Starting phenix.real_space_refine on Thu Mar 5 16:52:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7saa_24946/03_2026/7saa_24946.cif Found real_map, /net/cci-nas-00/data/ceres_data/7saa_24946/03_2026/7saa_24946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7saa_24946/03_2026/7saa_24946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7saa_24946/03_2026/7saa_24946.map" model { file = "/net/cci-nas-00/data/ceres_data/7saa_24946/03_2026/7saa_24946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7saa_24946/03_2026/7saa_24946.cif" } resolution = 2.97 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= 0.006 sd= 0.620 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 128 5.16 5 C 15128 2.51 5 N 3913 2.21 5 O 4449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s 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: 23618 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5937 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 437 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 15, 'HIS:plan': 4, 'GLU:plan': 14, 'GLN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 249 Chain: "B" Number of atoms: 5807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5807 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 414 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 24, 'HIS:plan': 5, 'PHE:plan': 5, 'ASN:plan1': 3, 'ARG:plan': 5, 'GLN:plan1': 7, 'TYR:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 296 Chain: "C" Number of atoms: 5910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5910 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 391 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 344 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 15, 'HIS:plan': 5, 'GLU:plan': 11, 'GLN:plan1': 7, 'PHE:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 7, 'TRP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 264 Chain: "D" Number of atoms: 5738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5738 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 485 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 24, 'HIS:plan': 5, 'PHE:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 5, 'GLN:plan1': 9, 'TYR:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 340 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: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 47 Unusual residues: {'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.34, per 1000 atoms: 0.23 Number of scatterers: 23618 At special positions: 0 Unit cell: (124.12, 154.08, 182.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 4449 8.00 N 3913 7.00 C 15128 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=2.53 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 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=2.03 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 436 " - pdb=" SG CYS C 455 " distance=2.18 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=1.42 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.02 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=1.88 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 B 901 " - " ASN B 491 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN C 368 " " NAG G 1 " - " ASN D 688 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 992.2 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: 5908 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 29 sheets defined 44.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.906A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 104 through 114 removed outlier: 4.143A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.676A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.503A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.856A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.661A pdb=" N ALA A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.569A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 removed outlier: 3.570A pdb=" N ARG A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.677A pdb=" N GLN A 525 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 584 removed outlier: 3.530A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 580 " --> pdb=" O MET A 576 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.583A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 657 removed outlier: 3.582A pdb=" N ILE A 631 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 694 removed outlier: 3.877A pdb=" N PHE A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.561A pdb=" N ARG A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.573A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 removed outlier: 3.669A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 810 through 826 removed outlier: 3.641A pdb=" N ALA A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 841 removed outlier: 4.079A pdb=" N LEU A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.027A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.741A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 removed outlier: 4.088A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.860A pdb=" N SER B 130 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.596A pdb=" N MET B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 3.531A pdb=" N GLU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.558A pdb=" N LYS B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.226A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 312 removed outlier: 3.534A pdb=" N ARG B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.595A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR B 330 " --> pdb=" O LYS B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 326 through 330' Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.554A pdb=" N ASN B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.547A pdb=" N ILE B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 517 through 522 removed outlier: 3.901A pdb=" N GLU B 521 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 522 " --> pdb=" O ARG B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 579 removed outlier: 4.056A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET B 565 " --> pdb=" O MET B 561 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 614 removed outlier: 3.527A pdb=" N ILE B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.513A pdb=" N ILE B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.586A pdb=" N ASN B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 706 removed outlier: 3.709A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 710 removed outlier: 3.944A pdb=" N ASN B 710 " --> pdb=" O GLY B 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.560A pdb=" N GLY B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.434A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.806A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 845 removed outlier: 4.018A pdb=" N MET B 818 " --> pdb=" O ASP B 814 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLY B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL B 821 " --> pdb=" O ASN B 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 86 removed outlier: 3.703A pdb=" N MET C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.886A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.895A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 