Starting phenix.real_space_refine on Fri Jun 20 23:21:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3a_46529/06_2025/9d3a_46529.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3a_46529/06_2025/9d3a_46529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d3a_46529/06_2025/9d3a_46529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3a_46529/06_2025/9d3a_46529.map" model { file = "/net/cci-nas-00/data/ceres_data/9d3a_46529/06_2025/9d3a_46529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3a_46529/06_2025/9d3a_46529.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 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 82 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 136 5.16 5 C 15548 2.51 5 N 4077 2.21 5 O 4509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24270 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 6161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6161 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 34, 'TRANS': 754} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 5879 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 28, 'TRANS': 747} Chain breaks: 3 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 166 Chain: "C" Number of atoms: 6246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6246 Classifications: {'peptide': 801} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 35, 'TRANS': 765} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 5870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 5870 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 726} Chain breaks: 4 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 80 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: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 14.33, per 1000 atoms: 0.59 Number of scatterers: 24270 At special positions: 0 Unit cell: (122.408, 148.944, 184.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 4509 8.00 N 4077 7.00 C 15548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.02 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 348 " distance=2.03 Simple disulfide: pdb=" SG CYS D 455 " - pdb=" SG CYS D 483 " distance=2.03 Simple disulfide: pdb=" SG CYS D 462 " - pdb=" SG CYS D 484 " distance=2.03 Simple disulfide: pdb=" SG CYS D 773 " - pdb=" SG CYS D 828 " 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-ASN " NAG A 902 " - " ASN A 471 " " NAG B 902 " - " ASN B 688 " " NAG C 902 " - " ASN C 771 " " NAG D 902 " - " ASN D 715 " " NAG E 1 " - " ASN A 771 " Time building additional restraints: 5.52 Conformation dependent library (CDL) restraints added in 2.9 seconds 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5832 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 27 sheets defined 42.6% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.824A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.929A pdb=" N ALA A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 removed outlier: 3.507A pdb=" N GLN A 86 " --> pdb=" O ILE A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 104 through 112 removed outlier: 3.591A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.726A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 removed outlier: 3.605A pdb=" N HIS A 146 " --> pdb=" O PRO A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 146' Processing helix chain 'A' and resid 147 through 158 removed outlier: 4.335A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.524A pdb=" N LEU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.747A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.867A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 removed outlier: 3.558A pdb=" N ARG A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 470 removed outlier: 3.917A pdb=" N ILE A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 4.023A pdb=" N LEU A 505 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 501 through 506' Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.540A pdb=" N TRP A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 567 " --> pdb=" O TRP A 563 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 575 " --> pdb=" O HIS A 571 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.697A pdb=" N VAL A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 657 removed outlier: 3.530A pdb=" N ARG A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 4.051A 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 688 through 696 removed outlier: 3.771A pdb=" N ARG A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.877A pdb=" N ARG A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.665A pdb=" N ILE A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 removed outlier: 4.257A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 removed outlier: 4.249A pdb=" N LEU A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 792 removed outlier: 3.995A pdb=" N LYS A 790 " --> pdb=" O GLU A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 837 removed outlier: 