Starting phenix.real_space_refine on Mon Aug 25 01:01:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfi_33791/08_2025/7yfi_33791_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfi_33791/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yfi_33791/08_2025/7yfi_33791_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfi_33791/08_2025/7yfi_33791_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yfi_33791/08_2025/7yfi_33791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfi_33791/08_2025/7yfi_33791.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.17, per 1000 atoms: 0.26 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.99 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: 4.81 Time building geometry restraints manager: 2.85 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 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.530 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.080 ------------------------------------------------------------------------------- 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 : 8.80 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.000 ARG A 260 TYR 0.029 0.001 TYR D 384 PHE 0.019 0.001 PHE A 197 TRP 0.028 0.001 TRP B 609 HIS 0.013 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00405 (24672) covalent geometry : angle 0.70189 (33480) SS BOND : bond 0.00310 ( 11) SS BOND : angle 1.29125 ( 22) hydrogen bonds : bond 0.13543 ( 1051) hydrogen bonds : angle 5.81178 ( 3003) Misc. bond : bond 0.00015 ( 1) 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) link_NAG-ASN : bond 0.03988 ( 32) link_NAG-ASN : angle 5.09598 ( 96) *********************** 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 : 0.978 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: 0.1898 time to fit residues: 76.7247 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 : 0.975 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 404 HIS C 371 HIS D 320 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.087306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.064107 restraints weight = 87565.169| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.41 r_work: 0.3207 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1438 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= 0.132 Angle : 0.646 11.774 33637 Z= 0.314 Chirality : 0.046 0.394 3891 Planarity : 0.005 0.074 4211 Dihedral : 9.091 104.046 4174 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.55 % Favored : 94.14 % Rotamer: Outliers : 2.41 % Allowed : 18.59 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.16), residues: 2954 helix: 1.81 (0.15), residues: 1175 sheet: -0.61 (0.25), residues: 427 loop : -1.68 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 233 TYR 0.017 0.001 TYR C 703 PHE 0.014 0.001 PHE A 554 TRP 0.020 0.001 TRP B 55 HIS 0.010 0.001 HIS C 449 Details of bonding type rmsd covalent geometry : bond 0.00286 (24672) covalent geometry : angle 0.61196 (33480) SS BOND : bond 0.00557 ( 11) SS BOND : angle 1.68706 ( 22) hydrogen bonds : bond 0.03697 ( 1051) hydrogen bonds : angle 4.66207 ( 3003) Misc. bond : bond 0.00025 ( 1) link_ALPHA1-4 : bond 0.01349 ( 2) link_ALPHA1-4 : angle 1.56364 ( 6) link_BETA1-4 : bond 0.00856 ( 11) link_BETA1-4 : angle 2.02874 ( 33) link_NAG-ASN : bond 0.00845 ( 32) link_NAG-ASN : angle 3.68452 ( 96) *********************** 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 209 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 147 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.6014 (OUTLIER) cc_final: 0.5675 (mp) REVERT: A 512 MET cc_start: 0.8082 (ttm) cc_final: 0.7877 (ttm) REVERT: A 554 PHE cc_start: 0.6105 (t80) cc_final: 0.5517 (t80) REVERT: A 555 MET cc_start: 0.5510 (OUTLIER) cc_final: 0.4863 (ppp) REVERT: B 40 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7669 (tp) REVERT: B 307 LEU cc_start: 0.7227 (mm) cc_final: 0.6979 (pp) REVERT: B 630 MET cc_start: 0.3756 (ttt) cc_final: 0.3491 (ttm) REVERT: C 74 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8629 (tpp) REVERT: C 209 MET cc_start: 0.7843 (mmp) cc_final: 0.7217 (mmm) REVERT: C 641 MET cc_start: 0.7210 (ttp) cc_final: 0.6758 (ttm) REVERT: D 190 TYR cc_start: 0.6427 (OUTLIER) cc_final: 0.5992 (m-80) REVERT: D 634 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.6947 (t80) outliers start: 62 outliers final: 19 residues processed: 194 average time/residue: 0.1630 time to fit residues: 51.7106 Evaluate side-chains 153 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 555 MET 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 245 SER 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 C residue 40 GLN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 92 VAL 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 608 TRP Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 747 VAL 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 634 PHE Chi-restraints excluded: chain D residue 678 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 224 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 189 optimal weight: 0.3980 chunk 75 optimal weight: 8.9990 chunk 216 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 278 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 294 optimal weight: 6.