147 removed outlier: 3.546A pdb=" N HIS C 146 " --> pdb=" O PRO C 143 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN C 147 " --> pdb=" O TYR C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 143 through 147' Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.886A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 214 removed outlier: 4.178A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 236 removed outlier: 3.974A pdb=" N VAL C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.629A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 296 removed outlier: 3.592A pdb=" N VAL C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 removed outlier: 3.631A pdb=" N LYS C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.197A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 removed outlier: 3.632A pdb=" N ASP C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 462 " --> pdb=" O PHE C 458 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 463 " --> pdb=" O CYS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.693A pdb=" N LEU C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.671A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 584 removed outlier: 3.735A pdb=" N VAL C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 580 " --> pdb=" O MET C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 615 removed outlier: 3.713A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP C 611 " --> pdb=" O MET C 607 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 657 removed outlier: 3.924A pdb=" N GLY C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 640 " --> pdb=" O TRP C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.783A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 removed outlier: 4.206A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.625A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.668A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 783 removed outlier: 3.583A pdb=" N LEU C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 809 through 811 No H-bonds generated for 'chain 'C' and resid 809 through 811' Processing helix chain 'C' and resid 812 through 841 removed outlier: 3.517A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 825 " --> pdb=" O ALA C 821 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE C 828 " --> pdb=" O ILE C 824 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 830 " --> pdb=" O ALA C 826 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG C 839 " --> pdb=" O ILE C 835 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS C 841 " --> pdb=" O TYR C 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 77 through 93 Processing helix chain 'D' and resid 106 through 119 removed outlier: 4.330A pdb=" N PHE D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 149 through 164 removed outlier: 4.154A pdb=" N MET D 161 " --> pdb=" O MET D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 removed outlier: 3.899A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (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 259 through 264 removed outlier: 4.327A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 311 removed outlier: 3.937A pdb=" N HIS D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 removed outlier: 3.782A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR D 330 " --> pdb=" O LYS D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 330' Processing helix chain 'D' and resid 334 through 339 Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.678A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 518 through 522 removed outlier: 3.691A pdb=" N GLU D 521 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 555 through 579 removed outlier: 3.588A pdb=" N LEU D 567 " --> pdb=" O PHE D 563 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 612 removed outlier: 3.696A pdb=" N ILE D 606 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 655 removed outlier: 3.580A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 638 " --> pdb=" O VAL D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 699 through 706 Processing helix chain 'D' and resid 707 through 710 removed outlier: 4.135A pdb=" N ASN D 710 " --> pdb=" O GLY D 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 707 through 710' Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.725A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 786 removed outlier: 4.686A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY D 785 " --> pdb=" O LEU D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.765A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 845 removed outlier: 3.735A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 3.765A pdb=" N VAL A 65 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 7.157A pdb=" N ILE A 163 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.822A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 478 removed outlier: 3.506A pdb=" N VAL A 401 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 514 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.941A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.424A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 73 removed outlier: 6.433A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 40 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 144 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 203 removed outlier: 8.075A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 227 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 280 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.541A 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 405 through 410 removed outlier: 4.416A pdb=" N LEU B 478 " --> pdb=" O PRO B 435 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ARG B 439 " --> pdb=" O LEU B 480 " (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 508 through 509 Processing sheet with id=AB5, first strand: chain 'B' and resid 530 through 532 removed outlier: 4.345A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.774A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 60 through 65 removed outlier: 3.631A pdb=" N GLN C 61 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C 63 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 194 through 197 removed outlier: 8.716A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AC1, first strand: chain 'C' and resid 473 through 478 Processing sheet with id=AC2, first strand: chain 'C' and resid 410 through 413 removed outlier: 3.568A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AC4, first strand: chain 'C' and resid 534 through 535 removed outlier: 4.059A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.941A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 67 through 73 removed outlier: 3.738A pdb=" N VAL D 42 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE D 126 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N PHE D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 198 through 205 removed outlier: 6.903A pdb=" N PHE D 169 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU D 201 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE D 227 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE D 257 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 418 through 421 removed outlier: 4.256A pdb=" N LEU D 478 " --> pdb=" O PRO D 435 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ARG D 439 " --> pdb=" O LEU D 480 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR D 479 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET D 508 " --> pdb=" O SER D 407 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD1, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.591A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.591A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 1067 hydrogen bonds defined for protein. 