3.535A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 removed outlier: 3.555A pdb=" N ILE B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.684A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.666A pdb=" N SER B 130 " --> pdb=" O HIS B 127 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 131 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 132' Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.547A pdb=" N ALA B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 3.610A pdb=" N ILE B 186 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 222 Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.892A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL B 243 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.193A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 removed outlier: 3.614A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER B 309 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 removed outlier: 4.235A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.952A pdb=" N LEU B 465 " --> pdb=" O CYS B 461 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 502 removed outlier: 4.037A pdb=" N VAL B 501 " --> pdb=" O MET B 497 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL B 502 " --> pdb=" O ILE B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'B' and resid 555 through 576 removed outlier: 3.873A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL B 569 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 612 removed outlier: 3.515A pdb=" N ALA B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.651A pdb=" N LYS B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 638 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 692 through 699 removed outlier: 3.593A pdb=" N ASN B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 4.135A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 724 removed outlier: 3.565A pdb=" N LEU B 719 " --> pdb=" O ASP B 715 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 741 removed outlier: 3.808A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 747 removed outlier: 7.820A pdb=" N GLY B 745 " --> pdb=" O ARG B 742 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS B 747 " --> pdb=" O GLU B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 786 removed outlier: 3.696A pdb=" N LEU B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.609A pdb=" N ALA B 794 " --> pdb=" O GLU B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 830 removed outlier: 4.111A pdb=" N ALA B 830 " --> pdb=" O GLY B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 841 removed outlier: 3.530A pdb=" N THR B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N HIS B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B 841 " --> pdb=" O ILE B 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 38 Processing helix chain 'C' and resid 39 through 47 removed outlier: 3.620A pdb=" N GLU C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.666A pdb=" N LYS C 51 " --> pdb=" O GLN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.510A pdb=" N MET C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 75' Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.214A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 155 removed outlier: 3.550A pdb=" N GLN C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 189 removed outlier: 3.531A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 210 through 214 removed outlier: 4.136A pdb=" N LEU C 214 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 238 removed outlier: 4.044A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 254 Processing helix chain 'C' and resid 255 through 260 removed outlier: 3.610A pdb=" N ALA C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 296 removed outlier: 4.070A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 327 removed outlier: 4.345A pdb=" N LEU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.830A pdb=" N THR C 419 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 470 removed outlier: 3.686A pdb=" N ILE C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 508 removed outlier: 4.162A pdb=" N LEU C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.745A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 584 removed outlier: 3.873A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 565 " --> pdb=" O THR C 561 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET C 576 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 579 " --> pdb=" O VAL C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 616 removed outlier: 3.701A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP C 611 " --> pdb=" O MET C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 651 removed outlier: 3.791A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL C 635 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET C 641 " --> pdb=" O ALA C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 656 removed outlier: 3.536A pdb=" N VAL