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS B 106 GLN B 621 ASN B 671 GLN C 492 ASN D 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.085109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.061221 restraints weight = 86472.079| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.87 r_work: 0.3120 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24729 Z= 0.166 Angle : 0.635 11.473 33637 Z= 0.312 Chirality : 0.046 0.359 3891 Planarity : 0.005 0.058 4211 Dihedral : 8.014 121.991 4166 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.16 % Favored : 93.57 % Rotamer: Outliers : 2.83 % Allowed : 18.79 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.16), residues: 2954 helix: 1.94 (0.15), residues: 1177 sheet: -0.69 (0.26), residues: 413 loop : -1.60 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 670 TYR 0.015 0.001 TYR A 526 PHE 0.020 0.002 PHE B 756 TRP 0.013 0.001 TRP A 381 HIS 0.006 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00380 (24672) covalent geometry : angle 0.60819 (33480) SS BOND : bond 0.00322 ( 11) SS BOND : angle 1.43802 ( 22) hydrogen bonds : bond 0.03615 ( 1051) hydrogen bonds : angle 4.40005 ( 3003) Misc. bond : bond 0.00017 ( 1) link_ALPHA1-4 : bond 0.01560 ( 2) link_ALPHA1-4 : angle 2.27775 ( 6) link_BETA1-4 : bond 0.00378 ( 11) link_BETA1-4 : angle 1.58841 ( 33) link_NAG-ASN : bond 0.00655 ( 32) link_NAG-ASN : angle 3.25481 ( 96) *********************** 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 207 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 134 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5498 (OUTLIER) cc_final: 0.5268 (tp) REVERT: A 29 ILE cc_start: 0.6226 (OUTLIER) cc_final: 0.5736 (mp) REVERT: A 209 MET cc_start: 0.8929 (tpt) cc_final: 0.8525 (tpt) REVERT: A 354 MET cc_start: 0.7121 (mpp) cc_final: 0.6755 (mmm) REVERT: A 555 MET cc_start: 0.5369 (mmt) cc_final: 0.4775 (mmm) REVERT: A 576 MET cc_start: 0.4336 (ppp) cc_final: 0.3934 (tmm) REVERT: B 40 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7937 (tp) REVERT: B 200 MET cc_start: 0.8280 (ttp) cc_final: 0.8042 (ttp) REVERT: B 307 LEU cc_start: 0.7450 (mm) cc_final: 0.7242 (pp) REVERT: B 369 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7618 (t70) REVERT: B 462 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: B 630 MET cc_start: 0.3885 (ttt) cc_final: 0.3662 (ttm) REVERT: C 74 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8402 (tpp) REVERT: C 101 HIS cc_start: 0.5966 (OUTLIER) cc_final: 0.4754 (m-70) REVERT: C 193 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8334 (tptm) REVERT: D 190 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.6286 (m-80) REVERT: D 634 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6872 (t80) REVERT: D 651 MET cc_start: 0.7682 (mmm) cc_final: 0.7359 (mmt) outliers start: 73 outliers final: 33 residues processed: 197 average time/residue: 0.1556 time to fit residues: 50.8286 Evaluate side-chains 168 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 288 VAL Chi-restraints excluded: chain A residue 338 VAL 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 245 SER Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 462 ASP 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 C residue 35 THR Chi-restraints excluded: chain C residue 74 MET 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 193 LYS 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 608 TRP Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 195 LEU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 6 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 269 optimal weight: 0.9980 chunk 267 optimal weight: 0.1980 chunk 206 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 46 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 724 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.084427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.060519 restraints weight = 