3063 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: 4.85 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 338 1.22 - 1.37: 7752 1.37 - 1.53: 12510 1.53 - 1.68: 3287 1.68 - 1.83: 217 Bond restraints: 24104 Sorted by residual: bond pdb=" C GLU C 406 " pdb=" O GLU C 406 " ideal model delta sigma weight residual 1.244 1.097 0.147 9.80e-03 1.04e+04 2.25e+02 bond pdb=" C GLN C 405 " pdb=" O GLN C 405 " ideal model delta sigma weight residual 1.235 1.069 0.166 1.13e-02 7.83e+03 2.15e+02 bond pdb=" C LEU D 736 " pdb=" O LEU D 736 " ideal model delta sigma weight residual 1.237 1.083 0.154 1.19e-02 7.06e+03 1.68e+02 bond pdb=" C GLN B 437 " pdb=" O GLN B 437 " ideal model delta sigma weight residual 1.234 1.074 0.160 1.25e-02 6.40e+03 1.64e+02 bond pdb=" C ILE D 408 " pdb=" O ILE D 408 " ideal model delta sigma weight residual 1.236 1.108 0.128 1.01e-02 9.80e+03 1.60e+02 ... (remaining 24099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.55: 32622 5.55 - 11.09: 214 11.09 - 16.64: 26 16.64 - 22.19: 1 22.19 - 27.74: 3 Bond angle restraints: 32866 Sorted by residual: angle pdb=" N GLU C 406 " pdb=" CA GLU C 406 " pdb=" C GLU C 406 " ideal model delta sigma weight residual 113.16 133.70 -20.54 1.42e+00 4.96e-01 2.09e+02 angle pdb=" C ASN B 495 " pdb=" CA ASN B 495 " pdb=" CB ASN B 495 " ideal model delta sigma weight residual 111.22 83.48 27.74 2.02e+00 2.45e-01 1.89e+02 angle pdb=" C ASP A 690 " pdb=" CA ASP A 690 " pdb=" CB ASP A 690 " ideal model delta sigma weight residual 110.85 88.62 22.23 1.70e+00 3.46e-01 1.71e+02 angle pdb=" CA GLU C 406 " pdb=" C GLU C 406 " pdb=" O GLU C 406 " ideal model delta sigma weight residual 118.34 106.63 11.71 9.70e-01 1.06e+00 1.46e+02 angle pdb=" C LYS A 743 " pdb=" N CYS A 744 " pdb=" CA CYS A 744 " ideal model delta sigma weight residual 120.38 135.04 -14.66 1.37e+00 5.33e-01 1.14e+02 ... (remaining 32861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 13637 23.98 - 47.96: 692 47.96 - 71.94: 105 71.94 - 95.92: 17 95.92 - 119.90: 6 Dihedral angle restraints: 14457 sinusoidal: 5304 harmonic: 9153 Sorted by residual: dihedral pdb=" C ASN B 495 " pdb=" N ASN B 495 " pdb=" CA ASN B 495 " pdb=" CB ASN B 495 " ideal model delta harmonic sigma weight residual -122.60 -88.33 -34.27 0 2.50e+00 1.60e-01 1.88e+02 dihedral pdb=" N SER A 610 " pdb=" C SER A 610 " pdb=" CA SER A 610 " pdb=" CB SER A 610 " ideal model delta harmonic sigma weight residual 122.80 151.06 -28.26 0 2.50e+00 1.60e-01 1.28e+02 dihedral pdb=" C SER A 610 " pdb=" N SER A 610 " pdb=" CA SER A 610 " pdb=" CB SER A 610 " ideal model delta harmonic sigma weight residual -122.60 -148.76 26.16 0 2.50e+00 1.60e-01 1.10e+02 ... (remaining 14454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.241: 3814 0.241 - 0.482: 97 0.482 - 0.723: 4 0.723 - 0.964: 2 0.964 - 1.205: 1 Chirality restraints: 3918 Sorted by residual: chirality pdb=" CA SER A 610 " pdb=" N SER A 610 " pdb=" C SER A 610 " pdb=" CB SER A 610 " both_signs ideal model delta sigma weight residual False 2.51 1.31 1.21 2.00e-01 2.50e+01 3.63e+01 chirality pdb=" CB VAL D 523 " pdb=" CA VAL D 523 " pdb=" CG1 VAL D 523 " pdb=" CG2 VAL D 523 " both_signs ideal model delta sigma weight residual False -2.63 -1.82 -0.81 2.00e-01 2.50e+01 1.64e+01 chirality pdb=" CA LEU C 603 " pdb=" N LEU C 603 " pdb=" C LEU C 603 " pdb=" CB LEU C 603 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.52e+01 ... (remaining 3915 not shown) Planarity restraints: 4170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 678 " 0.032 2.00e-02 2.50e+03 6.58e-02 4.32e+01 pdb=" C SER D 678 " -0.114 2.00e-02 2.50e+03 pdb=" O SER D 678 " 0.042 2.00e-02 2.50e+03 pdb=" N PRO D 679 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 269 " -0.096 5.00e-02 4.00e+02 1.42e-01 3.23e+01 pdb=" N PRO D 270 " 0.246 5.00e-02 4.00e+02 pdb=" CA PRO D 270 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO D 270 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 706 " 0.027 2.00e-02 2.50e+03 5.58e-02 3.11e+01 pdb=" C MET A 706 " -0.096 2.00e-02 2.50e+03 pdb=" O MET A 706 " 0.037 2.00e-02 2.50e+03 pdb=" N GLU A 707 " 0.032 2.00e-02 2.50e+03 ... (remaining 4167 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 39 2.36 - 2.99: 12205 2.99 - 3.63: 33144 3.63 - 4.26: 48704 4.26 - 4.90: 83287 Nonbonded interactions: 177379 Sorted by model distance: nonbonded pdb=" NH2 ARG A 695 " pdb=" OE1 GLN D 782 " model vdw 1.720 3.120 nonbonded pdb=" OG SER A 610 " pdb=" NE1 TRP A 636 " model vdw 1.736 3.120 nonbonded pdb=" NH1 ARG A 115 " pdb=" CD1 LEU A 135 " model vdw 2.007 3.540 nonbonded pdb=" CE2 PHE C 554 " pdb=" CD1 LEU C 819 " model vdw 2.007 3.760 nonbonded pdb=" CG2 THR B 544 " pdb=" CG2 VAL B 808 " model vdw 2.052 3.880 ... (remaining 177374 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 98 or (resid 99 through 102 and (name N or name CA or name C or name O or nam \ e CB )) or resid 103 through 177 or (resid 178 through 179 and (name N or name C \ A or name C or name O or name CB )) or resid 180 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 (name N or name CA or name C or name \ O or name CB )) or resid 292 or (resid 293 through 294 and (name N or name CA or \ name C or name O or name CB )) or resid 295 through 325 or (resid 326 and (name \ N or name CA or name C or name O or name CB )) or resid 327 through 550 or (res \ id 551 through 552 and (name N or name CA or name C or name O or name CB )) or r \ esid 553 through 555 or (resid 556 and (name N or name CA or name C or name O or \ name CB )) or resid 557 through 575 or (resid 576 and (name N or name CA or nam \ e C or name O or name CB )) or resid 577 through 660 or (resid 661 and (name N o \ r name CA or name C or name O or name CB )) or resid 662 through 677 or (resid 6 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 679 through \ 798 or (resid 799 and (name N or name CA or name C or name O or name CB )) or r \ esid 800 through 902 or resid 904)) 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 82 or (resid 83 and ( \ name N or name CA or name C or name O or name CB )) or resid 84 through 155 or ( \ resid 156 and (name N or name CA or name C or name O or name CB )) or resid 157 \ through 184 or (resid 185 through 186 and (name N or name CA or name C or name O \ or name CB )) or resid 187 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 (resid 272 and (name \ N or name CA or name C or name O or name CB )) or resid 273 through 386 or (resi \ d 387 and (name N or name CA or name C or name O or name CB )) or resid 388 thro \ ugh 633 or (resid 634 and (name N or name CA or name C or name O or name CB )) o \ r resid 635 through 903)) } ncs_group { reference = (chain 'B' and (resid 34 through 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 or (resid 69 and (name