C 656 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.725A pdb=" N ARG C 673 " --> pdb=" O ASP C 669 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN C 674 " --> pdb=" O PRO C 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 669 through 674' Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.849A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 707 Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.908A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 743 removed outlier: 4.478A pdb=" N SER C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 770 removed outlier: 4.331A pdb=" N GLN C 770 " --> pdb=" O PRO C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 782 removed outlier: 3.897A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER C 779 " --> pdb=" O SER C 775 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN C 782 " --> pdb=" O LYS C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 793 removed outlier: 3.564A pdb=" N ASP C 789 " --> pdb=" O MET C 785 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS C 790 " --> pdb=" O GLU C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 823 Processing helix chain 'C' and resid 823 through 839 removed outlier: 3.837A pdb=" N GLY C 827 " --> pdb=" O GLY C 823 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE C 828 " --> pdb=" O ILE C 824 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 836 " --> pdb=" O PHE C 832 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 63 Processing helix chain 'D' and resid 68 through 75 removed outlier: 4.110A pdb=" N ALA D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA D 75 " --> pdb=" O PRO D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 111 removed outlier: 5.353A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N CYS D 104 " --> pdb=" O VAL D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 126 through 138 removed outlier: 3.911A pdb=" N GLN D 136 " --> pdb=" O PHE D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 removed outlier: 4.152A pdb=" N LEU D 150 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 182 removed outlier: 4.055A pdb=" N VAL D 174 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU D 177 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 209 removed outlier: 4.073A pdb=" N PHE D 200 " --> pdb=" O GLY D 196 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 201 " --> pdb=" O HIS D 197 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU D 207 " --> pdb=" O TYR D 203 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR D 208 " --> pdb=" O ILE D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 227 Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 252 through 264 removed outlier: 4.011A pdb=" N VAL D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 336 removed outlier: 3.798A pdb=" N VAL D 327 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU D 334 " --> pdb=" O GLY D 330 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 335 " --> pdb=" O ALA D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 347 removed outlier: 3.978A pdb=" N ASP D 347 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 499 removed outlier: 3.813A pdb=" N ARG D 494 " --> pdb=" O ASP D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 530 removed outlier: 3.531A pdb=" N TYR D 530 " --> pdb=" O GLY D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 578 removed outlier: 4.524A pdb=" N PHE D 577 " --> pdb=" O PRO D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 588 removed outlier: 4.181A pdb=" N TRP D 586 " --> pdb=" O SER D 582 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET D 588 " --> pdb=" O ALA D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 605 removed outlier: 3.773A pdb=" N MET D 592 " --> pdb=" O MET D 588 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS D 593 " --> pdb=" O MET D 589 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 601 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 637 removed outlier: 3.515A pdb=" N TRP D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 640 No H-bonds generated for 'chain 'D' and resid 638 through 640' Processing helix chain 'D' and resid 654 through 683 removed outlier: 3.582A pdb=" N LEU D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 661 " --> pdb=" O ILE D 657 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP D 662 " --> pdb=" O MET D 658 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 665 " --> pdb=" O VAL D 661 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN D 683 " --> pdb=" O ALA D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 700 Processing helix chain 'D' and resid 701 through 704 removed outlier: 3.838A pdb=" N GLN D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 701 through 704' Processing helix chain 'D' and resid 716 through 724 removed outlier: 4.025A pdb=" N ILE D 722 " --> pdb=" O THR D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 734 removed outlier: 4.058A pdb=" N