86233.474| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.85 r_work: 0.3101 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24729 Z= 0.165 Angle : 0.606 11.388 33637 Z= 0.296 Chirality : 0.045 0.352 3891 Planarity : 0.004 0.057 4211 Dihedral : 7.418 114.821 4163 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.19 % Favored : 93.53 % Rotamer: Outliers : 2.83 % Allowed : 18.67 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.16), residues: 2954 helix: 2.00 (0.15), residues: 1175 sheet: -0.73 (0.26), residues: 425 loop : -1.55 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.015 0.001 TYR B 286 PHE 0.017 0.001 PHE C 753 TRP 0.011 0.001 TRP A 381 HIS 0.004 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00382 (24672) covalent geometry : angle 0.57886 (33480) SS BOND : bond 0.00356 ( 11) SS BOND : angle 1.82549 ( 22) hydrogen bonds : bond 0.03431 ( 1051) hydrogen bonds : angle 4.35448 ( 3003) Misc. bond : bond 0.00031 ( 1) link_ALPHA1-4 : bond 0.01250 ( 2) link_ALPHA1-4 : angle 2.21715 ( 6) link_BETA1-4 : bond 0.00564 ( 11) link_BETA1-4 : angle 1.59601 ( 33) link_NAG-ASN : bond 0.00591 ( 32) link_NAG-ASN : angle 3.11976 ( 96) *********************** 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 206 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 133 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.6276 (OUTLIER) cc_final: 0.5739 (mp) REVERT: A 554 PHE cc_start: 0.6125 (t80) cc_final: 0.5741 (t80) REVERT: A 555 MET cc_start: 0.5751 (mmt) cc_final: 0.5096 (ppp) REVERT: A 576 MET cc_start: 0.4333 (ppp) cc_final: 0.3955 (tmm) REVERT: B 40 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7977 (tp) REVERT: B 361 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8762 (mm) REVERT: B 462 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: B 649 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7461 (tt) REVERT: C 74 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8388 (tpp) REVERT: C 101 HIS cc_start: 0.5858 (OUTLIER) cc_final: 0.4775 (m90) REVERT: D 190 TYR cc_start: 0.6672 (OUTLIER) cc_final: 0.6232 (m-80) REVERT: D 197 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6695 (p0) REVERT: D 634 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6864 (t80) REVERT: D 651 MET cc_start: 0.7723 (mmm) cc_final: 0.7498 (mmt) outliers start: 73 outliers final: 42 residues processed: 196 average time/residue: 0.1495 time to fit residues: 49.2954 Evaluate side-chains 178 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 126 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 288 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 420 CYS Chi-restraints excluded: chain A residue 450 THR 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 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 361 LEU Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 462 ASP Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 609 TRP Chi-restraints excluded: chain B residue 649 LEU 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 74 MET 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 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 415 MET Chi-restraints excluded: chain C residue 421 LYS Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 747 VAL 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 156 optimal weight: 0.0010 chunk 112 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 280 optimal weight: 0.6980 chunk 235 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 770 GLN D 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.085269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.061651 restraints weight = 85179.075| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 3.83 r_work: 0.3127 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3364 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= 0.110 Angle : 0.562 11.401 33637 Z= 0.274 Chirality : 0.044 0.352 3891 Planarity : 0.004 0.058 4211 Dihedral : 6.959 113.285 4163 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.03 % Favored : 93.70 % Rotamer: Outliers : 2.33 % Allowed : 19.29 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.16), residues: 2954 helix: 2.14 (0.15), residues: 1175 sheet: -0.71 (0.25), residues: 427 loop : -1.50 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.013 0.001 TYR B 286 PHE 0.012 0.001 PHE D 678 TRP 0.010 0.001 TRP A 381 HIS 0.003 0.001 HIS A 449 Details of bonding type rmsd covalent geometry : bond 0.00243 (24672) covalent geometry : angle 0.53731 (33480) SS BOND : bond 0.00229 ( 11) SS BOND : angle 1.40650 ( 22) hydrogen bonds : bond 0.03077 ( 1051) hydrogen bonds : angle 