N or name CA or nam \ e C or name O or name CB )) or resid 70 through 117 or (resid 118 and (name N or \ name CA or name C or name O or name CB )) or resid 119 through 136 or (resid 13 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 138 or (resi \ d 139 and (name N or name CA or name C or name O or name CB )) or resid 140 thro \ ugh 179 or (resid 180 and (name N or name CA or name C or name O or name CB )) o \ r resid 181 through 212 or (resid 213 and (name N or name CA or name C or name O \ or name CB )) or resid 214 through 264 or (resid 265 and (name N or name CA or \ name C or name O or name CB )) or resid 266 through 305 or (resid 306 through 30 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 309 or (resi \ d 310 through 311 and (name N or name CA or name C or name O or name CB )) or re \ sid 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 nam \ e CA or name C or name O or name CB )) or resid 335 through 346 or (resid 347 an \ d (name N or name CA or name C or name O or name CB )) or resid 348 through 381 \ or (resid 382 and (name N or name CA or name C or name O or name CB )) or resid \ 383 through 440 or (resid 441 and (name N or name CA or name C or name O or name \ CB )) or resid 442 through 469 or (resid 470 and (name N or name CA or name C o \ r name O or name CB )) or resid 471 through 556 or (resid 557 and (name N or nam \ e CA or name C or name O or name CB )) or resid 558 through 562 or (resid 563 an \ d (name N or name CA or name C or name O or name CB )) or resid 564 through 603 \ or (resid 604 through 605 and (name N or name CA or name C or name O or name CB \ )) or resid 606 through 658 or (resid 659 and (name N or name CA or name C or na \ me O or name CB )) or resid 660 through 724 or (resid 725 and (name N or name CA \ or name C or name O or name CB )) or resid 726 through 802 or (resid 803 throug \ h 807 and (name N or name CA or name C or name O or name CB )) or resid 808 thro \ ugh 811 or (resid 812 and (name N or name CA or name C or name O or name CB )) o \ r resid 813 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 an \ d (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 or (resid 838 through 845 and (name N or name CA or name C or name O or name \ CB )) or resid 901 through 902)) selection = (chain 'D' and (resid 34 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 197 or (resid 198 and (name N or n \ ame CA or name C or name O or name CB )) or resid 199 or (resid 200 through 201 \ and (name N or name CA or name C or name O or name CB )) or resid 202 through 20 \ 6 or (resid 207 and (name N or name CA or name C or name O or name CB )) or resi \ d 208 or (resid 209 through 211 and (name N or name CA or name C or name O or na \ me CB )) or resid 212 through 241 or (resid 242 and (name N or name CA or name C \ or name O or name CB )) or resid 243 through 502 or (resid 503 and (name N or n \ ame CA or name C or name O or name CB )) or resid 504 through 530 or (resid 531 \ and (name N or name CA or name C or name O or name CB )) or resid 532 through 56 \ 0 or (resid 561 and (name N or name CA or name C or name O or name CB )) or resi \ d 562 through 574 or (resid 575 and (name N or name CA or name C or name O or na \ me CB )) or resid 576 through 661 or (resid 662 and (name N or name CA or name C \ or name O or name CB )) or resid 663 through 672 or (resid 673 and (name N or n \ ame CA or name C or name O or name CB )) or resid 674 through 901 or resid 903)) \ } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.920 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 22.090 Find NCS groups from input model: 0.570 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:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 : 0.013 0.616 24127 Z= 0.860 Angle : 1.205 35.324 32920 Z= 0.759 Chirality : 0.079 1.205 3918 Planarity : 0.008 0.142 4165 Dihedral : 14.407 119.897 8504 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.85 % Favored : 94.90 % Rotamer: Outliers : 2.99 % Allowed : 2.40 % Favored : 94.61 % Cbeta Deviations : 1.49 % 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: -0.87 (0.15), residues: 3136 helix: 0.41 (0.14), residues: 1228 sheet: 0.01 (0.27), residues: 416 loop : -1.61 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 755 TYR 0.033 0.002 TYR A 692 PHE 0.033 0.002 PHE C 758 TRP 0.024 0.002 TRP C 611 HIS 0.008 0.001 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.01152 (24104) covalent geometry : angle 1.16147 (32866) SS BOND : bond 0.21243 ( 15) SS BOND : angle 10.46182 ( 30) hydrogen bonds : bond 0.24724 ( 1063) hydrogen bonds : angle 7.39696 ( 3063) link_BETA1-4 : bond 0.00360 ( 3) link_BETA1-4 : angle 1.28570 ( 9) link_NAG-ASN : bond 0.00357 ( 5) link_NAG-ASN : angle 3.07511 ( 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 458 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 387 time to evaluate : 0.984 Fit side-chains REVERT: B 180 GLN cc_start: 0.7753 (tp40) cc_final: 0.7439 (pm20) REVERT: B 621 GLN cc_start: 0.7499 (tt0) cc_final: 0.7128 (mp10) REVERT: B 730 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.8997 (mm) REVERT: B 814 ASP cc_start: 0.7144 (m-30) cc_final: 0.6776 (p0) REVERT: B 824 MET cc_start: 0.5923 (mmp) cc_final: 0.5381 (mmt) REVERT: D 798 THR cc_start: 0.8938 (t) cc_final: 0.8723 (m) outliers start: 71 outliers final: 47 residues processed: 449 average time/residue: 0.5378 time to fit residues: 281.4693 Evaluate side-chains 334 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 286 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 608 TRP Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 708 LYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 696 GLN Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 700 SER Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 177 PRO Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 735 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 313 ASN A 742 GLN A 796 GLN B 437 GLN B 495 ASN B 656 GLN C 313 ASN C 696 GLN C 770 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.164416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.121170 restraints weight = 35097.329| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.86 r_work: 0.3091 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 24127 Z= 0.170 Angle : 0.638 7.933 32920 Z= 0.338 Chirality : 0.046 0.232 3918 Planarity : 0.006 0.122 4165 Dihedral : 8.717 102.877 3722 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.13 % Favored : 94.64 % Rotamer: Outliers : 3.79 % Allowed : 11.76 % Favored : 84.45 % 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: 0.93 (0.15), residues: 1270 sheet: 0.00 (0.27), residues: 422 loop : -1.60 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 695 TYR 0.024 0.001 TYR A 795 PHE 0.026 0.002 PHE B 642 TRP 0.015 0.001 TRP D 610 HIS 0.007 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00402 (24104) covalent geometry : angle 0.63419 (32866) SS BOND : bond 0.00957 ( 15) SS BOND : angle 1.78391 ( 30) hydrogen bonds : bond 0.06119 ( 1063) hydrogen bonds : angle 5.26457 ( 3063) link_BETA1-4 : bond 0.00452 ( 3) link_BETA1-4 : angle 1.02898 ( 9) link_NAG-ASN : bond 0.00385 ( 5) link_NAG-ASN : angle 2.51534 ( 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 409 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 319 