TYR D 732 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL D 734 " --> pdb=" O HIS D 730 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 750 removed outlier: 4.079A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 748 " --> pdb=" O ALA D 744 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 749 " --> pdb=" O LEU D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 767 removed outlier: 3.645A pdb=" N TYR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 781 No H-bonds generated for 'chain 'D' and resid 779 through 781' Processing helix chain 'D' and resid 799 through 813 removed outlier: 3.539A pdb=" N LEU D 808 " --> pdb=" O ASP D 804 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 811 " --> pdb=" O LEU D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 823 removed outlier: 3.536A pdb=" N ARG D 821 " --> pdb=" O GLU D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 845 removed outlier: 3.715A pdb=" N ASN D 844 " --> pdb=" O LEU D 840 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET D 845 " --> pdb=" O ASP D 841 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 840 through 845' Processing helix chain 'D' and resid 845 through 872 removed outlier: 3.822A pdb=" N PHE D 849 " --> pdb=" O MET D 845 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR D 850 " --> pdb=" O ALA D 846 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET D 851 " --> pdb=" O GLY D 847 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 852 " --> pdb=" O VAL D 848 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU D 860 " --> pdb=" O MET D 856 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 120 removed outlier: 5.953A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 195 removed outlier: 3.719A pdb=" N SER A 222 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.623A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.098A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 412 removed outlier: 3.558A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 451 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS A 455 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 489 removed outlier: 3.545A pdb=" N GLU A 488 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.595A pdb=" N ALA A 682 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 730 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 542 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 72 removed outlier: 3.521A pdb=" N ARG B 67 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 39 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 41 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.590A 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 200 removed outlier: 3.704A pdb=" N GLU B 200 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE B 171 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE B 168 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU B 229 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 257 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU B 362 " --> pdb=" O TRP B 379 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B 364 " --> pdb=" O GLY B 377 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 405 through 410 removed outlier: 3.508A pdb=" N ASP B 477 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 408 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 410 " --> pdb=" O TYR B 479 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB3, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.809A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B 729 " --> pdb=" O MET B 537 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 64 through 66 removed outlier: 6.883A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 91 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 119 through 120 Processing sheet with id=AB6, first strand: chain 'C' and resid 194 through 197 removed outlier: 3.672A pdb=" N PHE C 197 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 400 through 402 removed outlier: 5.770A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 412 through 413 removed outlier: 4.008A pdb=" N HIS C 449 " --> pdb=" O ASN C 440 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 487 through 488 Processing sheet with id=AC1, first strand: chain 'C' and resid 527 through 528 Processing sheet with id=AC2, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.508A pdb=" N ALA C 682 " --> pdb=" O ALA C 728 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 54 through 57 removed outlier: 3.719A pdb=" N GLU D 118 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 141 through 143 removed outlier: 6.255A pdb=" N ILE D 141 " --> pdb=" O LEU D 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 188 through 189 removed outlier: 7.229A pdb=" N VAL D 188 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D 244 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 307 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU D 