (mttp) REVERT: e 91 ASP cc_start: 0.9094 (m-30) cc_final: 0.8562 (m-30) REVERT: f 91 ASP cc_start: 0.9176 (m-30) cc_final: 0.8826 (m-30) outliers start: 42 outliers final: 26 residues processed: 229 average time/residue: 0.6093 time to fit residues: 155.4940 Evaluate side-chains 205 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 679 GLU Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 84 MET Chi-restraints excluded: chain e residue 60 ASN Chi-restraints excluded: chain e residue 84 MET Chi-restraints excluded: chain f residue 84 MET Chi-restraints excluded: chain f residue 94 VAL Chi-restraints excluded: chain f residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 166 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.093285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.062297 restraints weight = 44857.007| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.20 r_work: 0.2846 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19845 Z= 0.235 Angle : 0.647 17.232 26970 Z= 0.333 Chirality : 0.043 0.191 2997 Planarity : 0.004 0.048 3471 Dihedral : 4.708 58.614 3212 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.13 % Allowed : 14.68 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.17), residues: 2385 helix: 2.41 (0.20), residues: 672 sheet: 0.29 (0.20), residues: 642 loop : -0.07 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG f 112 TYR 0.021 0.001 TYR B 179 PHE 0.032 0.001 PHE A 770 TRP 0.014 0.001 TRP d 101 HIS 0.005 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00545 (19800) covalent geometry : angle 0.64291 (26856) SS BOND : bond 0.00746 ( 21) SS BOND : angle 0.95116 ( 42) hydrogen bonds : bond 0.03592 ( 948) hydrogen bonds : angle 4.90959 ( 2760) link_BETA1-4 : bond 0.00263 ( 12) link_BETA1-4 : angle 1.59061 ( 36) link_NAG-ASN : bond 0.00314 ( 12) link_NAG-ASN : angle 1.21895 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 792 PHE cc_start: 0.9194 (m-10) cc_final: 0.8855 (m-80) REVERT: A 806 MET cc_start: 0.3418 (mtt) cc_final: 0.0799 (ttt) REVERT: B 163 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8524 (ptm) REVERT: B 177 HIS cc_start: 0.8494 (m90) cc_final: 0.8230 (m90) REVERT: B 421 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7516 (mpp) REVERT: B 535 GLU cc_start: 0.8855 (mp0) cc_final: 0.8485 (mp0) REVERT: C 182 PHE cc_start: 0.8977 (m-80) cc_final: 0.8737 (m-80) REVERT: C 742 MET cc_start: 0.7904 (tmt) cc_final: 0.7238 (pp-130) REVERT: C 754 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8765 (tpp) REVERT: C 792 PHE cc_start: 0.9270 (m-10) cc_final: 0.8947 (m-80) REVERT: C 806 MET cc_start: 0.2232 (ptp) cc_final: 0.0464 (ttt) REVERT: d 88 LYS cc_start: 0.9170 (mttp) cc_final: 0.8869 (mttp) REVERT: d 91 ASP cc_start: 0.9096 (m-30) cc_final: 0.8721 (m-30) REVERT: e 66 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8536 (mtmm) REVERT: e 88 LYS cc_start: 0.9175 (mttp) cc_final: 0.8829 (mttp) REVERT: e 91 ASP cc_start: 0.9170 (m-30) cc_final: 0.8895 (m-30) REVERT: f 91 ASP cc_start: 0.9158 (m-30) cc_final: 0.8839 (m-30) outliers start: 43 outliers final: 24 residues processed: 209 average time/residue: 0.6250 time to fit residues: 145.8210 Evaluate side-chains 201 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 694 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain d residue 3 GLN Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 84 MET Chi-restraints excluded: chain e residue 84 MET Chi-restraints excluded: chain f residue 3 GLN Chi-restraints excluded: chain f residue 84 MET Chi-restraints excluded: chain f residue 94 VAL Chi-restraints excluded: chain f residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 111 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 162 optimal weight: 0.1980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.093876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.062553 restraints weight = 44220.268| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.44 r_work: 0.2775 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19845 Z= 0.156 Angle : 0.635 17.096 26970 