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 89 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7289 (ttt) REVERT: B 180 GLN cc_start: 0.7935 (tp40) cc_final: 0.7599 (pm20) REVERT: B 622 ASN cc_start: 0.6615 (OUTLIER) cc_final: 0.6402 (m110) REVERT: B 721 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9067 (mp) REVERT: B 814 ASP cc_start: 0.7125 (m-30) cc_final: 0.6800 (p0) REVERT: B 824 MET cc_start: 0.5975 (mmp) cc_final: 0.5429 (mmt) REVERT: C 181 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7829 (tm-30) outliers start: 90 outliers final: 41 residues processed: 376 average time/residue: 0.5410 time to fit residues: 238.6674 Evaluate side-chains 331 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 287 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 663 ARG Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 622 ASN Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 753 SER Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 735 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 36 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 239 optimal weight: 8.9990 chunk 235 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 145 optimal weight: 0.0570 chunk 97 optimal weight: 5.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 276 ASN A 313 ASN A 742 GLN A 796 GLN C 313 ASN D 152 GLN D 348 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.161738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116080 restraints weight = 34915.575| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.93 r_work: 0.3053 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 24127 Z= 0.230 Angle : 0.684 9.770 32920 Z= 0.361 Chirality : 0.048 0.268 3918 Planarity : 0.006 0.120 4165 Dihedral : 7.294 100.387 3670 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.80 % Favored : 93.97 % Rotamer: Outliers : 4.72 % Allowed : 13.99 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.67 (0.15), residues: 3136 helix: 0.91 (0.15), residues: 1271 sheet: -0.20 (0.26), residues: 429 loop : -1.82 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 115 TYR 0.023 0.002 TYR C 109 PHE 0.031 0.002 PHE C 753 TRP 0.015 0.002 TRP B 197 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00569 (24104) covalent geometry : angle 0.67627 (32866) SS BOND : bond 0.00860 ( 15) SS BOND : angle 3.05389 ( 30) hydrogen bonds : bond 0.05996 ( 1063) hydrogen bonds : angle 4.99896 ( 3063) link_BETA1-4 : bond 0.00336 ( 3) link_BETA1-4 : angle 1.14461 ( 9) link_NAG-ASN : bond 0.00440 ( 5) link_NAG-ASN : angle 2.55136 ( 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 419 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 307 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 89 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7402 (ttt) REVERT: B 180 GLN cc_start: 0.7876 (tp40) cc_final: 0.7514 (pm20) REVERT: B 439 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7869 (ptp-170) REVERT: B 562 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8204 (ppp) REVERT: B 721 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9020 (mp) REVERT: B 814 ASP cc_start: 0.7390 (m-30) cc_final: 0.6900 (p0) REVERT: B 824 MET cc_start: 0.6169 (mmp) cc_final: 0.5953 (mmp) REVERT: C 181 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7839 (tm-30) REVERT: C 350 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6420 (mp-120) REVERT: D 62 LEU cc_start: 0.4691 (OUTLIER) cc_final: 0.4393 (mt) REVERT: D 86 CYS cc_start: 0.7016 (p) cc_final: 0.6038 (t) REVERT: D 430 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8234 (mmt) outliers start: 112 outliers final: 47 residues processed: 381 average time/residue: 0.5303 time to fit residues: 238.3933 Evaluate side-chains 344 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 290 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 663 ARG Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 251 GLU Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 421 SER Chi-restraints excluded: chain D residue 430 MET Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 735 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 307 optimal weight: 0.6980 chunk 234 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 chunk 306 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.164553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123662 restraints weight = 34925.048| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.14 r_work: 0.3077 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 24127 Z= 0.120 Angle : 0.574 11.508 32920 Z= 0.301 Chirality : 0.043 0.232 3918 Planarity : 0.005 0.119 4165 Dihedral : 6.512 100.493 3658 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.66 % Favored : 95.12 % Rotamer: Outliers : 3.62 % Allowed : 16.10 % Favored : 80.28 % 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: -0.36 (0.15), residues: 3136 helix: 1.20 (0.15), residues: 1280 sheet: 0.01 (0.26), residues: 411 loop : -1.71 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 390 TYR 0.015 0.001 TYR A 795 PHE 0.030 0.001 PHE B 550 TRP 0.011 0.001 TRP D 610 HIS 0.004 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00286 (24104) covalent geometry : angle 0.56716 (32866) SS BOND : bond 0.00829 ( 15) SS BOND : angle 2.54103 ( 30) hydrogen bonds : bond 0.04224 ( 1063) hydrogen bonds : angle 4.69188 ( 3063) link_BETA1-4 : bond 0.00466 ( 3) link_BETA1-4 : angle 1.14963 ( 9) link_NAG-ASN : bond 0.00438 ( 5) link_NAG-ASN : angle 2.41666 ( 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 397 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 311 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 157 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8384 (mtp) REVERT: B 180 GLN cc_start: 0.7878 (tp40) cc_final: 0.7642 (pm20) REVERT: B 439 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7978 (ptp-170) REVERT: B 562 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8222 (ppp) REVERT: B 721 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8997 (mm) REVERT: B 814 ASP cc_start: 0.7231 (m-30) cc_final: 0.6806 (p0) REVERT: B 824 MET cc_start: 0.6115 (mmp) cc_final: 0.5889 (mmp) REVERT: C 181 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7915 (tm-30) REVERT: C 350 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.6482 (mp-120) REVERT: D 62 LEU cc_start: 0.4541 (OUTLIER) cc_final: 0.4192 (mt) REVERT: D 189 THR cc_start: 0.9260 (m) cc_final: 0.9031 (m) REVERT: D 233 THR cc_start: 0.5861 (OUTLIER) cc_final: 0.5473 (t) REVERT: D 531 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: D 715 ASP cc_start: 0.8797 (p0) cc_final: 0.8566 (p0) outliers start: 86 outliers final: 35 residues processed: 366 average time/residue: 0.5161 time to fit residues: 222.2620 Evaluate side-chains 334 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 291 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 663 ARG Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 735 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 276 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 81 optimal weight: 40.0000 chunk 121 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 GLN A 556 GLN C 313 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.163109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118856 restraints weight = 34712.134| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.91 