304 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL D 389 " --> pdb=" O VAL D 401 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG D 410 " --> pdb=" O SER D 403 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 434 through 435 Processing sheet with id=AC7, first strand: chain 'D' and resid 444 through 447 removed outlier: 3.673A pdb=" N VAL D 460 " --> pdb=" O CYS D 484 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 515 through 516 removed outlier: 3.665A pdb=" N LYS D 515 " --> pdb=" O ASN D 522 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN D 522 " --> pdb=" O LYS D 515 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 710 through 711 removed outlier: 6.949A pdb=" N GLY D 711 " --> pdb=" O ILE D 757 " (cutoff:3.500A) 723 hydrogen bonds defined for protein. 2049 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: 8.95 Time building geometry restraints manager: 6.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7846 1.34 - 1.46: 5448 1.46 - 1.58: 11284 1.58 - 1.70: 0 1.70 - 1.82: 233 Bond restraints: 24811 Sorted by residual: bond pdb=" CA GLY C 333 " pdb=" C GLY C 333 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.60e+00 bond pdb=" N GLY C 333 " pdb=" CA GLY C 333 " ideal model delta sigma weight residual 1.464 1.448 0.016 1.12e-02 7.97e+03 2.09e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" CG GLN A 536 " pdb=" CD GLN A 536 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.74e+00 bond pdb=" C1 NAG C 902 " pdb=" O5 NAG C 902 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 ... (remaining 24806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 33016 1.41 - 2.81: 556 2.81 - 4.22: 110 4.22 - 5.62: 22 5.62 - 7.03: 2 Bond angle restraints: 33706 Sorted by residual: angle pdb=" N CYS D 348 " pdb=" CA CYS D 348 " pdb=" C CYS D 348 " ideal model delta sigma weight residual 114.56 110.35 4.21 1.27e+00 6.20e-01 1.10e+01 angle pdb=" C MET A 470 " pdb=" N ASN A 471 " pdb=" CA ASN A 471 " ideal model delta sigma weight residual 121.54 126.77 -5.23 1.91e+00 2.74e-01 7.51e+00 angle pdb=" N GLU C 621 " pdb=" CA GLU C 621 " pdb=" C GLU C 621 " ideal model delta sigma weight residual 114.56 111.13 3.43 1.27e+00 6.20e-01 7.29e+00 angle pdb=" C ASP A 130 " pdb=" N LYS A 131 " pdb=" CA LYS A 131 " ideal model delta sigma weight residual 121.54 126.52 -4.98 1.91e+00 2.74e-01 6.80e+00 angle pdb=" N THR C 103 " pdb=" CA THR C 103 " pdb=" C THR C 103 " ideal model delta sigma weight residual 109.81 115.00 -5.19 2.21e+00 2.05e-01 5.52e+00 ... (remaining 33701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.43: 14233 22.43 - 44.85: 540 44.85 - 67.28: 41 67.28 - 89.70: 16 89.70 - 112.13: 5 Dihedral angle restraints: 14835 sinusoidal: 5787 harmonic: 9048 Sorted by residual: dihedral pdb=" CB CYS C 744 " pdb=" SG CYS C 744 " pdb=" SG CYS C 798 " pdb=" CB CYS C 798 " ideal model delta sinusoidal sigma weight residual -86.00 -43.93 -42.07 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA GLY D 796 " pdb=" C GLY D 796 " pdb=" N SER D 797 " pdb=" CA SER D 797 " ideal model delta harmonic sigma weight residual -180.00 -155.46 -24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA PRO B 679 " pdb=" C PRO B 679 " pdb=" N PRO B 680 " pdb=" CA PRO B 680 " ideal model delta harmonic sigma weight residual -180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 14832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2222 0.029 - 0.058: 1071 0.058 - 0.087: 304 0.087 - 0.116: 222 0.116 - 0.145: 33 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA ILE D 791 " pdb=" N ILE D 791 " pdb=" C ILE D 791 " pdb=" CB ILE D 791 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" CA ILE B 534 " pdb=" N ILE B 534 " pdb=" C ILE B 534 " pdb=" CB ILE B 534 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE B 764 " pdb=" N ILE B 764 " pdb=" C ILE B 764 " pdb=" CB ILE B 764 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 3849 not shown) Planarity restraints: 4294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 318 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO C 319 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 319 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 319 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 176 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO B 177 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 177 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 177 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 669 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 670 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " 0.023 5.00e-02 4.00e+02 ... (remaining 4291 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1385 2.73 - 3.27: 25026 3.27 - 3.82: 36623 3.82 - 4.36: 42871 4.36 - 4.90: 73627 Nonbonded interactions: 179532 Sorted by model distance: nonbonded pdb=" OH TYR D 506 " pdb=" OE1 GLU D 527 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR D 718 " pdb=" OE1 GLU D 901 " model vdw 