4.17663 ( 3003) Misc. bond : bond 0.00007 ( 1) link_ALPHA1-4 : bond 0.01285 ( 2) link_ALPHA1-4 : angle 2.17940 ( 6) link_BETA1-4 : bond 0.00531 ( 11) link_BETA1-4 : angle 1.49224 ( 33) link_NAG-ASN : bond 0.00566 ( 32) link_NAG-ASN : angle 2.88712 ( 96) *********************** 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 191 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 131 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5543 (OUTLIER) cc_final: 0.5283 (tp) REVERT: A 29 ILE cc_start: 0.6107 (OUTLIER) cc_final: 0.5582 (mp) REVERT: A 354 MET cc_start: 0.7135 (mpp) cc_final: 0.6737 (mmm) REVERT: A 555 MET cc_start: 0.5662 (mmt) cc_final: 0.5000 (ppp) REVERT: A 576 MET cc_start: 0.4344 (ppp) cc_final: 0.3985 (tmm) REVERT: B 40 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8022 (tp) REVERT: B 72 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8206 (tp) REVERT: B 361 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8687 (mm) REVERT: B 462 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: B 630 MET cc_start: 0.3885 (ttt) cc_final: 0.3485 (ppp) REVERT: C 40 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8529 (mm-40) REVERT: C 74 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8374 (tpp) REVERT: C 101 HIS cc_start: 0.5736 (OUTLIER) cc_final: 0.4828 (m90) REVERT: C 193 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8320 (tptm) REVERT: D 190 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.6098 (m-80) REVERT: D 634 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6877 (t80) REVERT: D 651 MET cc_start: 0.7662 (mmm) cc_final: 0.7397 (mmt) outliers start: 60 outliers final: 32 residues processed: 183 average time/residue: 0.1520 time to fit residues: 46.7848 Evaluate side-chains 170 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 701 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 462 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 745 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 193 LYS 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 421 LYS Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 269 PHE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 219 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 171 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.084060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.060045 restraints weight = 85798.642| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.86 r_work: 0.3082 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24729 Z= 0.171 Angle : 0.599 11.436 33637 Z= 0.294 Chirality : 0.045 0.360 3891 Planarity : 0.004 0.060 4211 Dihedral : 6.897 110.751 4163 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.36 % Favored : 93.40 % Rotamer: Outliers : 2.76 % Allowed : 19.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.16), residues: 2954 helix: 2.05 (0.15), residues: 1174 sheet: -0.76 (0.26), residues: 415 loop : -1.49 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.012 0.001 TYR D 449 PHE 0.019 0.002 PHE C 753 TRP 0.010 0.001 TRP A 381 HIS 0.022 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00400 (24672) covalent geometry : angle 0.57592 (33480) SS BOND : bond 0.00246 ( 11) SS BOND : angle 1.40736 ( 22) hydrogen bonds : bond 0.03432 ( 1051) hydrogen bonds : angle 4.27660 ( 3003) Misc. bond : bond 0.00018 ( 1) link_ALPHA1-4 : bond 0.01452 ( 2) link_ALPHA1-4 : angle 1.87386 ( 6) link_BETA1-4 : bond 0.00559 ( 11) link_BETA1-4 : angle 1.57687 ( 33) link_NAG-ASN : bond 0.00591 ( 32) link_NAG-ASN : angle 2.89305 ( 96) *********************** 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 199 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 128 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.5847 (mp) REVERT: A 165 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8543 (tt) REVERT: A 209 MET cc_start: 0.8717 (tpt) cc_final: 0.8279 (tpt) REVERT: A 354 MET cc_start: 0.7205 (mpp) cc_final: 0.6734 (mmm) REVERT: A 555 MET cc_start: 0.5609 (mmt) cc_final: 0.5293 (mmm) REVERT: A 576 MET cc_start: 0.4399 (ppp) cc_final: 0.4041 (tmm) REVERT: A 641 MET cc_start: 0.7675 (tmm) cc_final: 0.7474 (tmm) REVERT: A 709 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.6727 (p-80) REVERT: B 40 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8050 (tp) REVERT: B 361 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8660 (mm) REVERT: B 462 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8254 (m-30) REVERT: B 630 MET cc_start: 0.3934 (ttt) cc_final: 0.3536 (ppp) REVERT: C 40 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8344 (mp10) REVERT: C 74 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8379 (tpp) REVERT: C 101 HIS cc_start: 0.5814 (OUTLIER) cc_final: 0.4834 (m90) REVERT: C 193 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8369 (tptm) REVERT: C 297 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7996 (mt-10) REVERT: D 190 TYR cc_start: 0.6502 (OUTLIER) cc_final: 0.6092 (m-80) REVERT: D 634 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6954 (t80) REVERT: D 651 MET cc_start: 0.7878 (mmm) cc_final: 0.7676 (mmt) outliers start: 71 outliers final: 46 residues processed: 189 average time/residue: 0.1568 time to fit residues: 49.0006 Evaluate side-chains 181 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 123 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 165 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 338 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 219 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 450 MET Chi-restraints excluded: chain B residue 462 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 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 40 GLN Chi-restraints excluded: chain C residue 74 MET 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 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 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 421 LYS 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 733 SER Chi-restraints excluded: chain C residue 747 VAL 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 227 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 82 optimal weight: 0.0040 chunk 105 optimal weight: 0.3980 chunk 5 optimal weight: 6.9990 chunk 287 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 overall best weight: 0.6914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.085202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.061659 restraints weight = 85010.665| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.34 r_work: 0.3144 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24729 Z= 0.103 Angle : 0.551 11.410 33637 Z= 0.269 Chirality : 0.043 0.354 3891 Planarity : 0.004 0.061 4211 Dihedral : 6.595 110.437 4163 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.72 % Favored : 94.04 % Rotamer: Outliers : 2.56 % Allowed : 19.80 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.16), residues: 2954 helix: 2.18 (0.15), residues: 1181 sheet: -0.80 (0.25), residues: 441 loop : -1.46 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 52 TYR 0.016 0.001 TYR B 312 PHE 0.012 0.001 PHE D 678 TRP 0.009 0.001 TRP A 381 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00224 (24672) covalent geometry : angle 0.52957 (33480) SS BOND : bond 0.00222 ( 11) SS BOND : angle 1.20303 ( 22) hydrogen bonds : bond 0.02982 ( 1051) hydrogen bonds : angle 4.11855 ( 3003) Misc. bond : bond 0.00020 ( 1) link_ALPHA1-4 : bond 0.01372 ( 2) link_ALPHA1-4 : angle 1.67263 ( 6) link_BETA1-4 : bond 0.00521 ( 11) link_BETA1-4 : angle 1.54652 ( 33) link_NAG-ASN : bond 0.00557 ( 32) link_NAG-ASN : angle 2.70490 ( 96) *********************** 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 192 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 126 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5491 (OUTLIER) cc_final: 0.5219 (tp) REVERT: A 29 ILE cc_start: 0.6231 (OUTLIER) cc_final: 0.5706 (mp) REVERT: A 209 MET cc_start: 0.8663 (tpt) cc_final: 0.8191 (tpt) REVERT: A 354 MET cc_start: 0.7110 (mpp) cc_final: 0.6740 (mmm) REVERT: A 555 MET cc_start: 0.5526 (mmt) cc_final: 0.5246 (mmm) REVERT: A 576 MET cc_start: 0.4345 (ppp) cc_final: 0.3974 (tmm) REVERT: A 709 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.6730 (p-80) REVERT: B 40 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8074 (tp) REVERT: B 72 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8093 (tp) REVERT: B 361 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8633 (mm) REVERT: B 630 MET cc_start: 0.3888 (ttt) cc_final: 0.3467 (ppp) REVERT: C 40 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8263 (mp10) REVERT: C 74 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8405 (tpp) REVERT: C 101 HIS cc_start: 0.5637 (OUTLIER) cc_final: 0.4983 (m90) REVERT: C 193 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8334 (tptm) REVERT: C 297 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8021 (mt-10) REVERT: D 190 TYR cc_start: 0.6469 (OUTLIER) cc_final: 0.5954 (m-80) REVERT: D 445 ASP cc_start: 0.0466 (OUTLIER) cc_final: -0.0063 (m-30) REVERT: D 634 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6886 (t80) REVERT: D 651 MET cc_start: 0.7859 (mmm) cc_final: 