r_work: 0.3064 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 24127 Z= 0.159 Angle : 0.608 11.540 32920 Z= 0.318 Chirality : 0.045 0.223 3918 Planarity : 0.005 0.119 4165 Dihedral : 6.388 97.544 3652 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.23 % Favored : 94.55 % Rotamer: Outliers : 3.83 % Allowed : 17.15 % Favored : 79.01 % 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: -0.39 (0.15), residues: 3136 helix: 1.21 (0.15), residues: 1274 sheet: -0.13 (0.25), residues: 428 loop : -1.70 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 390 TYR 0.019 0.001 TYR C 109 PHE 0.034 0.002 PHE B 550 TRP 0.013 0.001 TRP D 610 HIS 0.005 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00394 (24104) covalent geometry : angle 0.60315 (32866) SS BOND : bond 0.00657 ( 15) SS BOND : angle 2.02303 ( 30) hydrogen bonds : bond 0.04741 ( 1063) hydrogen bonds : angle 4.66034 ( 3063) link_BETA1-4 : bond 0.00404 ( 3) link_BETA1-4 : angle 1.10264 ( 9) link_NAG-ASN : bond 0.00431 ( 5) link_NAG-ASN : angle 2.44991 ( 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 388 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 297 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8603 (tt0) cc_final: 0.8291 (mt-10) REVERT: A 744 CYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6889 (m) REVERT: B 86 CYS cc_start: 0.5694 (OUTLIER) cc_final: 0.5295 (m) REVERT: B 123 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7135 (pt) REVERT: B 157 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8375 (mtp) REVERT: B 180 GLN cc_start: 0.7884 (tp40) cc_final: 0.7575 (pm20) REVERT: B 439 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7980 (ptp-170) REVERT: B 562 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8249 (ppp) REVERT: B 721 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9005 (mm) REVERT: B 788 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8621 (mm-30) REVERT: B 814 ASP cc_start: 0.7241 (m-30) cc_final: 0.6798 (p0) REVERT: B 824 MET cc_start: 0.6212 (mmp) cc_final: 0.5984 (mmp) REVERT: C 181 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7858 (tm-30) REVERT: C 350 GLN cc_start: 0.6977 (OUTLIER) cc_final: 0.6433 (mp-120) REVERT: D 62 LEU cc_start: 0.4759 (OUTLIER) cc_final: 0.4386 (mt) REVERT: D 86 CYS cc_start: 0.6844 (p) cc_final: 0.6309 (m) REVERT: D 233 THR cc_start: 0.5913 (OUTLIER) cc_final: 0.5517 (t) REVERT: D 430 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8135 (mmt) REVERT: D 531 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8096 (tm-30) REVERT: D 715 ASP cc_start: 0.8794 (p0) cc_final: 0.8579 (p0) outliers start: 91 outliers final: 45 residues processed: 358 average time/residue: 0.5115 time to fit residues: 217.6355 Evaluate side-chains 350 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 292 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 663 ARG Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 750 THR Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 430 MET Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 735 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 120 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 302 optimal weight: 2.9990 chunk 257 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 164 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 220 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 313 ASN A 556 GLN C 313 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.164423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123427 restraints weight = 34735.596| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.11 r_work: 0.3081 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 24127 Z= 0.125 Angle : 0.581 9.993 32920 Z= 0.301 Chirality : 0.043 0.218 3918 Planarity : 0.005 0.118 4165 Dihedral : 6.123 95.067 3650 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.56 % Favored : 95.22 % Rotamer: Outliers : 3.46 % Allowed : 18.25 % Favored : 78.30 % 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: -0.21 (0.15), residues: 3136 helix: 1.37 (0.15), residues: 1267 sheet: 0.08 (0.26), residues: 410 loop : -1.64 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 390 TYR 0.016 0.001 TYR A 795 PHE 0.037 0.001 PHE B 550 TRP 0.011 0.001 TRP D 610 HIS 0.003 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00306 (24104) covalent geometry : angle 0.57652 (32866) SS BOND : bond 0.00546 ( 15) SS BOND : angle 1.69037 ( 30) hydrogen bonds : bond 0.04014 ( 1063) hydrogen bonds : angle 4.51861 ( 3063) link_BETA1-4 : bond 0.00420 ( 3) link_BETA1-4 : angle 1.12551 ( 9) link_NAG-ASN : bond 0.00443 ( 5) link_NAG-ASN : angle 2.49210 ( 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 394 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 312 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8608 (tt0) cc_final: 0.8354 (mt-10) REVERT: A 290 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7331 (tp40) REVERT: A 744 CYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6868 (m) REVERT: B 86 CYS cc_start: 0.5884 (p) cc_final: 0.5554 (m) REVERT: B 157 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8435 (mtp) REVERT: B 180 GLN cc_start: 0.7965 (tp40) cc_final: 0.7647 (pm20) REVERT: B 439 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7982 (ptp-170) REVERT: B 562 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8271 (ppp) REVERT: B 721 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8978 (mm) REVERT: B 814 ASP cc_start: 0.7251 (m-30) cc_final: 0.6845 (p0) REVERT: B 824 MET cc_start: 0.6319 (mmp) cc_final: 0.6090 (mmp) REVERT: C 181 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 350 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6481 (mp-120) REVERT: C 616 ASN cc_start: 0.8207 (p0) cc_final: 0.7943 (t0) REVERT: D 86 CYS cc_start: 0.6942 (p) cc_final: 0.6543 (m) REVERT: D 159 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8618 (m-40) REVERT: D 233 THR cc_start: 0.5912 (OUTLIER) cc_final: 0.5505 (t) REVERT: D 430 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8197 (mmt) REVERT: D 531 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: D 715 ASP cc_start: 0.8828 (p0) cc_final: 0.8580 (p0) outliers start: 82 outliers final: 35 residues processed: 368 average time/residue: 0.5114 time to fit residues: 223.7447 Evaluate side-chains 345 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 299 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 663 ARG Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 430 MET Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 735 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 117 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 284 optimal weight: 0.0570 chunk 39 optimal weight: 8.9990 chunk 221 optimal weight: 0.8980 chunk 109 optimal weight: 0.0970 chunk 313 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 310 optimal weight: 7.9990 chunk 184 optimal weight: 0.0980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 146 HIS A 556 GLN C 313 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.166931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115977 restraints weight = 35057.664| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.74 r_work: 0.3081 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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 : 0.002 0.096 