Starting phenix.real_space_refine on Thu Mar 5 15:41:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sad_24949/03_2026/7sad_24949.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sad_24949/03_2026/7sad_24949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sad_24949/03_2026/7sad_24949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sad_24949/03_2026/7sad_24949.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sad_24949/03_2026/7sad_24949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sad_24949/03_2026/7sad_24949.map" } resolution = 3.96 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= 0.004 sd= 0.493 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 298 atoms to isotropic. 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 118 5.16 5 C 14849 2.51 5 N 3799 2.21 5 O 4316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23082 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5807 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 594 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 22, 'HIS:plan': 4, 'GLU:plan': 23, 'GLN:plan1': 7, 'ASP:plan': 8, 'PHE:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 345 Chain: "B" Number of atoms: 5667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5667 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 556 Unresolved non-hydrogen angles: 677 Unresolved non-hydrogen dihedrals: 482 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 33, 'HIS:plan': 6, 'PHE:plan': 5, 'ARG:plan': 10, 'ASN:plan1': 6, 'GLN:plan1': 8, 'TYR:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 394 Chain: "C" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5751 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 550 Unresolved non-hydrogen angles: 659 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 25, 'HIS:plan': 6, 'GLU:plan': 28, 'GLN:plan1': 7, 'PHE:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 10, 'TRP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 387 Chain: "D" Number of atoms: 5634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5634 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 140} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 589 Unresolved non-hydrogen angles: 717 Unresolved non-hydrogen dihedrals: 508 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 19, 'GLU:plan': 35, 'HIS:plan': 6, 'PHE:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 8, 'GLN:plan1': 10, 'TYR:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 412 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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'377': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.42, per 1000 atoms: 0.23 Number of scatterers: 23082 At special positions: 0 Unit cell: (125.832, 154.936, 184.04, 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 118 16.00 O 4316 8.00 N 3799 7.00 C 14849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 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 A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.04 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.04 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 903 " - " ASN A 368 " " NAG D 901 " - " ASN D 491 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN C 368 " " NAG G 1 " - " ASN D 688 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 889.2 milliseconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5904 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 28 sheets defined 43.8% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 103 through 113 Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.739A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.922A pdb=" N GLN A 147 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.597A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.522A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.595A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.695A pdb=" N GLU A 253 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.002A pdb=" N LEU A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.982A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 459 through 471 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.068A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 584 removed outlier: 3.700A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 3.860A pdb=" N MET A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 655 removed outlier: 3.948A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.790A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 4.232A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 4.627A pdb=" N GLN A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 739 Processing helix chain 'A' and resid 766 through 782 removed outlier: 4.324A pdb=" N GLN A 770 " --> pdb=" O SER A 766 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 809 through 841 removed outlier: 4.154A pdb=" N MET A 813 " --> pdb=" O THR A 809 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.310A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.592A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 119 removed outlier: 3.679A pdb=" N ILE B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.767A pdb=" N SER B 130 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.895A pdb=" N MET B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 4.005A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 233 through 248 removed outlier: 4.031A pdb=" N GLU B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B 243 " --> pdb=" O TYR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.974A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 312 removed outlier: 3.554A pdb=" N HIS B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 460 through 472 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 558 through 579 removed outlier: 3.665A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 612 removed outlier: 3.640A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.904A pdb=" N LYS B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL B 634 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TRP B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 removed outlier: 3.625A pdb=" N GLN B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 668 through 673' Processing helix chain 'B' and resid 689 through 699 removed outlier: 4.049A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 709 removed outlier: 4.348A pdb=" N ALA B 704 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET B 706 " --> pdb=" O HIS B 703 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 707 " --> pdb=" O ALA B 704 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS B 708 " --> pdb=" O TYR B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.505A pdb=" N ALA B 740 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG B 742 " --> pdb=" O TYR B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 787 removed outlier: 4.503A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 783 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.951A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 845 removed outlier: 3.529A pdb=" N MET B 818 " --> pdb=" O ASP B 814 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLY B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL B 821 " --> pdb=" O ASN B 817 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 86 removed outlier: 4.244A pdb=" N MET C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 removed outlier: 3.758A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.561A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 removed outlier: 3.616A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 204 through 213 removed outlier: 3.885A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET C 209 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 237 removed outlier: 3.629A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.874A pdb=" N ALA C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 296 removed outlier: 3.538A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 removed outlier: 3.591A pdb=" N SER C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 500 through 508 removed outlier: 3.587A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 