2.220 3.040 nonbonded pdb=" O VAL B 243 " pdb=" OG SER B 246 " model vdw 2.235 3.040 nonbonded pdb=" ND2 ASN C 499 " pdb=" OE1 GLN C 686 " model vdw 2.250 3.120 nonbonded pdb=" N ASN D 52 " pdb=" O ASP D 83 " model vdw 2.261 3.120 ... (remaining 179527 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 and (name N or name CA or name C or name O or name CB \ )) or resid 26 through 35 or (resid 36 and (name N or name CA or name C or name \ O or name CB )) or resid 37 through 186 or (resid 187 through 188 and (name N or \ name CA or name C or name O or name CB )) or resid 189 through 494 or (resid 49 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 496 through \ 624 or (resid 625 and (name N or name CA or name C or name O or name CB )) or re \ sid 626 through 660 or (resid 661 through 662 and (name N or name CA or name C o \ r name O or name CB )) or resid 663 through 837 or resid 901 or resid 902)) selection = (chain 'C' and (resid 25 through 259 or (resid 260 and (name N or name CA or nam \ e C or name O or name CB )) or resid 261 through 544 or (resid 545 and (name N o \ r name CA or name C or name O or name CB )) or resid 546 through 548 or (resid 5 \ 49 and (name N or name CA or name C or name O or name CB )) or resid 550 through \ 585 or resid 602 through 703 or (resid 704 and (name N or name CA or name C or \ name O or name CB )) or resid 705 through 750 or (resid 751 and (name N or name \ CA or name C or name O or name CB )) or resid 752 through 798 or resid 807 throu \ gh 808 or (resid 809 and (name N or name CA or name C or name O or name CB )) or \ resid 810 or (resid 811 through 812 and (name N or name CA or name C or name O \ or name CB )) or resid 813 through 831 or (resid 832 through 833 and (name N or \ name CA or name C or name O or name CB )) or resid 834 through 836 or (resid 837 \ and (name N or name CA or name C or name O or name CB )) or resid 901 or resid \ 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.040 Extract box with map and model: 1.080 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 53.560 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 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 : 0.003 0.040 24833 Z= 0.137 Angle : 0.496 7.030 33756 Z= 0.258 Chirality : 0.042 0.145 3852 Planarity : 0.003 0.061 4289 Dihedral : 11.557 112.130 8955 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.48 % Favored : 93.49 % Rotamer: Outliers : 1.55 % Allowed : 5.52 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.15), residues: 3101 helix: -0.81 (0.16), residues: 1052 sheet: -1.16 (0.29), residues: 347 loop : -1.61 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 247 HIS 0.006 0.001 HIS C 404 PHE 0.020 0.001 PHE A 458 TYR 0.012 0.001 TYR D 581 ARG 0.002 0.000 ARG D 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 5) link_NAG-ASN : angle 2.09457 ( 15) link_BETA1-4 : bond 0.00378 ( 1) link_BETA1-4 : angle 0.98412 ( 3) hydrogen bonds : bond 0.32048 ( 723) hydrogen bonds : angle 8.85938 ( 2049) SS BOND : bond 0.00269 ( 16) SS BOND : angle 1.02714 ( 32) covalent geometry : bond 0.00315 (24811) covalent geometry : angle 0.49323 (33706) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 312 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 818 MET cc_start: 0.3845 (ppp) cc_final: 0.3626 (ppp) REVERT: B 567 LEU cc_start: 0.7508 (pp) cc_final: 0.7160 (pp) REVERT: C 492 ASN cc_start: 0.6799 (OUTLIER) cc_final: 0.6524 (p0) outliers start: 40 outliers final: 27 residues processed: 350 average time/residue: 0.3068 time to fit residues: 176.3658 Evaluate side-chains 276 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 248 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 731 TRP Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 492 ASN Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 550 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 80 optimal weight: 30.0000 chunk 159 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 243 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 148 optimal weight: 0.0470 chunk 181 optimal weight: 7.9990 chunk 282 optimal weight: 0.9980 overall best weight: 2.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.189495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.172516 restraints weight = 37969.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.170859 restraints weight = 71995.