Starting phenix.real_space_refine on Fri Jun 20 23:08:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfi_33791/06_2025/7yfi_33791_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfi_33791/06_2025/7yfi_33791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yfi_33791/06_2025/7yfi_33791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfi_33791/06_2025/7yfi_33791.map" model { file = "/net/cci-nas-00/data/ceres_data/7yfi_33791/06_2025/7yfi_33791_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfi_33791/06_2025/7yfi_33791_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 15374 2.51 5 N 4066 2.21 5 O 4567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24135 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 5941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 5941 Classifications: {'peptide': 748} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 714} Chain breaks: 2 Chain: "B" Number of atoms: 5805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5805 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 27, 'TRANS': 706} Chain breaks: 2 Chain: "C" Number of atoms: 5920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5920 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 711} Chain breaks: 2 Chain: "D" Number of atoms: 5815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5815 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 39, 'TRANS': 709} Chain breaks: 1 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 103 Unusual residues: {'NAG': 7} Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {'NAG': 5} Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 103 Unusual residues: {'NAG': 7} Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 13.76, per 1000 atoms: 0.57 Number of scatterers: 24135 At special positions: 0 Unit cell: (155.295, 180.999, 125.307, 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 128 16.00 O 4567 8.00 N 4066 7.00 C 15374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 800 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 317 " distance=2.03 Simple disulfide: pdb=" SG CYS D 426 " - pdb=" SG CYS D 453 " distance=2.03 Simple disulfide: pdb=" SG CYS D 433 " - pdb=" SG CYS D 454 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG O 2 " - " MAN O 3 " BETA1-4 " 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 A 801 " - " ASN A 203 " " NAG A 802 " - " ASN A 239 " " NAG A 803 " - " ASN A 276 " " NAG A 804 " - " ASN A 300 " " NAG A 805 " - " ASN A 350 " " NAG A 806 " - " ASN A 440 " " NAG A 807 " - " ASN A 491 " " NAG B 901 " - " ASN B 75 " " NAG B 902 " - " ASN B 340 " " NAG B 903 " - " ASN B 380 " " NAG B 904 " - " ASN B 444 " " NAG B 905 " - " ASN B 443 " " NAG C 801 " - " ASN C 239 " " NAG C 802 " - " ASN C 300 " " NAG C 803 " - " ASN C 368 " " NAG C 804 " - " ASN C 350 " " NAG C 805 " - " ASN C 440 " " NAG C 806 " - " ASN C 491 " " NAG C 807 " - " ASN C 771 " " NAG D 901 " - " ASN D 70 " " NAG D 902 " - " ASN D 438 " " NAG E 1 " - " ASN A 61 " " NAG F 1 " - " ASN A 368 " " NAG G 1 " - " ASN A 471 " " NAG H 1 " - " ASN A 771 " " NAG I 1 " - " ASN B 687 " " NAG J 1 " - " ASN C 276 " " NAG K 1 " - " ASN C 61 " " NAG L 1 " - " ASN C 203 " " NAG M 1 " - " ASN C 471 " " NAG N 1 " - " ASN D 337 " " NAG O 1 " - " ASN D 685 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.89 Conformation dependent library (CDL) restraints added in 3.3 seconds 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5556 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 32 sheets defined 42.2% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.16 Creating SS restraints... Processing helix chain 'A' and resid 35 through 52 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.996A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.642A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.890A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 188 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.894A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.744A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.817A pdb=" N ARG A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 297 Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 457 through 470 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 550 through 556 removed outlier: 4.104A pdb=" N SER A 553 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 584 Processing helix chain 'A' and resid 603 through 613 Processing helix chain 'A' and resid 628 through 655 Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.548A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 708 removed outlier: 4.026A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.955A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.735A pdb=" N VAL B 46 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.734A pdb=" N LEU B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.744A pdb=" N GLN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 116 " --> pdb=" O MET B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 213 through 221 removed outlier: 4.526A pdb=" N VAL B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 247 Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 287 through 310 removed outlier: 3.538A pdb=" N LYS B 309 " --> pdb=" O SER B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 495 through 502 Processing helix chain 'B' and resid 515 through 520 Processing helix chain 'B' and resid 603 through 613 removed outlier: 3.876A pdb=" N LEU B 607 " --> pdb=" O LYS B 603 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE B 613 " --> pdb=" O TRP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 655 Processing helix chain 'B' and resid 667 through 672 Processing helix chain 'B' and resid 673 through 676 Processing helix chain 'B' and resid 688 through 698 Processing helix chain 'B' and resid 698 through 706 Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 770 through 785 removed outlier: 4.730A pdb=" N GLN B 774 " --> pdb=" O PRO B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 796 Processing helix chain 'B' and resid 814 through 834 Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 104 through 114 removed outlier: 4.175A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.527A pdb=" N SER C 129 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 158 removed outlier: 4.052A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.635A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 251 through 260 