584 removed outlier: 3.704A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 removed outlier: 4.654A pdb=" N MET C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 657 removed outlier: 3.726A pdb=" N ALA C 640 " --> pdb=" O TRP C 636 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET C 641 " --> pdb=" O ALA C 637 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 654 " --> pdb=" O ASN C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.597A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 709 removed outlier: 3.996A pdb=" N HIS C 709 " --> pdb=" O HIS C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.600A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 766 through 782 removed outlier: 4.273A pdb=" N GLN C 770 " --> pdb=" O SER C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 removed outlier: 4.017A pdb=" N ASP C 787 " --> pdb=" O GLY C 783 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 788 " --> pdb=" O PHE C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 841 removed outlier: 3.592A pdb=" N MET C 813 " --> pdb=" O THR C 809 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE C 828 " --> pdb=" O ILE C 824 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.940A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 93 removed outlier: 3.514A pdb=" N ILE D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 removed outlier: 3.886A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 removed outlier: 3.539A pdb=" N SER D 130 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.867A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 removed outlier: 3.836A pdb=" N ILE D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 324 through 329 removed outlier: 3.509A pdb=" N LYS D 327 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 324 through 329' Processing helix chain 'D' and resid 334 through 339 Processing helix chain 'D' and resid 460 through 473 Processing helix chain 'D' and resid 495 through 503 removed outlier: 3.694A pdb=" N VAL D 502 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET D 503 " --> pdb=" O GLY D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 555 through 579 removed outlier: 3.539A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.710A pdb=" N ALA D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 656 Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.749A pdb=" N ASN D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN D 698 " --> pdb=" O ASN D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.880A pdb=" N HIS D 703 " --> pdb=" O TYR D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 removed outlier: 3.951A pdb=" N LYS D 722 " --> pdb=" O LEU D 718 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR D 723 " --> pdb=" O LEU D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 743 removed outlier: 3.631A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 787 removed outlier: 4.100A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN D 782 " --> pdb=" O LEU D 778 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU D 783 " --> pdb=" O ALA D 779 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY D 785 " --> pdb=" O LEU D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 798 removed outlier: 3.677A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 798 " --> pdb=" O ALA D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 817 Processing helix chain 'D' and resid 818 through 845 removed outlier: 4.423A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 6.171A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 197 removed outlier: 3.751A pdb=" N PHE A 197 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 3.551A pdb=" N GLN A 270 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 366 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 340 through 341 removed outlier: 4.051A pdb=" N ASP A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 478 removed outlier: 6.724A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 removed outlier: 3.635A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 412 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS A 454 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.985A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.466A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 747 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 73 removed outlier: 3.579A pdb=" N GLU B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 40 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 203 removed outlier: 7.981A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 227 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 228 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB2, first strand: chain 'B' and resid 417 through 420 removed outlier: 3.910A pdb=" N GLU B 420 " --> pdb=" O CYS B 456 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N LEU B 480 " --> pdb=" O PRO B 435 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N GLN B 437 " --> pdb=" O LEU B 480 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR B 410 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET B 508 " --> pdb=" O SER B 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB5, first strand: chain 'B' and resid 683 through 684 removed outlier: 3.778A pdb=" N GLY B 684 " --> pdb=" O ALA B 728 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE B 730 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 59 through 65 removed outlier: 3.540A pdb=" N THR C 63 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 65 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 197 removed outlier: 6.515A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 168 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.383A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 339 through 340 removed outlier: 4.662A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 473 through 478 removed outlier: 7.000A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET C 512 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL C 401 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL C 514 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET C 762 " --> pdb=" O GLU C 528 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU C 528 " --> pdb=" O MET C 762 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.668A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS C 455 " --> pdb=" O VAL C 434 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 535 through 536 removed outlier: 3.527A pdb=" N GLN C 536 " --> pdb=" O SER C 756 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER C 756 " --> pdb=" O GLN C 536 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.921A pdb=" N ALA C 682 " --> pdb=" O ALA C 728 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 539 " --> pdb=" O TRP C 731 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 749 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 542 " --> pdb=" O VAL C 747 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 747 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 67 through 73 removed outlier: 3.636A pdb=" N LEU D 41 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET D 73 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N PHE D 99 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE D 40 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ILE D 123 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 198 through 205 removed outlier: 7.970A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU D 205 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR D 173 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR D 231 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 174 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE D 278 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL D 280 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 366 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU D 374 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 405 through 410 removed outlier: 6.819A pdb=" N LEU D 406 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N TYR D 479 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 417 through 420 removed outlier: 4.037A pdb=" N GLU D 420 " --> pdb=" O CYS D 456 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS D 456 " --> pdb=" O GLU D 420 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS D 455 " --> pdb=" O CYS D 436 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.800A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 538 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.800A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 990 hydrogen bonds defined for protein. 