0.7595 (mmt) outliers start: 66 outliers final: 39 residues processed: 183 average time/residue: 0.1361 time to fit residues: 42.5503 Evaluate side-chains 177 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 125 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 135 LEU Chi-restraints excluded: chain A residue 338 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 72 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 384 SER 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 40 GLN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 193 LYS 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 421 LYS 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 733 SER Chi-restraints excluded: chain C residue 747 VAL 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 269 PHE Chi-restraints excluded: chain D residue 276 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 718 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 66 optimal weight: 8.9990 chunk 229 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 255 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.084573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.060874 restraints weight = 85417.275| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.81 r_work: 0.3107 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24729 Z= 0.133 Angle : 0.571 13.083 33637 Z= 0.279 Chirality : 0.044 0.358 3891 Planarity : 0.004 0.057 4211 Dihedral : 6.503 109.748 4163 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.33 % Favored : 93.43 % Rotamer: Outliers : 2.41 % Allowed : 20.23 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.16), residues: 2954 helix: 2.18 (0.15), residues: 1180 sheet: -0.75 (0.25), residues: 431 loop : -1.45 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.021 0.001 TYR B 312 PHE 0.015 0.001 PHE B 756 TRP 0.009 0.001 TRP A 381 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00305 (24672) covalent geometry : angle 0.55062 (33480) SS BOND : bond 0.00188 ( 11) SS BOND : angle 1.23455 ( 22) hydrogen bonds : bond 0.03124 ( 1051) hydrogen bonds : angle 4.16088 ( 3003) Misc. bond : bond 0.00023 ( 1) link_ALPHA1-4 : bond 0.01347 ( 2) link_ALPHA1-4 : angle 1.50666 ( 6) link_BETA1-4 : bond 0.00519 ( 11) link_BETA1-4 : angle 1.56766 ( 33) link_NAG-ASN : bond 0.00557 ( 32) link_NAG-ASN : angle 2.70377 ( 96) *********************** 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 187 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 125 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5499 (OUTLIER) cc_final: 0.5213 (tp) REVERT: A 29 ILE cc_start: 0.6269 (OUTLIER) cc_final: 0.5715 (mp) REVERT: A 209 MET cc_start: 0.8697 (tpt) cc_final: 0.8203 (tpt) REVERT: A 555 MET cc_start: 0.5630 (mmt) cc_final: 0.5402 (mmm) REVERT: A 576 MET cc_start: 0.4251 (ppp) cc_final: 0.3878 (tmm) REVERT: A 709 HIS cc_start: 0.8062 (OUTLIER) cc_final: 0.6761 (p-80) REVERT: B 40 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8084 (tp) REVERT: B 361 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8661 (mm) REVERT: B 630 MET cc_start: 0.3798 (ttt) cc_final: 0.3366 (ppp) REVERT: C 40 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8289 (mp10) REVERT: C 74 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8401 (tpp) REVERT: C 193 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8392 (tptm) REVERT: C 297 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8028 (mt-10) REVERT: D 190 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.6005 (m-80) REVERT: D 445 ASP cc_start: 0.0573 (OUTLIER) cc_final: 0.0118 (m-30) REVERT: D 634 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6886 (t80) REVERT: D 651 MET cc_start: 0.7908 (mmm) cc_final: 0.7678 (mmt) outliers start: 62 outliers final: 40 residues processed: 177 average time/residue: 0.1440 time to fit residues: 43.2003 Evaluate side-chains 175 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 124 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 70 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 338 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 200 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 384 SER 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 40 GLN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 79 CYS 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 326 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 ASN Chi-restraints excluded: chain C residue 421 LYS 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 733 SER 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 276 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 