removed outlier: 6.574A pdb=" N GLY C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASN C 257 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 297 removed outlier: 3.795A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 457 through 470 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 551 through 556 Processing helix chain 'C' and resid 561 through 584 Processing helix chain 'C' and resid 606 through 613 Processing helix chain 'C' and resid 628 through 658 removed outlier: 3.507A pdb=" N ASP C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.660A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 removed outlier: 4.167A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 768 through 782 removed outlier: 3.632A pdb=" N VAL C 772 " --> pdb=" O TRP C 768 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'D' and resid 73 through 86 Processing helix chain 'D' and resid 102 through 116 removed outlier: 4.376A pdb=" N GLN D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 145 through 160 removed outlier: 3.568A pdb=" N GLN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 189 Processing helix chain 'D' and resid 203 through 207 removed outlier: 3.704A pdb=" N GLY D 206 " --> pdb=" O LEU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 217 Processing helix chain 'D' and resid 229 through 244 Processing helix chain 'D' and resid 255 through 260 removed outlier: 3.797A pdb=" N LEU D 259 " --> pdb=" O PRO D 255 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY D 260 " --> pdb=" O ASN D 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 260' Processing helix chain 'D' and resid 284 through 307 Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 456 through 470 Processing helix chain 'D' and resid 493 through 500 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 601 through 611 removed outlier: 4.221A pdb=" N LEU D 605 " --> pdb=" O LYS D 601 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 611 " --> pdb=" O TRP D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 653 Processing helix chain 'D' and resid 665 through 670 removed outlier: 3.510A pdb=" N GLN D 669 " --> pdb=" O ASP D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 696 through 705 removed outlier: 4.358A pdb=" N LYS D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 721 Processing helix chain 'D' and resid 730 through 739 Processing helix chain 'D' and resid 768 through 783 removed outlier: 4.724A pdb=" N ALA D 772 " --> pdb=" O HIS D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 793 Processing helix chain 'D' and resid 811 through 835 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 7.990A pdb=" N VAL A 87 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 196 removed outlier: 3.846A pdb=" N LYS A 193 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 270 removed outlier: 6.751A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 478 removed outlier: 5.353A pdb=" N ALA A 515 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLY A 759 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU A 517 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLY A 757 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N PHE A 754 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 538 " --> pdb=" O PHE A 754 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 528 through 529 removed outlier: 5.810A pdb=" N PHE A 754 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 538 " --> pdb=" O PHE A 754 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 487 through 490 removed outlier: 3.874A pdb=" N LYS A 495 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 73 removed outlier: 6.522A pdb=" N ILE B 36 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU B 72 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 38 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 98 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.744A pdb=" N PHE B 170 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASN B 202 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 172 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL B 363 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 342 through 343 Processing sheet with id=AB2, first strand: chain 'B' and resid 474 through 479 removed outlier: 3.895A pdb=" N ILE B 408 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 507 " --> pdb=" O SER B 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB4, first strand: chain 'B' and resid 486 through 489 Processing sheet with id=AB5, first strand: chain 'B' and resid 529 through 531 removed outlier: 4.196A pdb=" N VAL B 529 " --> pdb=" O TYR B 761 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 759 " --> pdb=" O THR B 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 682 through 683 removed outlier: 6.281A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 59 through 66 removed outlier: 6.267A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR C 63 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 193 through 197 removed outlier: 7.061A pdb=" N ILE C 163 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.370A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 339 through 340 removed outlier: 4.269A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 474 through 478 removed outlier: 6.876A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 514 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU C 517 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLY C 757 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG C 755 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLN C 536 " --> pdb=" O ARG C 755 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY C 757 " --> pdb=" O LYS C 534 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS C 534 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 528 through 529 removed outlier: 5.080A pdb=" N ARG C 755 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLN C 536 " --> pdb=" O ARG C 755 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY C 757 " --> pdb=" O LYS C 534 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS C 534 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC5, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AC6, first strand: chain 'D' and resid 62 through 68 removed outlier: 3.639A pdb=" N GLY D 92 " --> pdb=" O THR D 31 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE D 119 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 