2865 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: 4.59 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3756 1.30 - 1.43: 6047 1.43 - 1.56: 13568 1.56 - 1.70: 2 1.70 - 1.83: 198 Bond restraints: 23571 Sorted by residual: bond pdb=" CA ALA B 648 " pdb=" C ALA B 648 " ideal model delta sigma weight residual 1.524 1.423 0.101 1.27e-02 6.20e+03 6.32e+01 bond pdb=" CG PRO C 142 " pdb=" CD PRO C 142 " ideal model delta sigma weight residual 1.503 1.264 0.239 3.40e-02 8.65e+02 4.93e+01 bond pdb=" N PHE D 642 " pdb=" CA PHE D 642 " ideal model delta sigma weight residual 1.459 1.379 0.080 1.20e-02 6.94e+03 4.48e+01 bond pdb=" C ALA C 649 " pdb=" O ALA C 649 " ideal model delta sigma weight residual 1.237 1.163 0.074 1.17e-02 7.31e+03 3.96e+01 bond pdb=" CA PRO A 557 " pdb=" C PRO A 557 " ideal model delta sigma weight residual 1.524 1.458 0.066 1.06e-02 8.90e+03 3.84e+01 ... (remaining 23566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.35: 32166 5.35 - 10.70: 69 10.70 - 16.05: 9 16.05 - 21.40: 2 21.40 - 26.75: 1 Bond angle restraints: 32247 Sorted by residual: angle pdb=" C THR D 647 " pdb=" CA THR D 647 " pdb=" CB THR D 647 " ideal model delta sigma weight residual 110.88 90.92 19.96 1.57e+00 4.06e-01 1.62e+02 angle pdb=" C GLN A 556 " pdb=" N PRO A 557 " pdb=" CA PRO A 557 " ideal model delta sigma weight residual 121.04 106.91 14.13 1.21e+00 6.83e-01 1.36e+02 angle pdb=" N PRO C 142 " pdb=" CD PRO C 142 " pdb=" CG PRO C 142 " ideal model delta sigma weight residual 103.20 87.33 15.87 1.50e+00 4.44e-01 1.12e+02 angle pdb=" CA LEU A 819 " pdb=" CB LEU A 819 " pdb=" CG LEU A 819 " ideal model delta sigma weight residual 116.30 89.55 26.75 3.50e+00 8.16e-02 5.84e+01 angle pdb=" N VAL C 656 " pdb=" CA VAL C 656 " pdb=" C VAL C 656 " ideal model delta sigma weight residual 113.10 120.24 -7.14 9.70e-01 1.06e+00 5.42e+01 ... (remaining 32242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 13399 24.69 - 49.37: 599 49.37 - 74.06: 54 74.06 - 98.75: 10 98.75 - 123.43: 3 Dihedral angle restraints: 14065 sinusoidal: 4917 harmonic: 9148 Sorted by residual: dihedral pdb=" C THR D 647 " pdb=" N THR D 647 " pdb=" CA THR D 647 " pdb=" CB THR D 647 " ideal model delta harmonic sigma weight residual -122.00 -99.45 -22.55 0 2.50e+00 1.60e-01 8.13e+01 dihedral pdb=" CB CYS C 744 " pdb=" SG CYS C 744 " pdb=" SG CYS C 798 " pdb=" CB CYS C 798 " ideal model delta sinusoidal sigma weight residual -86.00 -12.16 -73.84 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 455 " pdb=" CB CYS A 455 " ideal model delta sinusoidal sigma weight residual -86.00 -153.67 67.67 1 1.00e+01 1.00e-02 5.95e+01 ... (remaining 14062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 3892 0.145 - 0.290: 21 0.290 - 0.435: 7 0.435 - 0.580: 2 0.580 - 0.725: 2 Chirality restraints: 3924 Sorted by residual: chirality pdb=" CG LEU A 819 " pdb=" CB LEU A 819 " pdb=" CD1 LEU A 819 " pdb=" CD2 LEU A 819 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ASN C 650 " pdb=" N ASN C 650 " pdb=" C ASN C 650 " pdb=" CB ASN C 650 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA ILE B 655 " pdb=" N ILE B 655 " pdb=" C ILE B 655 " pdb=" CB ILE B 655 " both_signs ideal model delta sigma weight residual False 2.43 1.90 0.54 2.00e-01 2.50e+01 7.20e+00 ... (remaining 3921 not shown) Planarity restraints: 4070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 141 " -0.079 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO C 142 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 641 " 0.021 2.00e-02 2.50e+03 4.43e-02 1.97e+01 pdb=" C ILE D 641 " -0.077 2.00e-02 2.50e+03 pdb=" O ILE D 641 " 0.029 2.00e-02 2.50e+03 pdb=" N PHE D 642 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 559 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C GLN A 559 " -0.070 2.00e-02 2.50e+03 pdb=" O GLN A 559 " 0.026 2.00e-02 2.50e+03 pdb=" N SER A 560 " 0.024 2.00e-02 2.50e+03 ... (remaining 4067 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.19: 4 2.19 - 2.87: 8598 2.87 - 3.55: 31985 3.55 - 4.22: 44808 4.22 - 4.90: 77570 Nonbonded interactions: 162965 Sorted by model distance: nonbonded pdb=" O LEU A 562 " pdb=" N LEU A 564 " model vdw 1.515 3.120 nonbonded pdb=" N GLN A 559 " pdb=" OE1 GLN A 559 " model vdw 2.120 3.120 nonbonded pdb=" OG SER D 149 " pdb=" OE1 GLN D 152 " model vdw 2.172 3.040 nonbonded pdb=" OG1 THR C 550 " pdb=" OE1 GLU C 811 " model vdw 2.187 3.040 nonbonded pdb=" O ASP B 77 " pdb=" OG SER B 80 " model vdw 2.235 3.040 ... (remaining 162960 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 41 or (resid 42 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 or (resid 47 through 52 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 72 or (res \ id 73 and (name N or name CA or name C or name O or name CB )) or resid 74 throu \ gh 130 or (resid 131 and (name N or name CA or name C or name O or name CB )) or \ resid 132 through 171 or (resid 172 and (name N or name CA or name C or name O \ or name CB )) or resid 173 or (resid 174 through 176 and (name N or name CA or n \ ame C or name O or name CB )) or resid 177 through 180 or (resid 181 and (name N \ or name CA or name C or name O or name CB )) or resid 182 through 186 or (resid \ 187 through 188 and (name N or name CA or name C or name O or name CB )) or res \ id 189 or (resid 190 through 192 and (name N or name CA or name C or name O or n \ ame CB )) or resid 193 through 197 or (resid 198 and (name N or name CA or name \ C or name O or name CB )) or resid 199 through 214 or (resid 215 through 216 and \ (name N or name CA or name C or name O or name CB )) or resid 217 through 251 o \ r (resid 252 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 53 through 259 or (resid 260 and (name N or name CA or name C or name O or name \ CB )) or resid 261 through 274 or (resid 275 and (name N or name CA or name C or \ name O or name CB )) or resid 276 through 289 or (resid 290 through 291 and (na \ me N or name CA or name C or name O or name CB )) or resid 292 or (resid 293 thr \ ough 299 and (name N or name CA or name C or name O or name CB )) or resid 300 t \ hrough 336 or (resid 337 and (name N or name CA or name C or name O or name CB ) \ ) or resid 338 or (resid 339 and (name N or name CA or name C or name O or name \ CB )) or resid 340 through 416 or (resid 417 and (name N or name CA or name C or \ name O or name CB )) or resid 418 through 420 or (resid 421 through 423 and (na \ me N or name CA or name C or name O or name CB )) or resid 424 through 448 or (r \ esid 449 and (name N or name CA or name C or name O or name CB )) or resid 450 t \ hrough 543 or (resid 544 through 545 and (name N or name CA or name C or name O \ or name CB )) or resid 546 through 575 or (resid 576 and (name N or name CA or n \ ame C or name O or name CB )) or resid 577 through 580 or (resid 581 through 583 \ and (name N or name CA or name C or name O or name CB )) or resid 584 through 6 \ 61 or (resid 662 and (name N or name CA or name C or name O or name CB )) or res \ id 663 through 693 or (resid 694 through 695 and (name N or name CA or name C or \ name O or name CB )) or resid 696 through 703 or (resid 704 and (name N or name \ CA or name C or name O or name CB )) or resid 705 through 724 or (resid 725 and \ (name N or name CA or name C or name O or name CB )) or resid 726 through 736 o \ r (resid 737 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 38 or (resid 739 through 740 and (name N or name CA or name C or name O or name \ CB )) or resid 741 through 750 or (resid 751 and (name N or name CA or name C or \ name O or name CB )) or resid 752 through 780 or (resid 781 and (name N or name \ CA or name C or name O or name CB )) or resid 782 through 818 or (resid 819 and \ (name N or name CA or name C or name O or name CB )) or resid 820 