718 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 193 optimal weight: 0.0370 chunk 253 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 281 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 231 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.085331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.061757 restraints weight = 85547.969| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.83 r_work: 0.3128 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24729 Z= 0.100 Angle : 0.559 12.172 33637 Z= 0.271 Chirality : 0.043 0.355 3891 Planarity : 0.004 0.059 4211 Dihedral : 6.342 109.853 4163 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.72 % Favored : 94.04 % Rotamer: Outliers : 2.14 % Allowed : 20.54 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.16), residues: 2954 helix: 2.24 (0.15), residues: 1180 sheet: -0.69 (0.25), residues: 434 loop : -1.45 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.013 0.001 TYR B 312 PHE 0.012 0.001 PHE A 102 TRP 0.008 0.001 TRP A 381 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00217 (24672) covalent geometry : angle 0.53957 (33480) SS BOND : bond 0.00187 ( 11) SS BOND : angle 1.08823 ( 22) hydrogen bonds : bond 0.02913 ( 1051) hydrogen bonds : angle 4.08374 ( 3003) Misc. bond : bond 0.00015 ( 1) link_ALPHA1-4 : bond 0.01232 ( 2) link_ALPHA1-4 : angle 1.46136 ( 6) link_BETA1-4 : bond 0.00512 ( 11) link_BETA1-4 : angle 1.56183 ( 33) link_NAG-ASN : bond 0.00554 ( 32) link_NAG-ASN : angle 2.61150 ( 96) *********************** 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 180 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 125 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5487 (OUTLIER) cc_final: 0.5218 (tp) REVERT: A 29 ILE cc_start: 0.6272 (OUTLIER) cc_final: 0.5758 (mp) REVERT: A 209 MET cc_start: 0.8685 (tpt) cc_final: 0.8275 (tpt) REVERT: A 555 MET cc_start: 0.5630 (mmt) cc_final: 0.5388 (mmm) REVERT: A 576 MET cc_start: 0.4199 (ppp) cc_final: 0.3820 (tmm) REVERT: A 709 HIS cc_start: 0.7936 (OUTLIER) cc_final: 0.6790 (p-80) REVERT: B 40 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8102 (tp) REVERT: B 113 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8788 (mm) REVERT: B 361 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8638 (mm) REVERT: B 630 MET cc_start: 0.3803 (ttt) cc_final: 0.3371 (ppp) REVERT: C 40 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8276 (mp10) REVERT: C 74 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8432 (tpp) REVERT: C 193 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8377 (tptm) REVERT: C 297 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8010 (mt-10) REVERT: D 190 TYR cc_start: 0.6526 (OUTLIER) cc_final: 0.6025 (m-80) REVERT: D 445 ASP cc_start: 0.0587 (OUTLIER) cc_final: 0.0168 (m-30) REVERT: D 634 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6874 (t80) REVERT: D 651 MET cc_start: 0.7889 (mmm) cc_final: 0.7657 (mmt) REVERT: D 720 MET cc_start: 0.7542 (tmm) cc_final: 0.7165 (ptt) outliers start: 55 outliers final: 37 residues processed: 172 average time/residue: 0.1508 time to fit residues: 43.6358 Evaluate side-chains 172 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 123 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 70 ASN Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 338 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 113 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 251 TYR 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 40 GLN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 193 LYS 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 421 LYS 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 747 VAL 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 269 PHE Chi-restraints excluded: chain D residue 276 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 718 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 142 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 188 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 268 optimal weight: 0.6980 chunk 281 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.084405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.060761 restraints weight = 85521.050| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.34 r_work: 0.3122 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24729 Z= 0.142 Angle : 0.582 11.762 33637 Z= 0.284 Chirality : 0.044 0.360 3891 Planarity : 0.004 0.056 4211 Dihedral : 6.354 108.830 4163 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.40 % Favored : 93.40 % Rotamer: Outliers : 2.10 % Allowed : 20.34 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.16), residues: 2954 helix: 2.20 (0.15), residues: 1180 sheet: -0.71 (0.25), residues: 425 loop : -1.45 (0.17), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 52 TYR 0.011 0.001 TYR D 449 PHE 0.016 0.001 PHE C 753 TRP 0.009 0.001 TRP A 381 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00327 (24672) covalent geometry : angle 0.56291 (33480) SS BOND : bond 0.00189 ( 11) SS BOND : angle 1.13384 ( 22) hydrogen bonds : bond 0.03184 ( 1051) hydrogen bonds : angle 4.16692 ( 3003) Misc. bond : bond 0.00024 ( 1) link_ALPHA1-4 : bond 0.01163 ( 2) link_ALPHA1-4 : angle 1.39031 ( 6) link_BETA1-4 : bond 0.00472 ( 11) link_BETA1-4 : angle 1.58771 ( 33) link_NAG-ASN : bond 0.00553 ( 32) link_NAG-ASN : angle 2.64103 ( 96) ********************** 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 179 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.5527 (OUTLIER) cc_final: 0.5249 (tp) REVERT: A 29 ILE cc_start: 0.6391 (OUTLIER) cc_final: 0.5798 (mp) REVERT: A 209 MET cc_start: 0.8692 (tpt) cc_final: 0.8283 (tpt) REVERT: A 555 MET cc_start: 0.5672 (mmt) cc_final: 0.5432 (mmm) REVERT: A 576 MET cc_start: 0.4262 (ppp) cc_final: 0.3874 (tmm) REVERT: A 709 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.6859 (p-80) REVERT: B 40 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8112 (tp) REVERT: B 113 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8806 (mm) REVERT: B 361 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8684 (mm) REVERT: B 630 MET cc_start: 0.3789 (ttt) cc_final: 0.3375 (ppp) REVERT: C 40 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8256 (mp10) REVERT: C 74 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8392 (tpp) REVERT: C 193 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8450 (tptm) REVERT: C 297 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8037 (mt-10) REVERT: D 190 TYR cc_start: 0.6511 (OUTLIER) cc_final: 0.6029 (m-80) REVERT: D 197 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6632 (p0) REVERT: D 445 ASP cc_start: 0.0758 (OUTLIER) cc_final: 0.0303 (m-30) REVERT: D 634 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6902 (t80) REVERT: D 651 MET cc_start: 0.7947 (mmm) cc_final: 0.7724 (mmt) outliers start: 54 outliers final: 37 residues processed: 170 average time/residue: 0.1368 time to fit residues: 39.5343 Evaluate side-chains 171 residues out of total 2576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 121 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 338 VAL 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 113 LEU Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 384 SER 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 40 GLN Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 193 LYS 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 421 LYS 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 747 VAL 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 276 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 718 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 185 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 94 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.085238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.061710 restraints weight = 84919.319| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 4.03 r_work: 0.3116 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24729 Z= 0.110 Angle : 0.561 11.606 33637 Z= 0.273 Chirality : 0.044 0.356 3891 Planarity : 0.004 0.059 4211 Dihedral : 6.238 108.931 4163 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.03 % Favored : 93.77 % Rotamer: Outliers : 2.21 % Allowed : 20.42 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.16), residues: 2954 helix: 2.23 (0.15), residues: 1180 sheet: -0.69 (0.25), residues: 428 loop : -1.43 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 670 TYR 0.011 0.001 TYR B 676 PHE 0.016 0.001 PHE B 756 TRP 0.008 0.001 TRP A 381 HIS 0.005 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00247 (24672) covalent geometry : angle 0.54252 (33480) SS BOND : bond 0.00173 ( 11) SS BOND : angle 1.08293 ( 22) hydrogen bonds : bond 0.02969 ( 1051) hydrogen bonds : angle 4.10006 ( 3003) Misc. bond : bond 0.00019 ( 1) link_ALPHA1-4 : bond 0.00951 ( 2) link_ALPHA1-4 : angle 1.39973 ( 6) link_BETA1-4 : bond 0.00503 ( 11) link_BETA1-4 : angle 1.57820 ( 33) link_NAG-ASN : bond 0.00540 ( 32) link_NAG-ASN : angle 2.56202 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6194.99 seconds wall clock time: 107 minutes 2.56 seconds (6422.56 seconds total)