194 through 195 removed outlier: 9.045A pdb=" N LEU D 199 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL D 167 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU D 201 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR D 169 " --> pdb=" O LEU D 201 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 194 through 195 removed outlier: 4.038A pdb=" N VAL D 223 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 274 through 278 removed outlier: 6.693A pdb=" N MET D 358 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG D 374 " --> pdb=" O MET D 358 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL D 360 " --> pdb=" O VAL D 372 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AD2, first strand: chain 'D' and resid 415 through 417 removed outlier: 7.785A pdb=" N LEU D 477 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG D 434 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 403 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N TYR D 476 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL D 405 " --> pdb=" O TYR D 476 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 485 through 487 Processing sheet with id=AD4, first strand: chain 'D' and resid 527 through 529 removed outlier: 4.226A pdb=" N VAL D 527 " --> pdb=" O TYR D 759 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 680 through 681 removed outlier: 6.454A pdb=" N GLY D 681 " --> pdb=" O ILE D 727 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASP D 729 " --> pdb=" O GLY D 681 " (cutoff:3.500A) 1058 hydrogen bonds defined for protein. 3003 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: 9.41 Time building geometry restraints manager: 7.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3897 1.32 - 1.44: 6754 1.44 - 1.57: 13800 1.57 - 1.70: 4 1.70 - 1.83: 217 Bond restraints: 24672 Sorted by residual: bond pdb=" CA SER D 795 " pdb=" C SER D 795 " ideal model delta sigma weight residual 1.520 1.573 -0.053 1.16e-02 7.43e+03 2.11e+01 bond pdb=" C SER D 795 " pdb=" O SER D 795 " ideal model delta sigma weight residual 1.235 1.286 -0.052 1.13e-02 7.83e+03 2.09e+01 bond pdb=" C THR C 665 " pdb=" O THR C 665 " ideal model delta sigma weight residual 1.236 1.291 -0.055 1.28e-02 6.10e+03 1.85e+01 bond pdb=" C1 NAG D 901 " pdb=" O5 NAG D 901 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C THR A 302 " pdb=" O THR A 302 " ideal model delta sigma weight residual 1.234 1.274 -0.040 1.07e-02 8.73e+03 1.39e+01 ... (remaining 24667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 33027 2.61 - 5.23: 401 5.23 - 7.84: 39 7.84 - 10.46: 9 10.46 - 13.07: 4 Bond angle restraints: 33480 Sorted by residual: angle pdb=" N ILE C 667 " pdb=" CA ILE C 667 " pdb=" C ILE C 667 " ideal model delta sigma weight residual 113.16 101.44 11.72 1.49e+00 4.50e-01 6.19e+01 angle pdb=" C VAL D 431 " pdb=" N PRO D 432 " pdb=" CA PRO D 432 " ideal model delta sigma weight residual 119.85 113.77 6.08 1.01e+00 9.80e-01 3.62e+01 angle pdb=" N GLY C 666 " pdb=" CA GLY C 666 " pdb=" C GLY C 666 " ideal model delta sigma weight residual 112.54 119.21 -6.67 1.28e+00 6.10e-01 2.72e+01 angle pdb=" C ASN B 380 " pdb=" CA ASN B 380 " pdb=" CB ASN B 380 " ideal model delta sigma weight residual 117.23 110.29 6.94 1.36e+00 5.41e-01 2.60e+01 angle pdb=" N GLU A 299 " pdb=" CA GLU A 299 " pdb=" C GLU A 299 " ideal model delta sigma weight residual 109.96 118.00 -8.04 1.58e+00 4.01e-01 2.59e+01 ... (remaining 33475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.98: 14153 25.98 - 51.96: 954 51.96 - 77.94: 128 77.94 - 103.92: 53 103.92 - 129.90: 11 Dihedral angle restraints: 15299 sinusoidal: 6682 harmonic: 8617 Sorted by residual: dihedral pdb=" CB CYS B 745 " pdb=" SG CYS B 745 " pdb=" SG CYS B 800 " pdb=" CB CYS B 800 " ideal model delta sinusoidal sigma weight residual -86.00 -169.00 83.00 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CA TYR D 449 " pdb=" C TYR D 449 " pdb=" N THR D 450 " pdb=" CA THR D 450 " ideal model delta harmonic sigma weight residual 180.00 149.46 30.54 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA PHE B 756 " pdb=" C PHE B 756 " pdb=" N ALA B 757 " pdb=" CA ALA B 757 " ideal model delta harmonic sigma weight residual -180.00 -158.34 -21.66 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 15296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 3882 0.224 - 0.448: 7 0.448 - 0.672: 1 0.672 - 0.897: 0 0.897 - 1.121: 1 Chirality restraints: 3891 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.66e+01 chirality pdb=" C1 MAN J 3 " pdb=" O4 NAG J 2 " pdb=" C2 MAN J 3 " pdb=" O5 MAN J 3 " both_signs ideal model delta sigma weight residual False 2.40 2.23 0.17 2.00e-02 2.50e+03 6.95e+01 chirality pdb=" C1 NAG C 804 " pdb=" ND2 ASN C 350 " pdb=" C2 NAG C 804 " pdb=" O5 NAG C 804 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.14e+01 ... (remaining 3888 not shown) Planarity restraints: 4243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 806 " -0.351 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C 806 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C 806 " -0.068 2.00e-02 2.50e+03 pdb=" N2 NAG C 806 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG C 806 " -0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 802 " -0.331 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG C 802 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG C 802 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG C 802 " 0.497 2.00e-02 2.50e+03 pdb=" O7 NAG C 802 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.321 2.00e-02 2.50e+03 2.70e-01 9.12e+02 pdb=" C7 NAG G 1 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.025 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.452 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.227 2.00e-02 2.50e+03 ... (remaining 4240 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 388 2.66 - 3.22: 22705 3.22 - 3.78: 36800 3.78 - 4.34: 49424 4.34 - 4.90: 81855 Nonbonded interactions: 191172 Sorted by model distance: nonbonded pdb=" O THR C 665 " pdb=" OG1 THR C 749 " model vdw 2.097 3.040 nonbonded pdb=" OD1 ASN C 440 " pdb=" N ASP C 441 " model vdw 2.148 3.120 nonbonded pdb=" OG1 THR D 212 " pdb=" OE2 GLU D 239 " model vdw 2.175 3.040 nonbonded pdb=" OG SER A 126 " pdb=" OG SER A 145 " model vdw 2.177 3.040 nonbonded pdb=" OH TYR B 286 " pdb=" OD2 ASP B 294 " model vdw 2.184 3.040 ... (remaining 191167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 585 or resid 605 through 