through 902)) \ selection = (chain 'C' and (resid 25 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 or (resid 61 through 62 and (name N or nam \ e CA or name C or name O or name CB )) or resid 63 through 79 or (resid 80 and ( \ name N or name CA or name C or name O or name CB )) or resid 81 through 82 or (r \ esid 83 and (name N or name CA or name C or name O or name CB )) or resid 84 thr \ ough 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) \ or resid 103 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 123 or (resid 124 and (name N or name CA or \ name C or name O or name CB )) or resid 125 through 224 or (resid 225 and (name \ N or name CA or name C or name O or name CB )) or resid 226 through 271 or (res \ id 272 and (name N or name CA or name C or name O or name CB )) or resid 273 thr \ ough 276 or (resid 277 and (name N or name CA or name C or name O or name CB )) \ or resid 278 through 294 or (resid 295 through 299 and (name N or name CA or nam \ e C or name O or name CB )) or resid 300 through 310 or (resid 311 and (name N o \ r name CA or name C or name O or name CB )) or resid 312 or (resid 313 and (name \ N or name CA or name C or name O or name CB )) or resid 314 through 331 or (res \ id 332 and (name N or name CA or name C or name O or name CB )) or resid 333 thr \ ough 340 or (resid 341 through 342 and (name N or name CA or name C or name O or \ name CB )) or resid 343 through 345 or (resid 346 through 347 and (name N or na \ me CA or name C or name O or name CB )) or resid 348 through 376 or (resid 377 t \ hrough 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ through 386 or (resid 387 and (name N or name CA or name C or name O or name CB \ )) or resid 388 through 393 or (resid 394 and (name N or name CA or name C or n \ ame O or name CB )) or resid 395 through 396 or (resid 397 and (name N or name C \ A or name C or name O or name CB )) or resid 398 through 706 or (resid 707 and ( \ name N or name CA or name C or name O or name CB )) or resid 708 through 810 or \ (resid 811 and (name N or name CA or name C or name O or name CB )) or resid 812 \ through 816 or (resid 817 through 819 and (name N or name CA or name C or name \ O or name CB )) or resid 820 through 902)) } ncs_group { reference = (chain 'B' and (resid 34 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 117 or (resid 118 and (name N or n \ ame CA or name C or name O or name CB )) or resid 119 through 152 or (resid 153 \ through 154 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 5 through 212 or (resid 213 and (name N or name CA or name C or name O or name C \ B )) or resid 214 through 233 or (resid 234 through 237 and (name N or name CA o \ r name C or name O or name CB )) or resid 238 through 241 or (resid 242 and (nam \ e N or name CA or name C or name O or name CB )) or resid 243 through 244 or (re \ sid 245 and (name N or name CA or name C or name O or name CB )) or resid 246 th \ rough 305 or (resid 306 through 308 and (name N or name CA or name C or name O o \ r name CB )) or resid 309 or (resid 310 through 311 and (name N or name CA or na \ me C or name O or name CB )) or resid 312 through 315 or (resid 316 and (name N \ or name CA or name C or name O or name CB )) or resid 317 through 332 or (resid \ 333 through 334 and (name N or name CA or name C or name O or name CB )) or resi \ d 335 through 360 or (resid 361 and (name N or name CA or name C or name O or na \ me CB )) or resid 362 through 386 or (resid 387 and (name N or name CA or name C \ or name O or name CB )) or resid 388 through 411 or (resid 412 through 414 and \ (name N or name CA or name C or name O or name CB )) or resid 415 through 440 or \ (resid 441 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 2 through 466 or (resid 467 and (name N or name CA or name C or name O or name C \ B )) or resid 468 through 472 or (resid 473 and (name N or name CA or name C or \ name O or name CB )) or resid 474 through 499 or (resid 500 and (name N or name \ CA or name C or name O or name CB )) or resid 501 through 520 or (resid 521 and \ (name N or name CA or name C or name O or name CB )) or resid 522 through 556 or \ (resid 557 and (name N or name CA or name C or name O or name CB )) or resid 55 \ 8 through 707 or (resid 708 and (name N or name CA or name C or name O or name C \ B )) or resid 709 through 785 or (resid 786 and (name N or name CA or name C or \ name O or name CB )) or resid 787 or (resid 788 and (name N or name CA or name C \ or name O or name CB )) or resid 789 through 802 or (resid 803 through 807 and \ (name N or name CA or name C or name O or name CB )) or resid 808 through 811 or \ (resid 812 and (name N or name CA or name C or name O or name CB )) or resid 81 \ 3 through 817 or (resid 818 through 819 and (name N or name CA or name C or name \ O or name CB )) or resid 820 through 828 or (resid 829 through 830 and (name N \ or name CA or name C or name O or name CB )) or resid 831 through 835 or (resid \ 836 and (name N or name CA or name C or name O or name CB )) or resid 837 throug \ h 902)) selection = (chain 'D' and (resid 34 through 179 or (resid 180 and (name N or name CA or nam \ e C or name O or name CB )) or resid 181 through 190 or (resid 191 and (name N o \ r name CA or name C or name O or name CB )) or resid 192 through 197 or (resid 1 \ 98 and (name N or name CA or name C or name O or name CB )) or resid 199 or (res \ id 200 through 201 and (name N or name CA or name C or name O or name CB )) or r \ esid 202 through 208 or (resid 209 through 211 and (name N or name CA or name C \ or name O or name CB )) or resid 212 through 271 or (resid 272 and (name N or na \ me CA or name C or name O or name CB )) or resid 273 through 353 or (resid 354 a \ nd (name N or name CA or name C or name O or name CB )) or resid 355 through 367 \ or (resid 368 through 370 and (name N or name CA or name C or name O or name CB \ )) or resid 371 through 412 or (resid 413 through 414 and (name N or name CA or \ name C or name O or name CB )) or resid 415 through 422 or (resid 423 and (name \ N or name CA or name C or name O or name CB )) or resid 424 through 469 or (res \ id 470 and (name N or name CA or name C or name O or name CB )) or resid 471 thr \ ough 487 or (resid 488 and (name N or name CA or name C or name O or name CB )) \ or resid 489 through 539 or (resid 540 and (name N or name CA or name C or name \ O or name CB )) or resid 541 through 574 or (resid 575 and (name N or name CA or \ name C or name O or name CB )) or resid 576 through 628 or (resid 629 and (name \ N or name CA or name C or name O or name CB )) or resid 630 through 672 or (res \ id 673 and (name N or name CA or name C or name O or name CB )) or resid 674 thr \ ough 700 or (resid 701 and (name N or name CA or name C or name O or name CB )) \ or resid 702 through 767 or (resid 768 and (name N or name CA or name C or name \ O or name CB )) or resid 769 through 792 or (resid 793 through 794 and (name N o \ r name CA or name C or name O or name CB )) or resid 795 through 902)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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 group one per residue 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: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.180 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 : 0.006 0.239 23594 Z= 0.355 Angle : 0.784 26.753 32301 Z= 0.431 Chirality : 0.051 0.725 3924 Planarity : 0.005 0.113 4065 Dihedral : 13.287 123.434 8116 Min Nonbonded Distance : 1.515 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.42 % Favored : 94.39 % Rotamer: Outliers : 0.49 % Allowed : 0.49 % Favored : 99.02 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.15), residues: 3136 helix: 1.32 (0.15), residues: 1204 sheet: -0.16 (0.31), residues: 323 loop : -1.61 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 671 TYR 0.030 0.001 TYR B 646 PHE 0.043 0.002 PHE D 176 TRP 0.011 0.001 TRP A 608 HIS 0.008 0.001 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00581 (23571) covalent geometry : angle 0.78021 (32247) SS BOND : bond 0.00293 ( 15) SS BOND : angle 1.27145 ( 30) hydrogen bonds : bond 0.18160 ( 986) hydrogen bonds : angle 6.36459 ( 2865) link_BETA1-4 : bond 0.00686 ( 3) link_BETA1-4 : angle 1.65195 ( 9) link_NAG-ASN : bond 0.01216 ( 5) link_NAG-ASN : angle 2.92760 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 433 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 738 PHE cc_start: 0.8518 (t80) cc_final: 0.8291 (t80) REVERT: B 101 ASP cc_start: 0.7772 (m-30) cc_final: 0.6674 (t0) REVERT: B 537 MET cc_start: 0.8509 (tpt) cc_final: 0.8119 (tpt) REVERT: B 562 MET cc_start: 0.8938 (mmp) cc_final: 0.8663 (mmt) REVERT: B 702 MET cc_start: 0.8152 (ptp) cc_final: 0.7849 (ptp) REVERT: B 813 LEU cc_start: 0.8774 (mm) cc_final: 0.8086 (mm) REVERT: C 406 GLU cc_start: 0.7773 (tp30) cc_final: 0.7468 (tp30) REVERT: C 655 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9086 (tt) REVERT: C 674 ASN cc_start: 0.8522 (t0) cc_final: 0.8188 (t0) REVERT: C 724 ASN cc_start: 0.8091 (m-40) cc_final: 0.7773 (t0) REVERT: D 223 LEU cc_start: 0.8273 (mt) cc_final: 0.7935 (pp) REVERT: D 430 MET cc_start: 0.7777 (mtt) cc_final: 0.7510 (mtt) REVERT: D 742 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7894 (mmm-85) REVERT: D 777 ASP cc_start: 0.7855 (t70) cc_final: 0.7642 (t70) REVERT: D 789 MET cc_start: 0.7239 (ttp) cc_final: 0.7025 (ttp) outliers start: 11 outliers final: 7 residues processed: 443 average time/residue: 0.1208 time to fit residues: 92.1608 Evaluate side-chains 330 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 322 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 655 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B 218 ASN B 616 ASN C 28 ASN C 61 GLN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS D 486 HIS ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.123284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.097746 restraints weight = 68763.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099949 restraints weight = 41976.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101387 restraints weight = 28550.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.101747 restraints weight = 23991.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102300 restraints weight = 21635.487| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23594 Z= 0.207 Angle : 0.688 13.185 32301 Z= 0.357 Chirality : 0.045 0.281 3924 Planarity : 0.005 0.082 4065 Dihedral : 7.009 81.878 3679 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.76 % Favored : 93.08 % Rotamer: Outliers : 2.41 % Allowed : 10.74 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3136 helix: 1.06 (0.15), residues: 1233 sheet: -0.33 (0.27), residues: 401 loop : -1.77 (0.16), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 763 TYR 0.027 0.002 TYR B 479 PHE 0.031 0.002 PHE B 637 TRP 0.013 0.001 TRP A 608 HIS 0.009 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00472 (23571) covalent geometry : angle 0.68206 (32247) SS BOND : bond 0.00939 ( 15) SS BOND : angle 2.02800 ( 30) hydrogen bonds : bond 0.05058 ( 986) hydrogen bonds : angle 5.20451 ( 2865) link_BETA1-4 : bond 0.00496 ( 3) link_BETA1-4 : angle 1.98934 ( 9) link_NAG-ASN : bond 0.01118 ( 5) link_NAG-ASN : angle 2.79908 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 341 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 ILE cc_start: 0.9458 (mm) cc_final: 0.9235 (mm) REVERT: A 737 GLU cc_start: 0.8607 (tt0) cc_final: 0.8163 (tm-30) REVERT: B 101 ASP cc_start: 0.7797 (m-30) cc_final: 0.7392 (m-30) REVERT: B 358 MET cc_start: 0.7887 (mpp) cc_final: 0.7607 (mpp) REVERT: B 653 PHE cc_start: 0.8713 (t80) cc_final: 0.8492 (t80) REVERT: B 702 MET cc_start: 0.8246 (ptp) cc_final: 0.7967 (ptp) REVERT: C 177 GLN cc_start: 0.8294 (tm-30) cc_final: 0.8086 (tm-30) REVERT: C 463 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8841 (pp) REVERT: C 674 ASN cc_start: 0.8407 (t0) cc_final: 0.8071 (t0) REVERT: D 654 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7572 (ttm) REVERT: D 702 MET cc_start: 0.7587 (mmm) cc_final: 0.7125 (mpp) REVERT: D 742 ARG cc_start: 0.8283 (tpp80) cc_final: 0.7573 (mmm-85) outliers start: 54 outliers final: 36 residues processed: 372 average time/residue: 0.1174 time to fit residues: 75.8434 Evaluate side-chains 352 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 314 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 769 ASP Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 146 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 57 optimal weight: 0.0000 chunk 113 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 153 optimal weight: 40.0000 chunk 312 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.125661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099488 restraints weight = 68202.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.102882 restraints weight = 42357.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.103728 restraints weight = 27561.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.104639 restraints weight = 22649.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.104959 restraints weight = 19491.463| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 23594 Z= 0.114 Angle : 0.604 9.247 32301 Z= 0.306 Chirality : 0.043 0.270 3924 Planarity : 0.004 0.067 4065 Dihedral : 5.939 58.332 3669 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.77 % Favored : 94.07 % Rotamer: Outliers : 2.05 % Allowed : 14.04 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 3136 helix: 1.17 (0.15), residues: 1231 sheet: -0.18 (0.27), residues: 391 loop : -1.71 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 252 TYR 0.025 0.001 TYR B 479 PHE 0.024 0.001 PHE B 642 TRP 0.011 0.001 TRP C 768 HIS 0.010 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00249 (23571) covalent geometry : angle 0.59822 (32247) SS BOND : bond 0.00545 ( 15) SS BOND : angle 2.04227 ( 30) hydrogen bonds : bond 0.04283 ( 986) hydrogen bonds : angle 4.78140 ( 2865) link_BETA1-4 : bond 0.00485 ( 3) link_BETA1-4 : angle 1.72186 ( 9) link_NAG-ASN : bond 0.00977 ( 5) link_NAG-ASN : angle 2.50047 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 356 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 357 GLN cc_start: 0.7967 (pm20) cc_final: 0.7709 (pm20) REVERT: A 642 ILE cc_start: 0.9487 (mm) cc_final: 0.8977 (mm) REVERT: B 101 ASP cc_start: 0.7902 (m-30) cc_final: 0.7459 (m-30) REVERT: B 550 PHE cc_start: 0.9211 (p90) cc_final: 0.8805 (p90) REVERT: B 702 MET cc_start: 0.8126 (ptp) cc_final: 0.7806 (ptp) REVERT: C 130 ASP cc_start: 0.7168 (t0) cc_final: 0.6548 (p0) REVERT: C 237 MET cc_start: 0.7653 (ppp) cc_final: 0.7262 (ppp) REVERT: C 406 GLU cc_start: 0.7624 (tp30) cc_final: 0.7419 (tp30) REVERT: C 463 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8772 (pp) REVERT: C 674 ASN cc_start: 0.8316 (t0) cc_final: 0.8034 (t0) REVERT: D 89 MET cc_start: 0.5378 (tpt) cc_final: 0.5140 (tpt) REVERT: D 223 LEU cc_start: 0.7970 (mt) cc_final: 0.7750 (pp) REVERT: D 654 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7466 (ttm) REVERT: D 702 MET cc_start: 0.7554 (mmm) cc_final: 0.7162 (mpp) REVERT: D 742 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7538 (mmm-85) outliers start: 46 outliers final: 27 residues processed: 384 average time/residue: 0.1219 time to fit residues: 80.7861 Evaluate side-chains 347 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 318 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 769 ASP Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 290 optimal weight: 3.9990 chunk 275 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 219 optimal weight: 8.9990 chunk 229 optimal weight: 4.9990 chunk 297 optimal weight: 1.9990 chunk 228 optimal weight: 0.5980 chunk 214 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN D 127 HIS ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.126118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.100000 restraints weight = 67624.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.103285 restraints weight = 42351.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104171 restraints weight = 27743.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.104957 restraints weight = 22859.