Z= 0.324 Chirality : 0.043 0.299 2997 Planarity : 0.003 0.055 3471 Dihedral : 4.664 58.287 3212 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.64 % Allowed : 15.48 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.17), residues: 2385 helix: 2.38 (0.20), residues: 672 sheet: 0.52 (0.20), residues: 612 loop : -0.10 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 178 TYR 0.022 0.001 TYR C 179 PHE 0.033 0.001 PHE C 770 TRP 0.016 0.001 TRP d 101 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00361 (19800) covalent geometry : angle 0.63093 (26856) SS BOND : bond 0.00603 ( 21) SS BOND : angle 1.16781 ( 42) hydrogen bonds : bond 0.03288 ( 948) hydrogen bonds : angle 4.82691 ( 2760) link_BETA1-4 : bond 0.00293 ( 12) link_BETA1-4 : angle 1.52045 ( 36) link_NAG-ASN : bond 0.00272 ( 12) link_NAG-ASN : angle 1.14385 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 421 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7616 (mpp) REVERT: A 754 MET cc_start: 0.8845 (tpp) cc_final: 0.8614 (tpp) REVERT: A 792 PHE cc_start: 0.9191 (m-10) cc_final: 0.8854 (m-80) REVERT: A 806 MET cc_start: 0.2989 (mtt) cc_final: 0.0753 (ttt) REVERT: B 163 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8449 (ptm) REVERT: B 177 HIS cc_start: 0.8528 (m90) cc_final: 0.8273 (m90) REVERT: B 421 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7491 (mpp) REVERT: B 535 GLU cc_start: 0.8889 (mp0) cc_final: 0.8426 (mp0) REVERT: B 754 MET cc_start: 0.9283 (tpp) cc_final: 0.8962 (tpp) REVERT: C 182 PHE cc_start: 0.8882 (m-80) cc_final: 0.8616 (m-80) REVERT: C 366 MET cc_start: 0.9312 (mmm) cc_final: 0.9042 (mmm) REVERT: C 742 MET cc_start: 0.8050 (tmt) cc_final: 0.7341 (pp-130) REVERT: C 754 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8720 (tpp) REVERT: C 792 PHE cc_start: 0.9258 (m-10) cc_final: 0.8940 (m-80) REVERT: C 806 MET cc_start: 0.2093 (ptp) cc_final: 0.0448 (ttt) REVERT: d 5 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8809 (m) REVERT: d 88 LYS cc_start: 0.9120 (mttp) cc_final: 0.8786 (mttp) REVERT: d 91 ASP cc_start: 0.9075 (m-30) cc_final: 0.8576 (m-30) REVERT: e 66 LYS cc_start: 0.8862 (mtpp) cc_final: 0.8435 (mtmm) REVERT: e 74 ASP cc_start: 0.8215 (t0) cc_final: 0.8005 (t0) REVERT: e 88 LYS cc_start: 0.9073 (mttp) cc_final: 0.8692 (mttp) REVERT: e 91 ASP cc_start: 0.9148 (m-30) cc_final: 0.8768 (m-30) REVERT: f 3 GLN cc_start: 0.9144 (mt0) cc_final: 0.8661 (mp10) REVERT: f 74 ASP cc_start: 0.7995 (t0) cc_final: 0.7513 (t0) REVERT: f 91 ASP cc_start: 0.9175 (m-30) cc_final: 0.8859 (m-30) outliers start: 33 outliers final: 24 residues processed: 203 average time/residue: 0.6347 time to fit residues: 144.1694 Evaluate side-chains 200 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain d residue 3 GLN Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 84 MET Chi-restraints excluded: chain e residue 84 MET Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 84 MET Chi-restraints excluded: chain f residue 94 VAL Chi-restraints excluded: chain f residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 174 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 152 optimal weight: 0.0370 chunk 107 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 230 optimal weight: 0.3980 overall best weight: 1.0460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS A 217 ASN B 217 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.098042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.066305 restraints weight = 45504.884| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.45 r_work: 0.2915 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19845 Z= 0.148 Angle : 0.643 17.590 26970 Z= 0.325 Chirality : 0.042 0.309 2997 Planarity : 0.003 0.062 3471 Dihedral : 4.612 58.089 3212 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.59 % Allowed : 15.62 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.18 (0.17), residues: 2385 helix: 2.36 (0.20), residues: 672 sheet: 0.59 (0.20), residues: 612 loop : -0.04 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 178 TYR 0.018 0.001 TYR d 96 