798 or resid 801 throu \ gh 808)) selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 55.850 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.130 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.004 0.217 24729 Z= 0.222 Angle : 0.756 22.007 33637 Z= 0.391 Chirality : 0.051 1.121 3891 Planarity : 0.014 0.302 4211 Dihedral : 17.744 129.899 9710 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.09 % Favored : 93.50 % Rotamer: Outliers : 1.20 % Allowed : 19.41 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2954 helix: 1.70 (0.15), residues: 1148 sheet: -0.60 (0.25), residues: 440 loop : -1.66 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 609 HIS 0.013 0.001 HIS A 38 PHE 0.019 0.001 PHE A 197 TYR 0.029 0.001 TYR D 384 ARG 0.011 0.000 ARG A 260 Details of bonding type rmsd link_NAG-ASN : bond 0.03988 ( 32) link_NAG-ASN : angle 5.09598 ( 96) link_ALPHA1-4 : bond 0.01857 ( 2) link_ALPHA1-4 : angle 3.48735 ( 6) link_BETA1-4 : bond 0.00726 ( 11) link_BETA1-4 : angle 1.89574 ( 33) hydrogen bonds : bond 0.13543 ( 1051) hydrogen bonds : angle 5.81178 ( 3003) SS BOND : bond 0.00310 ( 11) SS BOND : angle 1.29125 ( 22) covalent geometry : bond 0.00405 (24672) covalent geometry : angle 0.70189 (33480) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.5144 (OUTLIER) cc_final: 0.4396 (ppp) outliers start: 31 outliers final: 5 residues processed: 263 average time/residue: 0.3762 time to fit residues: 151.5453 Evaluate side-chains 146 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain D residue 666 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 267 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 404 HIS B 106 GLN B 621 ASN C 477 HIS ** C 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 HIS C 719 GLN C 770 GLN D 172 HIS D 320 HIS D 653 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.083288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.059560 restraints weight = 86742.921| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.34 r_work: 0.3090 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 24729 Z= 0.328 Angle : 0.834 14.349 33637 Z= 0.407 Chirality : 0.053 0.472 3891 Planarity : 0.006 0.071 4211 Dihedral : 9.288 100.198 4174 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.99 % Favored : 93.70 % Rotamer: Outliers : 4.31 % Allowed : 18.28 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 2954 helix: 1.31 (0.15), residues: 1179 sheet: -0.86 (0.26), residues: 399 loop : -1.71 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 55 HIS 0.012 0.002 HIS C 449 PHE 0.027 0.003 PHE C 472 TYR 0.022 0.002 TYR C 703 ARG 0.016 0.001 ARG A 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00818 ( 32) link_NAG-ASN : angle 4.11527 ( 96) link_ALPHA1-4 : bond 0.01252 ( 2) link_ALPHA1-4 : angle 1.74467 ( 6) link_BETA1-4 : bond 0.00800 ( 11) link_BETA1-4 : angle 2.53616 ( 33) hydrogen bonds : bond 0.04607 ( 1051) hydrogen bonds : angle 4.99941 ( 3003) SS BOND : bond 0.01321 ( 11) SS BOND : angle 1.65454 ( 22) covalent geometry : bond 0.00762 (24672) covalent geometry : angle 0.80103 (33480) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 143 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.6295 (OUTLIER) cc_final: 0.5780 (mp) REVERT: A 354 MET cc_start: 0.7134 (mpp) cc_final: 0.6684 (mmm) REVERT: A 554 PHE cc_start: 0.5906 (t80) cc_final: 0.5610 (t80) REVERT: A 555 MET cc_start: 0.5599 (OUTLIER) cc_final: 0.4796 (ppp) REVERT: A 607 MET cc_start: 0.2287 (ptp) cc_final: 0.2033 (ttm) REVERT: B 40 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8031 (tp) REVERT: B 200 MET cc_start: 0.8063 (ttp) cc_final: 0.7844 (ttp) REVERT: B 307 LEU cc_start: 0.7554 (mm) cc_final: 0.7340 (pp) REVERT: C 101 HIS cc_start: 0.5947 (OUTLIER) cc_final: 0.4511 (m-70) REVERT: C 193 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8348 (tptm) REVERT: C 203 ASN cc_start: 0.7420 (OUTLIER) cc_final: 0.7016 (t160) REVERT: C 209 MET cc_start: 0.8387 (mmp) cc_final: 0.7803 (mmm) REVERT: D 190 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.6290 (m-80) REVERT: D 634 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6841 (t80) outliers start: 111 outliers final: 51 residues processed: 238 average time/residue: 0.3307 time to fit residues: 129.7427 Evaluate side-chains 183 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 124 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 TRP Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 281 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 247 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.084398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.060510 restraints weight = 85612.823| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.80 r_work: 0.3100 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24729 Z= 0.152 Angle : 0.625 11.597 33637 Z= 0.307 Chirality : 0.045 0.353 3891 Planarity : 0.004 0.061 4211 Dihedral : 8.699 117.579 4168 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.72 % Favored : 94.01 % Rotamer: Outliers : 2.72 % Allowed : 19.18 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2954 helix: 1.72 (0.15), residues: 1176 sheet: -0.96 (0.25), residues: 424 loop : -1.66 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 55 HIS 0.005 0.001 HIS A 449 PHE 0.018 0.001 PHE B 756 TYR 0.018 0.001 TYR B 286 ARG 0.003 0.000 ARG D 709 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 32) link_NAG-ASN : angle 3.54006 ( 96) link_ALPHA1-4 : bond 0.01205 ( 2) link_ALPHA1-4 : angle 2.05518 ( 6) link_BETA1-4 : bond 0.00578 ( 11) link_BETA1-4 : angle 1.61575 ( 33) hydrogen bonds : bond 0.03698 ( 1051) hydrogen bonds : angle 4.56986 ( 3003) SS BOND : bond 0.00743 ( 11) SS BOND : angle 1.64511 ( 22) covalent geometry : bond 0.00346 (24672) covalent geometry : angle 0.59332 (33480) Misc. bond : bond 0.00098 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 128 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5483 (OUTLIER) cc_final: 0.5178 (tp) REVERT: A 29 ILE cc_start: 0.6379 (OUTLIER) cc_final: 0.5841 (mp) REVERT: A 209 MET cc_start: 0.8999 (tpt) cc_final: 0.8645 (tpt) REVERT: A 354 MET cc_start: 0.7197 (mpp) cc_final: 0.6764 (mmm) REVERT: A 512 MET cc_start: 0.8644 (ttm) cc_final: 0.8438 (ttm) REVERT: A 555 MET cc_start: 0.5220 (mmt) cc_final: 0.4612 (mmm) REVERT: A 576 MET cc_start: 0.4345 (ppp) cc_final: 0.3928 (tmm) REVERT: B 40 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8034 (tp) REVERT: B 200 MET cc_start: 0.8189 (ttp) cc_final: 0.7939 (ttp) REVERT: B 307 LEU cc_start: 0.7576 (mm) cc_final: 0.7368 (pp) REVERT: B 361 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8750 (mm) REVERT: B 630 MET cc_start: 0.3844 (ttt) cc_final: 0.3600 (ttm) REVERT: C 74 MET cc_start: 0.9064 (tpp) cc_final: 0.8317 (tpp) REVERT: C 101 HIS cc_start: 0.6032 (OUTLIER) cc_final: 0.4737 (m90) REVERT: C 203 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.7016 (t160) REVERT: C 719 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7937 (tp40) REVERT: C 752 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8569 (mp) REVERT: D 190 TYR cc_start: 0.6723 (OUTLIER) cc_final: 0.6279 (m-80) REVERT: D 197 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6636 (p0) REVERT: D 634 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6887 (t80) REVERT: D 651 MET cc_start: 0.7698 (mmm) cc_final: 0.7398 (mmt) outliers start: 70 outliers final: 37 residues processed: 188 average time/residue: 0.3172 time to fit residues: 100.7077 Evaluate side-chains 171 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 123 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 531 ILE Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 718 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 217 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 262 optimal weight: 7.9990 chunk 271 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 70 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.084945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.061735 restraints weight = 85253.568| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.31 r_work: 0.3149 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24729 Z= 0.109 Angle : 0.577 11.596 33637 Z= 0.282 Chirality : 0.044 0.355 3891 Planarity : 0.004 0.057 4211 Dihedral : 7.661 114.968 4165 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.92 % Favored : 93.81 % Rotamer: Outliers : 2.45 % Allowed : 19.49 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.16), residues: 2954 helix: 1.99 (0.15), residues: 1175 sheet: -0.71 (0.26), residues: 428 loop : -1.58 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 55 HIS 0.004 0.001 HIS A 449 PHE 0.014 0.001 PHE B 396 TYR 0.013 0.001 TYR A 392 ARG 0.006 0.000 ARG B 52 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 32) link_NAG-ASN : angle 3.24735 ( 96) link_ALPHA1-4 : bond 0.01346 ( 2) link_ALPHA1-4 : angle 2.26902 ( 6) link_BETA1-4 : bond 0.00657 ( 11) link_BETA1-4 : angle 1.58711 ( 33) hydrogen bonds : bond 0.03186 ( 1051) hydrogen bonds : angle 4.28047 ( 3003) SS BOND : bond 0.00305 ( 11) SS BOND : angle 1.44792 ( 22) covalent geometry : bond 0.00236 (24672) covalent geometry : angle 0.54756 (33480) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 132 time to evaluate : 6.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5486 (OUTLIER) cc_final: 0.5201 (tp) REVERT: A 29 ILE cc_start: 0.6298 (OUTLIER) cc_final: 0.5823 (mp) REVERT: A 165 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8392 (tt) REVERT: A 354 MET cc_start: 0.7094 (mpp) cc_final: 0.6685 (mmm) REVERT: A 555 MET cc_start: 0.5667 (mmt) cc_final: 0.5249 (mmm) REVERT: A 576 MET cc_start: 0.4349 (ppp) cc_final: 0.3958 (tmm) REVERT: A 607 MET cc_start: 0.2347 (ptp) cc_final: 0.2039 (ttm) REVERT: B 40 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8047 (tp) REVERT: B 307 LEU cc_start: 0.7575 (mm) cc_final: 0.7322 (mt) REVERT: B 361 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8692 (mm) REVERT: B 649 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7467 (tt) REVERT: C 74 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8349 (tpp) REVERT: C 719 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7690 (tp40) REVERT: C 752 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8564 (mp) REVERT: D 190 TYR cc_start: 0.6602 (OUTLIER) cc_final: 0.6201 (m-80) REVERT: D 197 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6674 (p0) REVERT: D 634 PHE cc_start: 0.7221 (OUTLIER) cc_final: 0.6869 (t80) REVERT: D 651 MET cc_start: 0.7696 (mmm) cc_final: 0.7451 (mmt) outliers start: 63 outliers final: 35 residues processed: 185 average time/residue: 0.4955 time to fit residues: 158.4216 Evaluate side-chains 171 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 4.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 718 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 8 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 279 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.083694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.060065 restraints weight = 86109.855| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.34 r_work: 0.3104 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24729 Z= 0.181 Angle : 0.617 11.653 33637 Z= 0.304 Chirality : 0.045 0.364 3891 Planarity : 0.004 0.059 4211 Dihedral : 7.432 114.208 4165 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.47 % Favored : 93.26 % Rotamer: Outliers : 3.45 % Allowed : 18.71 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2954 helix: 1.99 (0.15), residues: 1174 sheet: -0.81 (0.26), residues: 411 loop : -1.55 (0.17), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP B 55 HIS 0.006 0.001 HIS A 94 PHE 0.019 0.002 PHE C 753 TYR 0.013 0.001 TYR D 449 ARG 0.005 0.000 ARG B 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00602 ( 32) link_NAG-ASN : angle 3.09190 ( 96) link_ALPHA1-4 : bond 0.01323 ( 2) link_ALPHA1-4 : angle 2.19232 ( 6) link_BETA1-4 : bond 0.00523 ( 11) link_BETA1-4 : angle 1.54258 ( 33) hydrogen bonds : bond 0.03571 ( 1051) hydrogen bonds : angle 4.37376 ( 3003) SS BOND : bond 0.00277 ( 11) SS BOND : angle 1.42561 ( 22) covalent geometry : bond 0.00421 (24672) covalent geometry : angle 0.59211 (33480) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 125 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5546 (OUTLIER) cc_final: 0.5227 (tp) REVERT: A 29 ILE cc_start: 0.6471 (OUTLIER) cc_final: 0.5934 (mp) REVERT: A 354 MET cc_start: 0.7162 (mpp) cc_final: 0.6587 (mmm) REVERT: A 555 MET cc_start: 0.5555 (mmt) cc_final: 0.5195 (mmm) REVERT: A 576 MET cc_start: 0.4420 (ppp) cc_final: 0.4036 (tmm) REVERT: A 709 HIS cc_start: 0.8097 (OUTLIER) cc_final: 0.6636 (p-80) REVERT: B 40 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8107 (tp) REVERT: B 307 LEU cc_start: 0.7615 (mm) cc_final: 0.7370 (mt) REVERT: B 361 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8706 (mm) REVERT: C 74 MET cc_start: 0.9076 (tpp) cc_final: 