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105380 restraints weight = 19740.394| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23594 Z= 0.109 Angle : 0.594 9.071 32301 Z= 0.299 Chirality : 0.042 0.261 3924 Planarity : 0.004 0.061 4065 Dihedral : 5.598 59.851 3669 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.22 % Favored : 93.65 % Rotamer: Outliers : 2.18 % Allowed : 15.83 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 3136 helix: 1.29 (0.15), residues: 1225 sheet: -0.15 (0.27), residues: 406 loop : -1.68 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 252 TYR 0.022 0.001 TYR B 479 PHE 0.023 0.001 PHE B 637 TRP 0.012 0.001 TRP A 636 HIS 0.004 0.001 HIS D 802 Details of bonding type rmsd covalent geometry : bond 0.00242 (23571) covalent geometry : angle 0.58833 (32247) SS BOND : bond 0.00530 ( 15) SS BOND : angle 1.96671 ( 30) hydrogen bonds : bond 0.03890 ( 986) hydrogen bonds : angle 4.59652 ( 2865) link_BETA1-4 : bond 0.00296 ( 3) link_BETA1-4 : angle 1.75273 ( 9) link_NAG-ASN : bond 0.00925 ( 5) link_NAG-ASN : angle 2.32715 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 357 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8385 (tpp) cc_final: 0.7322 (mmt) REVERT: A 354 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7663 (ttm) REVERT: A 642 ILE cc_start: 0.9453 (mm) cc_final: 0.9201 (mm) REVERT: B 101 ASP cc_start: 0.7807 (m-30) cc_final: 0.7305 (m-30) REVERT: B 157 MET cc_start: 0.8220 (ptt) cc_final: 0.7876 (ptm) REVERT: B 430 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.5993 (mmt) REVERT: B 436 CYS cc_start: 0.5101 (OUTLIER) cc_final: 0.4783 (t) REVERT: B 550 PHE cc_start: 0.9206 (p90) cc_final: 0.8773 (p90) REVERT: B 551 LEU cc_start: 0.9086 (mp) cc_final: 0.8594 (mp) REVERT: B 702 MET cc_start: 0.8168 (ptp) cc_final: 0.7852 (ptp) REVERT: C 130 ASP cc_start: 0.7132 (t0) cc_final: 0.6535 (p0) REVERT: C 237 MET cc_start: 0.7639 (ppp) cc_final: 0.7350 (ppp) REVERT: C 354 MET cc_start: 0.7907 (tmm) cc_final: 0.7645 (tpp) REVERT: C 406 GLU cc_start: 0.7612 (tp30) cc_final: 0.7350 (tp30) REVERT: C 436 CYS cc_start: 0.6855 (m) cc_final: 0.6632 (m) REVERT: C 463 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8768 (pp) REVERT: C 575 VAL cc_start: 0.9537 (t) cc_final: 0.9333 (p) REVERT: C 674 ASN cc_start: 0.8274 (t0) cc_final: 0.8013 (t0) REVERT: D 157 MET cc_start: 0.8473 (tmm) cc_final: 0.8260 (tmm) REVERT: D 223 LEU cc_start: 0.7918 (mt) cc_final: 0.7714 (pp) REVERT: D 257 ILE cc_start: 0.9138 (mm) cc_final: 0.8930 (mt) REVERT: D 524 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: D 600 PHE cc_start: 0.7892 (t80) cc_final: 0.7669 (t80) REVERT: D 702 MET cc_start: 0.7609 (mmm) cc_final: 0.7237 (mpp) REVERT: D 742 ARG cc_start: 0.8194 (tpp80) cc_final: 0.7580 (mmm-85) outliers start: 49 outliers final: 35 residues processed: 388 average time/residue: 0.1210 time to fit residues: 81.4992 Evaluate side-chains 377 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 337 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 769 ASP Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 75 optimal weight: 7.9990 chunk 282 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 312 optimal weight: 9.9990 chunk 261 optimal weight: 3.9990 chunk 173 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.121722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.095424 restraints weight = 68557.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098759 restraints weight = 43166.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.099404 restraints weight = 28158.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100120 restraints weight = 24247.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.100589 restraints weight = 21020.245| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23594 Z= 0.224 Angle : 0.676 9.328 32301 Z= 0.353 Chirality : 0.045 0.248 3924 Planarity : 0.005 0.067 4065 Dihedral : 6.048 59.867 3666 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.91 % Favored : 92.00 % Rotamer: Outliers : 3.70 % Allowed : 16.41 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.15), residues: 3136 helix: 0.99 (0.14), residues: 1243 sheet: -0.55 (0.27), residues: 407 loop : -1.85 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 663 TYR 0.019 0.002 TYR B 479 PHE 0.025 0.002 PHE A 533 TRP 0.012 0.002 TRP D 494 HIS 0.012 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00514 (23571) covalent geometry : angle 0.66958 (32247) SS BOND : bond 0.00693 ( 15) SS BOND : angle 2.25897 ( 30) hydrogen bonds : bond 0.05015 ( 986) hydrogen bonds : angle 4.92584 ( 2865) link_BETA1-4 : bond 0.00364 ( 3) link_BETA1-4 : angle 2.21810 ( 9) link_NAG-ASN : bond 0.00996 ( 5) link_NAG-ASN : angle 2.63639 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 327 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 354 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7653 (ttm) REVERT: A 641 MET cc_start: 0.8808 (tmm) cc_final: 0.8445 (tmm) REVERT: A 642 ILE cc_start: 0.9523 (mm) cc_final: 0.9091 (mm) REVERT: A 711 TYR cc_start: 0.8301 (m-10) cc_final: 0.8048 (m-80) REVERT: B 101 ASP cc_start: 0.7601 (m-30) cc_final: 0.7197 (m-30) REVERT: B 157 MET cc_start: 0.8175 (ptt) cc_final: 0.7859 (ptm) REVERT: B 386 MET cc_start: 0.8760 (mmm) cc_final: 0.8388 (mmm) REVERT: B 430 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6984 (mtt) REVERT: B 702 MET cc_start: 0.8307 (ptp) cc_final: 0.7923 (ptp) REVERT: C 130 ASP cc_start: 0.7151 (t0) cc_final: 0.6620 (p0) REVERT: C 237 MET cc_start: 0.7616 (ppp) cc_final: 0.7396 (ppp) REVERT: C 240 MET cc_start: 0.7627 (mmm) cc_final: 0.7226 (mmm) REVERT: C 406 GLU cc_start: 0.7712 (tp30) cc_final: 0.7473 (tp30) REVERT: C 674 ASN cc_start: 0.8444 (t0) cc_final: 0.8101 (t0) REVERT: C 762 MET cc_start: 0.8496 (ptp) cc_final: 0.8163 (ptp) REVERT: D 162 GLU cc_start: 0.8853 (tp30) cc_final: 0.8611 (tm-30) REVERT: D 257 ILE cc_start: 0.9190 (mm) cc_final: 0.8938 (mt) REVERT: D 524 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: D 600 PHE cc_start: 0.7976 (t80) cc_final: 0.7742 (t80) REVERT: D 742 ARG cc_start: 0.8295 (tpp80) cc_final: 0.7571 (mmm-85) outliers start: 83 outliers final: 57 residues processed: 384 average time/residue: 0.1191 time to fit residues: 79.1927 Evaluate side-chains 376 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 316 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 772 TRP Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 769 ASP Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 147 optimal weight: 0.4980 chunk 175 optimal weight: 10.0000 chunk 46 optimal weight: 0.4980 chunk 191 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 277 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 280 HIS A 499 ASN A 650 ASN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.123352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.097082 restraints weight = 68730.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100344 restraints weight = 43044.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.101087 restraints weight = 28566.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.101795 restraints weight = 24495.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.102452 restraints weight = 20951.696| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23594 Z= 0.143 Angle : 0.624 9.622 32301 Z= 0.319 Chirality : 0.043 0.253 3924 Planarity : 0.004 0.065 4065 Dihedral : 5.727 58.578 3666 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.05 % Favored : 92.86 % Rotamer: Outliers : 3.43 % Allowed : 18.37 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3136 helix: 1.11 (0.15), residues: 1236 sheet: -0.42 (0.27), residues: 400 loop : -1.78 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 663 TYR 0.031 0.001 TYR B 479 PHE 0.022 0.002 PHE B 642 TRP 0.011 0.001 TRP C 768 HIS 0.007 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00325 (23571) covalent geometry : angle 0.61724 (32247) SS BOND : bond 0.00737 ( 15) SS BOND : angle 2.37494 ( 30) hydrogen bonds : bond 0.04365 ( 986) hydrogen bonds : angle 4.69826 ( 2865) link_BETA1-4 : bond 0.00382 ( 3) link_BETA1-4 : angle 1.97882 ( 9) link_NAG-ASN : bond 0.00881 ( 5) link_NAG-ASN : angle 2.39036 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 341 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7633 (ttm) REVERT: A 400 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.9165 (mt) REVERT: A 641 MET cc_start: 0.8795 (tmm) cc_final: 0.8392 (tmm) REVERT: A 642 ILE cc_start: 0.9503 (mm) cc_final: 0.9022 (mm) REVERT: B 101 ASP cc_start: 0.7546 (m-30) cc_final: 0.7170 (m-30) REVERT: B 157 MET cc_start: 0.8169 (ptt) cc_final: 0.7883 (ptm) REVERT: B 702 MET cc_start: 0.8199 (ptp) cc_final: 0.7855 (ptp) REVERT: C 130 ASP cc_start: 0.7133 (t0) cc_final: 0.6587 (p0) REVERT: C 237 MET cc_start: 0.7614 (ppp) cc_final: 0.7381 (ppp) REVERT: C 240 MET cc_start: 0.7622 (mmm) cc_final: 0.7214 (mmm) REVERT: C 354 MET cc_start: 0.7861 (tmm) cc_final: 0.7583 (tmm) REVERT: C 436 CYS cc_start: 0.6689 (m) cc_final: 0.6467 (m) REVERT: C 674 ASN cc_start: 0.8372 (t0) cc_final: 0.8051 (t0) REVERT: C 762 MET cc_start: 0.8474 (ptp) cc_final: 0.7821 (ptm) REVERT: D 162 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8651 (tm-30) REVERT: D 257 ILE cc_start: 0.9200 (mm) cc_final: 0.8993 (mt) REVERT: D 600 PHE cc_start: 0.7954 (t80) cc_final: 0.7735 (t80) REVERT: D 702 MET cc_start: 0.7533 (mmm) cc_final: 0.7175 (mpp) REVERT: D 742 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7529 (mmm-85) outliers start: 77 outliers final: 56 residues processed: 388 average time/residue: 0.1249 time to fit residues: 84.5161 Evaluate side-chains 382 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 323 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 134 MET Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 769 ASP Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 104 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 295 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 252 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 277 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.123457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097103 restraints weight = 67994.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100720 restraints weight = 42811.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101343 restraints weight = 27432.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.102040 restraints weight = 23583.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102660 restraints weight = 20516.669| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23594 Z= 0.138 Angle : 0.636 11.760 32301 Z= 0.321 Chirality : 0.044 0.399 3924 Planarity : 0.004 0.063 4065 Dihedral : 5.528 55.058 3666 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.37 % Favored : 92.54 % Rotamer: Outliers : 3.17 % Allowed : 19.57 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.15), residues: 3136 helix: 1.14 (0.15), residues: 1232 sheet: -0.46 (0.27), residues: 403 loop : -1.77 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 663 TYR 0.030 0.001 TYR B 479 PHE 0.022 0.002 PHE B 642 TRP 0.009 0.001 TRP C 768 HIS 0.010 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00316 (23571) covalent geometry : angle 0.62743 (32247) SS BOND : bond 0.00519 ( 15) SS BOND : angle 2.33989 ( 30) hydrogen bonds : bond 0.04254 ( 986) hydrogen bonds : angle 4.65666 ( 2865) link_BETA1-4 : bond 0.00446 ( 3) link_BETA1-4 : angle 1.90953 ( 9) link_NAG-ASN : bond 0.00883 ( 5) link_NAG-ASN : angle 3.38618 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 331 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 354 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7642 (ttm) REVERT: A 641 MET cc_start: 0.8787 (tmm) cc_final: 0.8392 (tmm) REVERT: A 642 ILE cc_start: 0.9498 (mm) cc_final: 0.8968 (mm) REVERT: A 650 ASN cc_start: 0.8264 (t0) cc_final: 0.8027 (t0) REVERT: B 101 ASP cc_start: 0.7549 (m-30) cc_final: 0.7158 (m-30) REVERT: B 157 MET cc_start: 0.8165 (ptt) cc_final: 0.7875 (ptm) REVERT: B 702 MET cc_start: 0.8180 (ptp) cc_final: 0.7841 (ptp) REVERT: C 240 MET cc_start: 0.7646 (mmm) cc_final: 0.7232 (mmm) REVERT: C 354 MET cc_start: 0.7789 (tmm) cc_final: 0.7556 (tmm) REVERT: C 436 CYS cc_start: 0.6744 (m) cc_final: 0.6517 (m) REVERT: C 674 ASN cc_start: 0.8354 (t0) cc_final: 0.8055 (t0) REVERT: C 762 MET cc_start: 0.8473 (ptp) cc_final: 0.7820 (ptm) REVERT: D 257 ILE cc_start: 0.9208 (mm) cc_final: 0.9001 (mt) REVERT: D 558 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7663 (p) REVERT: D 600 PHE cc_start: 0.7929 (t80) cc_final: 0.7727 (t80) REVERT: D 742 ARG cc_start: 0.8197 (tpp80) cc_final: 0.7555 (mmm-85) outliers start: 71 outliers final: 55 residues processed: 374 average time/residue: 0.1181 time to fit residues: 76.7368 Evaluate side-chains 380 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 323 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 732 ASP Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 769 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 287 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 247 optimal weight: 8.9990 chunk 292 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 190 optimal weight: 9.9990 chunk 195 optimal weight: 0.0060 chunk 242 optimal weight: 20.0000 chunk 156 optimal weight: 1.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.124752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.098613 restraints weight = 67539.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.101721 restraints weight = 42029.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.102671 restraints weight = 27684.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.103507 restraints weight = 23296.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.104251 restraints weight = 19984.929| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23594 Z= 0.116 Angle : 0.624 12.830 32301 Z= 0.313 Chirality : 0.043 0.332 3924 Planarity : 0.004 0.062 4065 Dihedral : 5.288 59.312 3666 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.70 % Favored : 93.21 % Rotamer: Outliers : 2.59 % Allowed : 20.20 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 3136 helix: 1.23 (0.15), residues: 1232 sheet: -0.19 (0.28), residues: 379 loop : -1.77 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 523 TYR 0.030 0.001 TYR B 479 PHE 0.027 0.001 PHE B 637 TRP 0.010 0.001 TRP C 768 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00262 (23571) covalent geometry : angle 0.61618 (32247) SS BOND : bond 0.00597 ( 15) SS BOND : angle 2.42788 ( 30) hydrogen bonds : bond 0.03820 ( 986) hydrogen bonds : angle 4.48327 ( 2865) link_BETA1-4 : bond 0.00457 ( 3) link_BETA1-4 : angle 1.76005 ( 9) link_NAG-ASN : bond 0.00982 ( 5) link_NAG-ASN : angle 3.00343 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 343 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 400 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9102 (mt) REVERT: A 641 MET cc_start: 0.8762 (tmm) cc_final: 0.8394 (tmm) REVERT: A 642 ILE cc_start: 0.9499 (mm) cc_final: 0.8945 (mm) REVERT: A 650 ASN cc_start: 0.7971 (t0) cc_final: 0.7676 (t0) REVERT: B 101 ASP cc_start: 0.7471 (m-30) cc_final: 0.7089 (m-30) REVERT: B 157 MET cc_start: 0.8161 (ptt) cc_final: 0.7865 (ptm) REVERT: B 702 MET cc_start: 0.8146 (ptp) cc_final: 0.7826 (ptp) REVERT: C 237 MET cc_start: 0.7158 (ppp) cc_final: 0.6884 (pmm) REVERT: C 240 MET cc_start: 0.7649 (mmm) cc_final: 0.7243 (mmm) REVERT: C 354 MET cc_start: 0.7735 (tmm) cc_final: 0.7494 (tmm) REVERT: C 436 CYS cc_start: 0.6820 (m) cc_final: 0.6570 (m) REVERT: C 674 ASN cc_start: 0.8350 (t0) cc_final: 0.8062 (t0) REVERT: C 762 MET cc_start: 0.8514 (ptp) cc_final: 0.7891 (ptm) REVERT: D 558 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7595 (p) REVERT: D 702 MET cc_start: 0.7449 (mmm) cc_final: 0.7138 (mpp) REVERT: D 742 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7580 (mmm-85) outliers start: 58 outliers final: 45 residues processed: 379 average time/residue: 0.1204 time to fit residues: 78.8774 Evaluate side-chains 371 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 324 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 735 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 106 optimal weight: 2.9990 chunk 253 optimal weight: 30.0000 chunk 64 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 184 optimal weight: 0.0970 chunk 161 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 chunk 286 optimal weight: 0.0170 chunk 171 optimal weight: 4.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.124721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.098409 restraints weight = 68315.