24127 Z= 0.104 Angle : 0.560 9.563 32920 Z= 0.287 Chirality : 0.042 0.212 3918 Planarity : 0.005 0.119 4165 Dihedral : 5.723 91.951 3649 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.53 % Favored : 95.25 % Rotamer: Outliers : 2.57 % Allowed : 19.76 % Favored : 77.67 % 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: -0.03 (0.15), residues: 3136 helix: 1.47 (0.15), residues: 1279 sheet: 0.31 (0.27), residues: 406 loop : -1.56 (0.16), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 489 TYR 0.019 0.001 TYR C 261 PHE 0.040 0.001 PHE B 550 TRP 0.012 0.001 TRP B 610 HIS 0.002 0.000 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00249 (24104) covalent geometry : angle 0.55605 (32866) SS BOND : bond 0.00437 ( 15) SS BOND : angle 1.26808 ( 30) hydrogen bonds : bond 0.03281 ( 1063) hydrogen bonds : angle 4.37621 ( 3063) link_BETA1-4 : bond 0.00538 ( 3) link_BETA1-4 : angle 1.09151 ( 9) link_NAG-ASN : bond 0.00438 ( 5) link_NAG-ASN : angle 2.61839 ( 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 379 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 318 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7118 (m-30) cc_final: 0.6909 (m-30) REVERT: A 192 GLU cc_start: 0.8580 (tt0) cc_final: 0.8341 (mt-10) REVERT: A 290 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7152 (tp40) REVERT: A 489 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6777 (ptp-110) REVERT: A 744 CYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6577 (m) REVERT: B 157 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8361 (mtp) REVERT: B 180 GLN cc_start: 0.7871 (tp40) cc_final: 0.7460 (pm20) REVERT: B 358 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7565 (ttt) REVERT: B 439 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8083 (ptp-170) REVERT: B 562 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8157 (ppp) REVERT: B 814 ASP cc_start: 0.7410 (m-30) cc_final: 0.6880 (p0) REVERT: C 181 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7824 (tm-30) REVERT: C 616 ASN cc_start: 0.8007 (p0) cc_final: 0.7774 (t0) REVERT: D 86 CYS cc_start: 0.7186 (p) cc_final: 0.6839 (m) REVERT: D 189 THR cc_start: 0.9198 (m) cc_final: 0.8973 (m) REVERT: D 233 THR cc_start: 0.5596 (OUTLIER) cc_final: 0.5210 (t) REVERT: D 430 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8077 (mmt) REVERT: D 531 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: D 715 ASP cc_start: 0.8802 (p0) cc_final: 0.8599 (p0) outliers start: 61 outliers final: 27 residues processed: 361 average time/residue: 0.5248 time to fit residues: 223.9671 Evaluate side-chains 333 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 663 ARG Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 430 MET Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 735 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 307 optimal weight: 0.0570 chunk 93 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 162 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 GLN A 313 ASN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN C 650 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.165833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125283 restraints weight = 34891.514| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.04 r_work: 0.3125 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 24127 Z= 0.119 Angle : 0.578 9.943 32920 Z= 0.294 Chirality : 0.043 0.213 3918 Planarity : 0.005 0.119 4165 Dihedral : 5.595 86.905 3647 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.62 % Favored : 95.18 % Rotamer: Outliers : 2.87 % Allowed : 20.23 % Favored : 76.91 % 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: -0.03 (0.15), residues: 3136 helix: 1.51 (0.15), residues: 1279 sheet: 0.28 (0.27), residues: 391 loop : -1.56 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 489 TYR 0.014 0.001 TYR B 646 PHE 0.042 0.001 PHE B 550 TRP 0.009 0.001 TRP B 285 HIS 0.003 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00295 (24104) covalent geometry : angle 0.57363 (32866) SS BOND : bond 0.00495 ( 15) SS BOND : angle 1.54953 ( 30) hydrogen bonds : bond 0.03569 ( 1063) hydrogen bonds : angle 4.35891 ( 3063) link_BETA1-4 : bond 0.00399 ( 3) link_BETA1-4 : angle 1.07028 ( 9) link_NAG-ASN : bond 0.00424 ( 5) link_NAG-ASN : angle 2.66879 ( 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 372 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 304 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8476 (tt0) cc_final: 0.8274 (mt-10) REVERT: A 290 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7340 (tp40) REVERT: A 744 CYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6698 (m) REVERT: B 142 MET cc_start: 0.8212 (mtp) cc_final: 0.7725 (mmm) REVERT: B 157 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8345 (mtp) REVERT: B 168 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8702 (mm) REVERT: B 180 GLN cc_start: 0.7922 (tp40) cc_final: 0.7653 (pm20) REVERT: B 408 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8278 (mm) REVERT: B 439 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8030 (ptp-170) REVERT: B 562 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8276 (ppp) REVERT: B 814 ASP cc_start: 0.7269 (m-30) cc_final: 0.6888 (p0) REVERT: C 181 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7784 (tm-30) REVERT: C 616 ASN cc_start: 0.8136 (p0) cc_final: 0.7931 (t0) REVERT: D 89 MET cc_start: 0.6899 (ptm) cc_final: 0.5983 (ppp) REVERT: D 189 THR cc_start: 0.9252 (m) cc_final: 0.9039 (m) REVERT: D 233 THR cc_start: 0.5972 (OUTLIER) cc_final: 0.5563 (t) REVERT: D 430 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8128 (mmt) REVERT: D 531 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: D 715 ASP cc_start: 0.8708 (p0) cc_final: 0.8477 (p0) outliers start: 68 outliers final: 34 residues processed: 346 average time/residue: 0.5049 time to fit residues: 206.3232 Evaluate side-chains 338 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 294 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 663 ARG Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 430 MET Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 686 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 123 optimal weight: 0.7980 chunk 221 optimal weight: 0.9980 chunk 240 optimal weight: 0.0070 chunk 290 optimal weight: 7.9990 chunk 276 optimal weight: 0.0670 chunk 165 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 273 optimal weight: 0.9990 chunk 238 optimal weight: 30.0000 chunk 197 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 GLN A 313 ASN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.166938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114844 restraints weight = 35174.685| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.64 r_work: 0.3112 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 24127 Z= 0.105 Angle : 0.570 10.865 32920 Z= 0.289 Chirality : 0.042 0.211 3918 Planarity : 0.005 0.119 4165 Dihedral : 5.333 80.100 3646 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.66 % Favored : 95.18 % Rotamer: Outliers : 2.49 % Allowed : 20.65 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.07 (0.15), residues: 3136 helix: 1.59 (0.15), residues: 1280 sheet: 0.23 (0.26), residues: 418 loop : -1.50 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 260 TYR 0.018 0.001 TYR C 