PHE 0.034 0.001 PHE A 770 TRP 0.015 0.001 TRP d 101 HIS 0.005 0.001 HIS A 724 Details of bonding type rmsd covalent geometry : bond 0.00343 (19800) covalent geometry : angle 0.63930 (26856) SS BOND : bond 0.00585 ( 21) SS BOND : angle 1.05045 ( 42) hydrogen bonds : bond 0.03242 ( 948) hydrogen bonds : angle 4.80575 ( 2760) link_BETA1-4 : bond 0.00307 ( 12) link_BETA1-4 : angle 1.50788 ( 36) link_NAG-ASN : bond 0.00262 ( 12) link_NAG-ASN : angle 1.14835 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 421 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.7674 (mpp) REVERT: A 792 PHE cc_start: 0.9227 (m-10) cc_final: 0.8875 (m-80) REVERT: A 806 MET cc_start: 0.3569 (mtt) cc_final: 0.0832 (ttt) REVERT: B 163 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8417 (ptm) REVERT: B 177 HIS cc_start: 0.8447 (m90) cc_final: 0.8217 (m90) REVERT: B 421 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.7466 (mpp) REVERT: B 535 GLU cc_start: 0.8933 (mp0) cc_final: 0.8673 (mp0) REVERT: C 182 PHE cc_start: 0.8974 (m-80) cc_final: 0.8704 (m-80) REVERT: C 742 MET cc_start: 0.7961 (tmt) cc_final: 0.7256 (pp-130) REVERT: C 754 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8752 (tpp) REVERT: C 792 PHE cc_start: 0.9265 (m-10) cc_final: 0.8938 (m-80) REVERT: C 806 MET cc_start: 0.2550 (ptp) cc_final: 0.0661 (ttt) REVERT: d 5 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.9011 (m) REVERT: d 66 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8393 (mtmm) REVERT: d 77 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8332 (tm-30) REVERT: d 88 LYS cc_start: 0.9118 (mttp) cc_final: 0.8825 (mttp) REVERT: d 91 ASP cc_start: 0.9107 (m-30) cc_final: 0.8728 (m-30) REVERT: e 66 LYS cc_start: 0.8820 (mtpp) cc_final: 0.8504 (mtmm) REVERT: e 88 LYS cc_start: 0.9125 (mttp) cc_final: 0.8724 (mttp) REVERT: e 91 ASP cc_start: 0.9209 (m-30) cc_final: 0.8846 (m-30) REVERT: f 1 GLN cc_start: 0.8408 (tp40) cc_final: 0.7720 (tp-100) REVERT: f 74 ASP cc_start: 0.8138 (t0) cc_final: 0.7527 (OUTLIER) REVERT: f 91 ASP cc_start: 0.9164 (m-30) cc_final: 0.8837 (m-30) outliers start: 32 outliers final: 24 residues processed: 196 average time/residue: 0.5944 time to fit residues: 130.6264 Evaluate side-chains 201 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 412 CYS Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 74 ASP Chi-restraints excluded: chain d residue 84 MET Chi-restraints excluded: chain e residue 84 MET Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 94 VAL Chi-restraints excluded: chain f residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 200 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 125 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 24 optimal weight: 0.0070 chunk 171 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.093265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.061842 restraints weight = 44156.958| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.47 r_work: 0.2794 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19845 Z= 0.137 Angle : 0.647 17.203 26970 Z= 0.326 Chirality : 0.043 0.303 2997 Planarity : 0.004 0.077 3471 Dihedral : 4.590 57.941 3212 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.49 % Allowed : 15.92 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.19 (0.17), residues: 2385 helix: 2.33 (0.20), residues: 672 sheet: 0.63 (0.20), residues: 612 loop : -0.03 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG f 112 TYR 0.023 0.001 TYR B 179 PHE 0.037 0.001 PHE C 770 TRP 0.014 0.001 TRP d 101 HIS 0.005 0.001 HIS A 724 Details of bonding type rmsd covalent geometry : bond 0.00317 (19800) covalent geometry : angle 0.64356 (26856) SS BOND : bond 0.00547 ( 21) SS BOND : angle 0.98819 ( 42) hydrogen bonds : bond 0.03205 ( 948) hydrogen bonds : angle 4.79234 ( 2760) link_BETA1-4 : bond 0.00322 ( 12) link_BETA1-4 : angle 1.49326 ( 36) link_NAG-ASN : bond 0.00266 ( 12) link_NAG-ASN : angle 1.15191 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6378.80 seconds wall clock time: 109 minutes 17.47 seconds (6557.47 seconds total)