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.169650 restraints weight = 60756.288| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 24833 Z= 0.241 Angle : 0.678 10.616 33756 Z= 0.355 Chirality : 0.047 0.253 3852 Planarity : 0.005 0.063 4289 Dihedral : 7.128 90.225 3511 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.48 % Favored : 92.49 % Rotamer: Outliers : 2.95 % Allowed : 9.25 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.14), residues: 3101 helix: -0.58 (0.15), residues: 1096 sheet: -1.34 (0.27), residues: 371 loop : -1.74 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 636 HIS 0.008 0.001 HIS C 404 PHE 0.037 0.002 PHE A 458 TYR 0.022 0.002 TYR B 479 ARG 0.004 0.001 ARG C 794 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 5) link_NAG-ASN : angle 2.30651 ( 15) link_BETA1-4 : bond 0.00307 ( 1) link_BETA1-4 : angle 1.41037 ( 3) hydrogen bonds : bond 0.06554 ( 723) hydrogen bonds : angle 6.06991 ( 2049) SS BOND : bond 0.00558 ( 16) SS BOND : angle 1.65683 ( 32) covalent geometry : bond 0.00571 (24811) covalent geometry : angle 0.67472 (33706) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 273 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 408 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8491 (tt) REVERT: C 238 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6798 (mm) REVERT: C 702 MET cc_start: 0.7748 (pmm) cc_final: 0.7545 (pmm) outliers start: 76 outliers final: 56 residues processed: 332 average time/residue: 0.3189 time to fit residues: 174.0001 Evaluate side-chains 301 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 563 TRP Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 848 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 291 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 199 optimal weight: 0.9980 chunk 116 optimal weight: 0.1980 chunk 296 optimal weight: 0.8980 chunk 279 optimal weight: 2.9990 chunk 107 optimal weight: 50.0000 chunk 130 optimal weight: 10.0000 chunk 166 optimal weight: 0.0370 chunk 30 optimal weight: 20.0000 chunk 298 optimal weight: 1.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN B 385 GLN C 162 HIS C 571 HIS ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.192719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.176110 restraints weight = 37291.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.174367 restraints weight = 66541.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.172606 restraints weight = 70225.283| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24833 Z= 0.118 Angle : 0.565 9.923 33756 Z= 0.288 Chirality : 0.043 0.196 3852 Planarity : 0.004 0.063 4289 Dihedral : 6.127 72.291 3504 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.97 % Favored : 95.00 % Rotamer: Outliers : 2.49 % Allowed : 11.93 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.15), residues: 3101 helix: -0.32 (0.15), residues: 1114 sheet: -1.21 (0.27), residues: 378 loop : -1.72 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 381 HIS 0.009 0.001 HIS B 802 PHE 0.020 0.001 PHE A 458 TYR 0.014 0.001 TYR C 578 ARG 0.005 0.000 ARG C 174 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 5) link_NAG-ASN : angle 1.90461 ( 15) link_BETA1-4 : bond 0.00519 ( 1) link_BETA1-4 : angle 1.23466 ( 3) hydrogen bonds : bond 0.05309 ( 723) hydrogen bonds : angle 5.42212 ( 2049) SS BOND : bond 0.00495 ( 16) SS BOND : angle 1.61448 ( 32) covalent geometry : bond 0.00253 (24811) covalent geometry : angle 0.56156 (33706) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 260 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 LEU cc_start: 0.7002 (mp) cc_final: 0.6684 (tt) REVERT: B 408 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8107 (tt) REVERT: B 418 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7897 (mt) REVERT: B 428 THR cc_start: 0.6610 (p) cc_final: 0.6406 (p) REVERT: D 821 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7251 (mtp85) outliers start: 64 outliers final: 47 residues processed: 311 average time/residue: 0.3234 time to fit residues: 165.1019 Evaluate side-chains 292 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 79 CYS Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 821 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 120 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 144 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 277 optimal weight: 0.8980 chunk 241 optimal weight: 7.9990 chunk 199 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.200285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.182176 restraints weight = 36874.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.180960 restraints weight = 62243.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.178737 restraints weight = 64598.354| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24833 Z= 0.113 Angle : 0.544 9.811 33756 Z= 0.275 Chirality : 0.043 0.225 3852 Planarity : 0.004 0.062 4289 Dihedral : 5.461 56.978 3501 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.32 % Rotamer: Outliers : 2.84 % Allowed : 12.12 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 3101 helix: -0.06 (0.15), residues: 1114 sheet: -1.21 (0.27), residues: 365 loop : -1.70 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 563 HIS 0.006 0.001 HIS B 802 PHE 0.025 0.001 PHE B 143 TYR 0.014 0.001 TYR D 203 ARG 0.004 0.000 ARG D 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 5) link_NAG-ASN : angle 1.88051 ( 15) link_BETA1-4 : bond 0.00468 ( 1) link_BETA1-4 : angle 1.31580 ( 3) hydrogen bonds : bond 0.04345 ( 723) hydrogen bonds : angle 5.01847 ( 2049) SS BOND : bond 