261 PHE 0.043 0.001 PHE B 550 TRP 0.011 0.001 TRP B 285 HIS 0.002 0.000 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00257 (24104) covalent geometry : angle 0.56473 (32866) SS BOND : bond 0.00482 ( 15) SS BOND : angle 1.65517 ( 30) hydrogen bonds : bond 0.03216 ( 1063) hydrogen bonds : angle 4.29046 ( 3063) link_BETA1-4 : bond 0.00449 ( 3) link_BETA1-4 : angle 1.03496 ( 9) link_NAG-ASN : bond 0.00435 ( 5) link_NAG-ASN : angle 2.81207 ( 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 368 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 309 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8460 (tt0) cc_final: 0.8255 (mt-10) REVERT: A 290 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7171 (tp40) REVERT: A 744 CYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6603 (m) REVERT: B 142 MET cc_start: 0.7558 (mtp) cc_final: 0.7243 (mmm) REVERT: B 168 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8662 (mm) REVERT: B 180 GLN cc_start: 0.7805 (tp40) cc_final: 0.7516 (pm20) REVERT: B 358 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7609 (ttt) REVERT: B 562 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8208 (ppp) REVERT: C 181 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7667 (tm-30) REVERT: C 237 MET cc_start: 0.8549 (tpp) cc_final: 0.8328 (ttt) REVERT: C 616 ASN cc_start: 0.8086 (p0) cc_final: 0.7859 (t0) REVERT: D 89 MET cc_start: 0.7109 (ptm) cc_final: 0.6059 (ppp) REVERT: D 159 ASN cc_start: 0.8802 (OUTLIER) cc_final: 0.8554 (m-40) REVERT: D 189 THR cc_start: 0.9240 (m) cc_final: 0.9017 (m) REVERT: D 233 THR cc_start: 0.5718 (OUTLIER) cc_final: 0.5363 (t) REVERT: D 430 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7985 (mmt) REVERT: D 531 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8219 (tm-30) REVERT: D 715 ASP cc_start: 0.8726 (p0) cc_final: 0.8510 (p0) outliers start: 59 outliers final: 34 residues processed: 346 average time/residue: 0.5097 time to fit residues: 208.6253 Evaluate side-chains 341 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 298 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 663 ARG Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 430 MET Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 178 optimal weight: 7.9990 chunk 3 optimal weight: 30.0000 chunk 312 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 305 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 207 optimal weight: 0.4980 chunk 169 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 235 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 196 GLN A 313 ASN A 350 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.162058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118264 restraints weight = 34796.822| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.96 r_work: 0.3054 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 24127 Z= 0.215 Angle : 0.675 12.753 32920 Z= 0.346 Chirality : 0.046 0.213 3918 Planarity : 0.006 0.119 4165 Dihedral : 5.684 63.719 3645 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.64 % Favored : 94.20 % Rotamer: Outliers : 2.19 % Allowed : 21.03 % Favored : 76.78 % 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: -0.28 (0.15), residues: 3136 helix: 1.30 (0.15), residues: 1271 sheet: 0.13 (0.26), residues: 402 loop : -1.68 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 139 TYR 0.026 0.002 TYR C 109 PHE 0.045 0.002 PHE B 550 TRP 0.018 0.002 TRP D 166 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00532 (24104) covalent geometry : angle 0.66818 (32866) SS BOND : bond 0.00750 ( 15) SS BOND : angle 2.28818 ( 30) hydrogen bonds : bond 0.05036 ( 1063) hydrogen bonds : angle 4.56038 ( 3063) link_BETA1-4 : bond 0.00299 ( 3) link_BETA1-4 : angle 1.14678 ( 9) link_NAG-ASN : bond 0.00508 ( 5) link_NAG-ASN : angle 3.08654 ( 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 341 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 289 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8567 (tt0) cc_final: 0.8299 (mt-10) REVERT: A 290 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7256 (tp40) REVERT: A 497 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7691 (pp20) REVERT: B 142 MET cc_start: 0.7985 (mtp) cc_final: 0.7640 (mmm) REVERT: B 168 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8871 (mm) REVERT: B 180 GLN cc_start: 0.7861 (tp40) cc_final: 0.7509 (pm20) REVERT: B 408 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8642 (mm) REVERT: B 562 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8307 (ppp) REVERT: B 814 ASP cc_start: 0.7256 (m-30) cc_final: 0.6859 (p0) REVERT: B 816 ASP cc_start: 0.7713 (p0) cc_final: 0.7026 (p0) REVERT: C 181 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7860 (tm-30) REVERT: C 415 MET cc_start: 0.8232 (mmm) cc_final: 0.7973 (mtt) REVERT: C 616 ASN cc_start: 0.8237 (p0) cc_final: 0.7939 (t0) REVERT: D 86 CYS cc_start: 0.6662 (p) cc_final: 0.6135 (p) REVERT: D 89 MET cc_start: 0.7028 (ptm) cc_final: 0.6083 (ppp) REVERT: D 159 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8539 (m-40) REVERT: D 233 THR cc_start: 0.6014 (OUTLIER) cc_final: 0.5651 (t) REVERT: D 430 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8135 (mmt) outliers start: 52 outliers final: 29 residues processed: 324 average time/residue: 0.4949 time to fit residues: 190.1525 Evaluate side-chains 328 residues out of total 2748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 291 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 663 ARG Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 430 MET Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 686 VAL 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 197 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 212 optimal weight: 0.0570 chunk 220 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 256 optimal weight: 8.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 313 ASN A 556 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 ASN D 336 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.165259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120783 restraints weight = 34872.738| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.94 r_work: 0.3126 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 24127 Z= 0.112 Angle : 0.588 11.231 32920 Z= 0.299 Chirality : 0.043 0.209 3918 Planarity : 0.005 0.118 4165 Dihedral : 5.233 55.712 3645 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.62 % Favored : 95.22 % Rotamer: Outliers : 1.77 % Allowed : 21.62 % Favored : 76.61 % 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: -0.05 (0.15), residues: 3136 helix: 1.48 (0.15), residues: 1282 sheet: 0.22 (0.26), residues: 418 loop : -1.58 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 139 TYR 0.017 0.001 TYR C 261 PHE 0.046 0.001 PHE B 550 TRP 0.010 0.001 TRP A 768 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00272 (24104) covalent geometry : angle 0.58160 (32866) SS BOND : bond 0.00405 ( 15) SS BOND : angle 1.64254 ( 30) hydrogen bonds : bond 0.03555 ( 1063) hydrogen bonds : angle 4.37924 ( 3063) link_BETA1-4 : bond 0.00475 ( 3) link_BETA1-4 : angle 1.06865 ( 9) link_NAG-ASN : bond 0.00434 ( 5) link_NAG-ASN : angle 3.27908 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9578.38 seconds wall clock time: 163 minutes 10.69 seconds (9790.69 seconds total)