0.8318 (tpp) REVERT: C 101 HIS cc_start: 0.5871 (OUTLIER) cc_final: 0.4812 (m90) REVERT: C 193 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8431 (tptm) REVERT: C 719 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7948 (tp40) REVERT: C 752 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8771 (mp) REVERT: D 190 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.6176 (m-80) REVERT: D 197 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.6759 (p0) REVERT: D 634 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6947 (t80) outliers start: 89 outliers final: 55 residues processed: 200 average time/residue: 0.3209 time to fit residues: 109.0189 Evaluate side-chains 190 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 123 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 2 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 287 optimal weight: 8.9990 chunk 233 optimal weight: 1.9990 chunk 225 optimal weight: 0.9980 chunk 249 optimal weight: 0.0980 chunk 278 optimal weight: 0.9980 chunk 284 optimal weight: 10.0000 chunk 217 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 332 HIS D 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.084660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.061118 restraints weight = 84981.524| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.78 r_work: 0.3115 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24729 Z= 0.113 Angle : 0.567 13.960 33637 Z= 0.277 Chirality : 0.044 0.357 3891 Planarity : 0.004 0.059 4211 Dihedral : 7.012 113.251 4165 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.72 % Favored : 94.01 % Rotamer: Outliers : 2.83 % Allowed : 19.88 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2954 helix: 2.11 (0.15), residues: 1180 sheet: -0.85 (0.26), residues: 402 loop : -1.49 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 55 HIS 0.006 0.001 HIS A 53 PHE 0.013 0.001 PHE B 396 TYR 0.017 0.001 TYR A 392 ARG 0.005 0.000 ARG B 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 32) link_NAG-ASN : angle 2.83032 ( 96) link_ALPHA1-4 : bond 0.01425 ( 2) link_ALPHA1-4 : angle 2.01241 ( 6) link_BETA1-4 : bond 0.00526 ( 11) link_BETA1-4 : angle 1.47776 ( 33) hydrogen bonds : bond 0.03120 ( 1051) hydrogen bonds : angle 4.21238 ( 3003) SS BOND : bond 0.00213 ( 11) SS BOND : angle 1.23129 ( 22) covalent geometry : bond 0.00251 (24672) covalent geometry : angle 0.54416 (33480) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 127 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5515 (OUTLIER) cc_final: 0.5209 (tp) REVERT: A 29 ILE cc_start: 0.6317 (OUTLIER) cc_final: 0.5781 (mp) REVERT: A 209 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8356 (tpt) REVERT: A 354 MET cc_start: 0.7139 (mpp) cc_final: 0.6741 (mmm) REVERT: A 555 MET cc_start: 0.5603 (mmt) cc_final: 0.5275 (mmm) REVERT: A 576 MET cc_start: 0.4422 (ppp) cc_final: 0.4053 (tmm) REVERT: A 641 MET cc_start: 0.7645 (tmm) cc_final: 0.7402 (tmm) REVERT: A 709 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.6623 (p-80) REVERT: B 40 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8138 (tp) REVERT: B 307 LEU cc_start: 0.7602 (mm) cc_final: 0.7354 (mt) REVERT: B 361 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8668 (mm) REVERT: B 630 MET cc_start: 0.3908 (ttt) cc_final: 0.3490 (ppp) REVERT: C 74 MET cc_start: 0.9070 (tpp) cc_final: 0.8357 (tpp) REVERT: C 101 HIS cc_start: 0.5836 (OUTLIER) cc_final: 0.5066 (m90) REVERT: C 490 VAL cc_start: 0.7144 (OUTLIER) cc_final: 0.6942 (p) REVERT: C 719 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7955 (tp40) REVERT: C 752 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8772 (mp) REVERT: D 190 TYR cc_start: 0.6499 (OUTLIER) cc_final: 0.6009 (m-80) REVERT: D 197 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6676 (p0) REVERT: D 445 ASP cc_start: 0.0028 (OUTLIER) cc_final: -0.0507 (m-30) REVERT: D 634 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6949 (t80) outliers start: 73 outliers final: 41 residues processed: 191 average time/residue: 0.3035 time to fit residues: 98.9490 Evaluate side-chains 177 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 122 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 269 PHE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 718 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 2 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 147 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 255 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 273 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 671 GLN C 147 GLN D 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.082077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.058292 restraints weight = 86055.575| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.77 r_work: 0.3039 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 24729 Z= 0.301 Angle : 0.708 11.667 33637 Z= 0.352 Chirality : 0.049 0.375 3891 Planarity : 0.005 0.058 4211 Dihedral : 7.377 112.032 4165 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.01 % Favored : 92.76 % Rotamer: Outliers : 3.18 % Allowed : 19.91 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2954 helix: 1.74 (0.15), residues: 1172 sheet: -1.09 (0.25), residues: 419 loop : -1.57 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 55 HIS 0.009 0.001 HIS A 53 PHE 0.025 0.002 PHE C 458 TYR 0.018 0.002 TYR B 754 ARG 0.006 0.001 ARG B 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 32) link_NAG-ASN : angle 3.09156 ( 96) link_ALPHA1-4 : bond 0.01472 ( 2) link_ALPHA1-4 : angle 1.44688 ( 6) link_BETA1-4 : bond 0.00493 ( 11) link_BETA1-4 : angle 1.70864 ( 33) hydrogen bonds : bond 0.04135 ( 1051) hydrogen bonds : angle 4.60434 ( 3003) SS BOND : bond 0.00351 ( 11) SS BOND : angle 1.49885 ( 22) covalent geometry : bond 0.00710 (24672) covalent geometry : angle 0.68654 (33480) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 124 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5461 (OUTLIER) cc_final: 0.5077 (tp) REVERT: A 29 ILE cc_start: 0.6514 (OUTLIER) cc_final: 0.5921 (mp) REVERT: A 209 MET cc_start: 0.8793 (tpt) cc_final: 0.8337 (tpt) REVERT: A 354 MET cc_start: 0.7238 (mpp) cc_final: 0.6652 (mmm) REVERT: A 392 TYR cc_start: 0.7181 (t80) cc_final: 0.6923 (t80) REVERT: A 555 MET cc_start: 0.5616 (mmt) cc_final: 0.5258 (mmm) REVERT: A 609 PHE cc_start: 0.6455 (OUTLIER) cc_final: 0.5468 (m-10) REVERT: A 641 MET cc_start: 0.7667 (tmm) cc_final: 0.7401 (tmm) REVERT: A 709 HIS cc_start: 0.8322 (OUTLIER) cc_final: 0.6908 (p-80) REVERT: B 40 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8189 (tp) REVERT: B 307 LEU cc_start: 0.7583 (mm) cc_final: 0.7332 (mt) REVERT: B 361 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8683 (mm) REVERT: C 74 MET cc_start: 0.9045 (tpp) cc_final: 0.8302 (tpp) REVERT: C 101 HIS cc_start: 0.5989 (OUTLIER) cc_final: 0.4783 (m90) REVERT: C 203 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7305 (t160) REVERT: C 297 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8010 (mt-10) REVERT: C 719 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8180 (tp40) REVERT: D 190 TYR cc_start: 0.6637 (OUTLIER) cc_final: 0.6128 (m-80) REVERT: D 197 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6822 (p0) REVERT: D 401 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.6976 (mpt180) REVERT: D 634 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7010 (t80) outliers start: 82 outliers final: 56 residues processed: 195 average time/residue: 0.3132 time to fit residues: 103.8634 Evaluate side-chains 191 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 122 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 259 optimal weight: 1.9990 chunk 126 optimal weight: 0.0070 chunk 210 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 291 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.083765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.060238 restraints weight = 85127.238| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.78 r_work: 0.3091 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24729 Z= 0.121 Angle : 0.588 11.560 33637 Z= 0.290 Chirality : 0.044 0.366 3891 Planarity : 0.004 0.061 4211 Dihedral : 6.973 112.355 4165 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.82 % Favored : 93.94 % Rotamer: Outliers : 2.37 % Allowed : 20.61 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2954 helix: 1.94 (0.15), residues: 1180 sheet: -0.95 (0.25), residues: 441 loop : -1.54 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.001 TRP B 55 HIS 0.004 0.001 HIS A 94 PHE 0.013 0.001 PHE A 102 TYR 0.015 0.001 TYR B 312 ARG 0.004 0.000 ARG B 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 32) link_NAG-ASN : angle 2.77117 ( 96) link_ALPHA1-4 : bond 0.01322 ( 2) link_ALPHA1-4 : angle 1.59396 ( 6) link_BETA1-4 : bond 0.00545 ( 11) link_BETA1-4 : angle 1.58600 ( 33) hydrogen bonds : bond 0.03287 ( 1051) hydrogen bonds : angle 4.30974 ( 3003) SS BOND : bond 0.00220 ( 11) SS BOND : angle 1.17805 ( 22) covalent geometry : bond 0.00270 (24672) covalent geometry : angle 0.56669 (33480) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 123 time to evaluate : 2.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5512 (OUTLIER) cc_final: 0.5150 (tp) REVERT: A 29 ILE cc_start: 0.6399 (OUTLIER) cc_final: 0.5802 (mp) REVERT: A 209 MET cc_start: 0.8708 (tpt) cc_final: 0.8232 (tpt) REVERT: A 354 MET cc_start: 0.7186 (mpp) cc_final: 0.6824 (mmm) REVERT: A 555 MET cc_start: 0.5622 (mmt) cc_final: 0.5283 (mmm) REVERT: A 609 PHE cc_start: 0.6430 (OUTLIER) cc_final: 0.5435 (m-10) REVERT: A 641 MET cc_start: 0.7782 (tmm) cc_final: 0.7532 (tmm) REVERT: A 709 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.6912 (p-80) REVERT: B 40 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8201 (tp) REVERT: B 55 TRP cc_start: 0.6521 (m-90) cc_final: 0.6302 (m-90) REVERT: B 307 LEU cc_start: 0.7530 (mm) cc_final: 0.7270 (mt) REVERT: B 361 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8604 (mm) REVERT: B 630 MET cc_start: 0.3944 (ttt) cc_final: 0.3552 (ppp) REVERT: C 74 MET cc_start: 0.9026 (tpp) cc_final: 0.8261 (tpp) REVERT: C 101 HIS cc_start: 0.5777 (OUTLIER) cc_final: 0.4837 (m90) REVERT: C 297 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7963 (mt-10) REVERT: C 663 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6894 (tpm170) REVERT: C 719 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8134 (tp40) REVERT: D 190 TYR cc_start: 0.6517 (OUTLIER) cc_final: 0.6031 (m-80) REVERT: D 197 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6616 (p0) REVERT: D 634 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6907 (t80) outliers start: 61 outliers final: 38 residues processed: 175 average time/residue: 0.3404 time to fit residues: 102.4184 Evaluate side-chains 172 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 122 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 718 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 154 optimal weight: 8.9990 chunk 263 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.081773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.058111 restraints weight = 85564.727| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.73 r_work: 0.3039 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 24729 Z= 0.282 Angle : 0.699 11.645 33637 Z= 0.346 Chirality : 0.048 0.379 3891 Planarity : 0.005 0.056 4211 Dihedral : 7.245 111.543 4165 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.35 % Favored : 92.42 % Rotamer: Outliers : 2.91 % Allowed : 20.26 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2954 helix: 1.76 (0.15), residues: 1170 sheet: -1.18 (0.25), residues: 430 loop : -1.58 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP B 55 HIS 0.006 0.001 HIS A 94 PHE 0.023 0.002 PHE C 753 TYR 0.024 0.002 TYR A 392 ARG 0.005 0.001 ARG D 434 Details of bonding type rmsd link_NAG-ASN : bond 0.00646 ( 32) link_NAG-ASN : angle 3.05559 ( 96) link_ALPHA1-4 : bond 0.01336 ( 2) link_ALPHA1-4 : angle 1.33376 ( 6) link_BETA1-4 : bond 0.00504 ( 11) link_BETA1-4 : angle 1.74725 ( 33) hydrogen bonds : bond 0.04026 ( 1051) hydrogen bonds : angle 4.58785 ( 3003) SS BOND : bond 0.00326 ( 11) SS BOND : angle 1.39966 ( 22) covalent geometry : bond 0.00659 (24672) covalent geometry : angle 0.67826 (33480) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 121 time to evaluate : 2.