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.101692 restraints weight = 42661.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102490 restraints weight = 27960.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.103294 restraints weight = 24019.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103982 restraints weight = 20476.243| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23594 Z= 0.120 Angle : 0.634 11.816 32301 Z= 0.317 Chirality : 0.043 0.306 3924 Planarity : 0.004 0.085 4065 Dihedral : 5.166 56.210 3665 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.82 % Favored : 93.08 % Rotamer: Outliers : 2.50 % Allowed : 20.55 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 3136 helix: 1.28 (0.15), residues: 1224 sheet: -0.15 (0.28), residues: 379 loop : -1.74 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 742 TYR 0.028 0.001 TYR B 479 PHE 0.024 0.001 PHE B 637 TRP 0.009 0.001 TRP C 768 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00274 (23571) covalent geometry : angle 0.62617 (32247) SS BOND : bond 0.00603 ( 15) SS BOND : angle 2.59463 ( 30) hydrogen bonds : bond 0.03821 ( 986) hydrogen bonds : angle 4.47483 ( 2865) link_BETA1-4 : bond 0.00445 ( 3) link_BETA1-4 : angle 1.74295 ( 9) link_NAG-ASN : bond 0.00905 ( 5) link_NAG-ASN : angle 2.78107 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 340 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8332 (tpp) cc_final: 0.7288 (mmt) REVERT: A 400 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9116 (mt) REVERT: A 641 MET cc_start: 0.8761 (tmm) cc_final: 0.8401 (tmm) REVERT: A 642 ILE cc_start: 0.9483 (mm) cc_final: 0.8917 (mm) REVERT: A 650 ASN cc_start: 0.7969 (t0) cc_final: 0.7673 (t0) REVERT: B 101 ASP cc_start: 0.7444 (m-30) cc_final: 0.7091 (m-30) REVERT: B 157 MET cc_start: 0.8153 (ptt) cc_final: 0.7864 (ptm) REVERT: B 386 MET cc_start: 0.8683 (mmm) cc_final: 0.8429 (mmm) REVERT: B 654 MET cc_start: 0.8364 (tmt) cc_final: 0.8132 (tmt) REVERT: B 702 MET cc_start: 0.8132 (ptp) cc_final: 0.7821 (ptp) REVERT: C 154 MET cc_start: 0.8002 (mtp) cc_final: 0.7706 (mtp) REVERT: C 237 MET cc_start: 0.7195 (ppp) cc_final: 0.5102 (ttm) REVERT: C 240 MET cc_start: 0.7613 (mmm) cc_final: 0.7178 (mmm) REVERT: C 354 MET cc_start: 0.7695 (tmm) cc_final: 0.7463 (tmm) REVERT: C 436 CYS cc_start: 0.6796 (m) cc_final: 0.6573 (m) REVERT: C 674 ASN cc_start: 0.8324 (t0) cc_final: 0.8040 (t0) REVERT: C 762 MET cc_start: 0.8528 (ptp) cc_final: 0.7897 (ptm) REVERT: D 144 PHE cc_start: 0.8497 (m-10) cc_final: 0.8097 (m-10) REVERT: D 558 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7556 (p) REVERT: D 702 MET cc_start: 0.7411 (mmm) cc_final: 0.7124 (mpp) REVERT: D 742 ARG cc_start: 0.8236 (tpp80) cc_final: 0.7590 (mmm-85) outliers start: 56 outliers final: 49 residues processed: 378 average time/residue: 0.1254 time to fit residues: 82.5671 Evaluate side-chains 379 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 328 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 735 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 141 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 185 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.123110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.096876 restraints weight = 68036.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100096 restraints weight = 42533.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.100819 restraints weight = 28014.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.101674 restraints weight = 24084.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102226 restraints weight = 20633.144| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23594 Z= 0.163 Angle : 0.666 12.055 32301 Z= 0.337 Chirality : 0.044 0.284 3924 Planarity : 0.005 0.063 4065 Dihedral : 5.405 57.017 3665 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.59 % Favored : 92.32 % Rotamer: Outliers : 2.41 % Allowed : 21.04 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.15), residues: 3136 helix: 1.10 (0.15), residues: 1236 sheet: -0.52 (0.27), residues: 405 loop : -1.79 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 763 TYR 0.029 0.001 TYR B 479 PHE 0.024 0.002 PHE B 637 TRP 0.011 0.001 TRP B 559 HIS 0.008 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00376 (23571) covalent geometry : angle 0.65839 (32247) SS BOND : bond 0.00635 ( 15) SS BOND : angle 2.68310 ( 30) hydrogen bonds : bond 0.04287 ( 986) hydrogen bonds : angle 4.62215 ( 2865) link_BETA1-4 : bond 0.00374 ( 3) link_BETA1-4 : angle 1.91747 ( 9) link_NAG-ASN : bond 0.00901 ( 5) link_NAG-ASN : angle 2.81638 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 332 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9146 (mt) REVERT: A 641 MET cc_start: 0.8807 (tmm) cc_final: 0.8484 (tmm) REVERT: A 642 ILE cc_start: 0.9507 (mm) cc_final: 0.8957 (mm) REVERT: A 650 ASN cc_start: 0.8110 (t0) cc_final: 0.7801 (t0) REVERT: B 101 ASP cc_start: 0.7323 (m-30) cc_final: 0.6978 (m-30) REVERT: B 157 MET cc_start: 0.8132 (ptt) cc_final: 0.7858 (ptm) REVERT: B 386 MET cc_start: 0.8713 (mmm) cc_final: 0.8482 (mmm) REVERT: B 562 MET cc_start: 0.8949 (mmp) cc_final: 0.8702 (mmt) REVERT: B 654 MET cc_start: 0.8396 (tmt) cc_final: 0.8078 (tmt) REVERT: B 702 MET cc_start: 0.8297 (ptp) cc_final: 0.7971 (ptp) REVERT: C 240 MET cc_start: 0.7664 (mmm) cc_final: 0.7224 (mmm) REVERT: C 354 MET cc_start: 0.7703 (tmm) cc_final: 0.7477 (tmm) REVERT: C 436 CYS cc_start: 0.6708 (m) cc_final: 0.6491 (m) REVERT: C 504 GLU cc_start: 0.8105 (mp0) cc_final: 0.7780 (mp0) REVERT: C 674 ASN cc_start: 0.8405 (t0) cc_final: 0.8079 (t0) REVERT: C 762 MET cc_start: 0.8502 (ptp) cc_final: 0.7873 (ptm) REVERT: D 144 PHE cc_start: 0.8562 (m-10) cc_final: 0.8142 (m-10) REVERT: D 558 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7559 (p) REVERT: D 702 MET cc_start: 0.7482 (mmm) cc_final: 0.7166 (mpp) REVERT: D 742 ARG cc_start: 0.8255 (tpp80) cc_final: 0.7611 (mmm-85) outliers start: 54 outliers final: 50 residues processed: 366 average time/residue: 0.1191 time to fit residues: 75.9682 Evaluate side-chains 378 residues out of total 2746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 326 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 405 GLN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 735 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 179 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 164 optimal weight: 0.0040 chunk 34 optimal weight: 7.9990 chunk 302 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 293 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 312 optimal weight: 9.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN B 616 ASN ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.124895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.098672 restraints weight = 68418.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.101950 restraints weight = 42805.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102812 restraints weight = 27890.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103606 restraints weight = 23891.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.104097 restraints weight = 20408.375| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23594 Z= 0.117 Angle : 0.641 13.203 32301 Z= 0.319 Chirality : 0.043 0.427 3924 Planarity : 0.004 0.062 4065 Dihedral : 5.091 54.691 3665 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.60 % Favored : 93.30 % Rotamer: Outliers : 2.41 % Allowed : 21.40 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.15), residues: 3136 helix: 1.27 (0.15), residues: 1222 sheet: -0.27 (0.28), residues: 386 loop : -1.73 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 763 TYR 0.027 0.001 TYR B 479 PHE 0.022 0.001 PHE B 637 TRP 0.011 0.001 TRP C 768 HIS 0.005 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00265 (23571) covalent geometry : angle 0.63400 (32247) SS BOND : bond 0.00574 ( 15) SS BOND : angle 2.38512 ( 30) hydrogen bonds : bond 0.03725 ( 986) hydrogen bonds : angle 4.45942 ( 2865) link_BETA1-4 : bond 0.00454 ( 3) link_BETA1-4 : angle 1.68870 ( 9) link_NAG-ASN : bond 0.00892 ( 5) link_NAG-ASN : angle 2.58737 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3884.47 seconds wall clock time: 67 minutes 45.58 seconds (4065.58 seconds total)