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5409 (OUTLIER) cc_final: 0.4999 (tp) REVERT: A 29 ILE cc_start: 0.6542 (OUTLIER) cc_final: 0.5877 (mp) REVERT: A 209 MET cc_start: 0.8822 (tpt) cc_final: 0.8380 (tpt) REVERT: A 354 MET cc_start: 0.7200 (mpp) cc_final: 0.6625 (mmm) REVERT: A 392 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.6922 (t80) REVERT: A 555 MET cc_start: 0.5701 (mmt) cc_final: 0.5342 (mmm) REVERT: A 609 PHE cc_start: 0.6528 (OUTLIER) cc_final: 0.5426 (m-10) REVERT: A 641 MET cc_start: 0.7774 (tmm) cc_final: 0.7535 (tmm) REVERT: A 709 HIS cc_start: 0.8275 (OUTLIER) cc_final: 0.6941 (p-80) REVERT: B 40 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8167 (tp) REVERT: B 48 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: B 307 LEU cc_start: 0.7576 (mm) cc_final: 0.7298 (mt) REVERT: B 361 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8662 (mm) REVERT: B 609 TRP cc_start: 0.6107 (OUTLIER) cc_final: 0.5721 (t60) REVERT: B 630 MET cc_start: 0.4007 (ttt) cc_final: 0.3636 (ppp) REVERT: C 74 MET cc_start: 0.9046 (tpp) cc_final: 0.8276 (tpp) REVERT: C 101 HIS cc_start: 0.5860 (OUTLIER) cc_final: 0.4862 (m90) REVERT: C 203 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7347 (t160) REVERT: C 297 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8004 (mt-10) REVERT: C 719 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8189 (tp40) REVERT: D 190 TYR cc_start: 0.6601 (OUTLIER) cc_final: 0.6160 (m-80) REVERT: D 197 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6824 (p0) REVERT: D 401 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.6978 (mpt180) REVERT: D 634 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.6928 (t80) outliers start: 75 outliers final: 51 residues processed: 186 average time/residue: 0.3250 time to fit residues: 101.5640 Evaluate side-chains 187 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 120 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 401 ARG Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 698 ASP Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 226 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 278 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 223 optimal weight: 0.4980 chunk 110 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.084401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.060965 restraints weight = 84874.003| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.27 r_work: 0.3136 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24729 Z= 0.113 Angle : 0.595 12.206 33637 Z= 0.292 Chirality : 0.044 0.364 3891 Planarity : 0.004 0.062 4211 Dihedral : 6.883 111.998 4165 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.92 % Favored : 93.87 % Rotamer: Outliers : 2.17 % Allowed : 20.96 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2954 helix: 1.95 (0.15), residues: 1179 sheet: -1.02 (0.25), residues: 443 loop : -1.53 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP B 55 HIS 0.005 0.001 HIS A 94 PHE 0.014 0.001 PHE A 102 TYR 0.023 0.001 TYR A 392 ARG 0.003 0.000 ARG B 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 32) link_NAG-ASN : angle 2.71494 ( 96) link_ALPHA1-4 : bond 0.01098 ( 2) link_ALPHA1-4 : angle 1.49579 ( 6) link_BETA1-4 : bond 0.00540 ( 11) link_BETA1-4 : angle 1.59900 ( 33) hydrogen bonds : bond 0.03224 ( 1051) hydrogen bonds : angle 4.30248 ( 3003) SS BOND : bond 0.00234 ( 11) SS BOND : angle 1.12918 ( 22) covalent geometry : bond 0.00247 (24672) covalent geometry : angle 0.57540 (33480) Misc. bond : bond 0.00020 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5908 Ramachandran restraints generated. 2954 Oldfield, 0 Emsley, 2954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 124 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5575 (OUTLIER) cc_final: 0.5212 (tp) REVERT: A 29 ILE cc_start: 0.6490 (OUTLIER) cc_final: 0.5883 (mp) REVERT: A 209 MET cc_start: 0.8655 (tpt) cc_final: 0.8176 (tpt) REVERT: A 354 MET cc_start: 0.7002 (mpp) cc_final: 0.6667 (mmm) REVERT: A 392 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.6657 (t80) REVERT: A 555 MET cc_start: 0.5687 (mmt) cc_final: 0.5354 (mmm) REVERT: A 609 PHE cc_start: 0.6455 (OUTLIER) cc_final: 0.5376 (m-10) REVERT: A 641 MET cc_start: 0.7768 (tmm) cc_final: 0.7532 (tmm) REVERT: A 709 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.6866 (p-80) REVERT: B 40 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8227 (tp) REVERT: B 307 LEU cc_start: 0.7554 (mm) cc_final: 0.7285 (mt) REVERT: B 630 MET cc_start: 0.3861 (ttt) cc_final: 0.3441 (ppp) REVERT: C 74 MET cc_start: 0.8963 (tpp) cc_final: 0.8236 (tpp) REVERT: C 101 HIS cc_start: 0.5806 (OUTLIER) cc_final: 0.5044 (m90) REVERT: C 297 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7975 (mt-10) REVERT: C 719 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8082 (tp40) REVERT: D 190 TYR cc_start: 0.6524 (OUTLIER) cc_final: 0.6088 (m-80) REVERT: D 634 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6902 (t80) outliers start: 56 outliers final: 43 residues processed: 172 average time/residue: 0.3061 time to fit residues: 89.9285 Evaluate side-chains 175 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 122 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 392 TYR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 634 PHE Chi-restraints excluded: chain D residue 640 LEU Chi-restraints excluded: chain D residue 678 PHE Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 718 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 101 optimal weight: 0.2980 chunk 169 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.084413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.061002 restraints weight = 85291.565| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.27 r_work: 0.3138 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24729 Z= 0.116 Angle : 0.584 11.770 33637 Z= 0.286 Chirality : 0.044 0.366 3891 Planarity : 0.004 0.057 4211 Dihedral : 6.620 111.214 4161 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.36 % Favored : 93.47 % Rotamer: Outliers : 2.25 % Allowed : 21.04 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2954 helix: 2.02 (0.15), residues: 1179 sheet: -0.98 (0.25), residues: 425 loop : -1.49 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP B 55 HIS 0.005 0.001 HIS A 94 PHE 0.019 0.001 PHE B 396 TYR 0.019 0.001 TYR A 392 ARG 0.003 0.000 ARG B 49 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 32) link_NAG-ASN : angle 2.64917 ( 96) link_ALPHA1-4 : bond 0.00978 ( 2) link_ALPHA1-4 : angle 1.37775 ( 6) link_BETA1-4 : bond 0.00511 ( 11) link_BETA1-4 : angle 1.54877 ( 33) hydrogen bonds : bond 0.03168 ( 1051) hydrogen bonds : angle 4.25095 ( 3003) SS BOND : bond 0.00198 ( 11) SS BOND : angle 1.10113 ( 22) covalent geometry : bond 0.00262 (24672) covalent geometry : angle 0.56513 (33480) Misc. bond : bond 0.00023 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12664.98 seconds wall clock time: 221 minutes 17.07 seconds (13277.07 seconds total)