0.00172 ( 16) SS BOND : angle 1.04588 ( 32) covalent geometry : bond 0.00250 (24811) covalent geometry : angle 0.54201 (33706) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 260 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.4593 (pmm) cc_final: 0.4336 (ttp) REVERT: A 317 THR cc_start: 0.4881 (OUTLIER) cc_final: 0.4564 (m) REVERT: A 614 LEU cc_start: 0.7160 (mp) cc_final: 0.6831 (tt) REVERT: B 408 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7855 (tt) REVERT: B 418 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7925 (mt) REVERT: B 428 THR cc_start: 0.6709 (p) cc_final: 0.6506 (p) REVERT: B 567 LEU cc_start: 0.7518 (pp) cc_final: 0.6683 (mt) REVERT: D 821 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7316 (mtp85) outliers start: 73 outliers final: 46 residues processed: 321 average time/residue: 0.3305 time to fit residues: 175.2817 Evaluate side-chains 293 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 243 time to evaluate : 3.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 821 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 95 optimal weight: 30.0000 chunk 253 optimal weight: 10.0000 chunk 45 optimal weight: 0.0570 chunk 288 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 chunk 309 optimal weight: 10.0000 chunk 266 optimal weight: 20.0000 chunk 187 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 190 optimal weight: 0.0670 chunk 251 optimal weight: 20.0000 overall best weight: 2.4240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 184 ASN B 622 ASN ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.197109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.179353 restraints weight = 36706.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.177720 restraints weight = 65706.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.176149 restraints weight = 65885.375| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24833 Z= 0.204 Angle : 0.618 9.524 33756 Z= 0.317 Chirality : 0.045 0.189 3852 Planarity : 0.004 0.074 4289 Dihedral : 5.589 58.006 3496 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.16 % Favored : 92.81 % Rotamer: Outliers : 3.26 % Allowed : 12.94 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.15), residues: 3101 helix: -0.05 (0.16), residues: 1112 sheet: -1.32 (0.27), residues: 372 loop : -1.76 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 563 HIS 0.009 0.001 HIS B 802 PHE 0.036 0.002 PHE A 458 TYR 0.018 0.001 TYR B 479 ARG 0.016 0.000 ARG A 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 5) link_NAG-ASN : angle 2.19849 ( 15) link_BETA1-4 : bond 0.00378 ( 1) link_BETA1-4 : angle 1.69648 ( 3) hydrogen bonds : bond 0.04664 ( 723) hydrogen bonds : angle 5.09787 ( 2049) SS BOND : bond 0.00344 ( 16) SS BOND : angle 1.75167 ( 32) covalent geometry : bond 0.00491 (24811) covalent geometry : angle 0.61420 (33706) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 249 time to evaluate : 3.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 THR cc_start: 0.5012 (OUTLIER) cc_final: 0.4708 (m) REVERT: B 408 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8222 (tt) REVERT: B 428 THR cc_start: 0.6915 (p) cc_final: 0.6691 (p) REVERT: B 567 LEU cc_start: 0.7572 (pp) cc_final: 0.6730 (mt) REVERT: B 824 MET cc_start: 0.2732 (mmp) cc_final: 0.2420 (mmt) REVERT: D 821 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7379 (mtp85) outliers start: 84 outliers final: 64 residues processed: 322 average time/residue: 0.5156 time to fit residues: 284.4938 Evaluate side-chains 306 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 239 time to evaluate : 4.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 821 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 184 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 290 optimal weight: 6.9990 chunk 217 optimal weight: 0.7980 chunk 209 optimal weight: 10.0000 chunk 228 optimal weight: 0.9990 chunk 308 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.199194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.178578 restraints weight = 36322.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.176631 restraints weight = 62744.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.175321 restraints weight = 60926.248| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24833 Z= 0.123 Angle : 0.569 12.386 33756 Z= 0.287 Chirality : 0.043 0.240 3852 Planarity : 0.004 0.060 4289 Dihedral : 5.281 59.072 3496 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.99 % Allowed : 13.40 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 3101 helix: 0.02 (0.16), residues: 1111 sheet: -1.30 (0.27), residues: 365 loop : -1.67 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 636 HIS 0.008 0.001 HIS A 171 PHE 0.022 0.001 PHE A 458 TYR 0.015 0.001 TYR D 203 ARG 0.004 0.000 ARG D 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 5) link_NAG-ASN : angle 2.09753 ( 15) link_BETA1-4 : bond 0.00404 ( 1) link_BETA1-4 : angle 1.50842 ( 3) hydrogen bonds : bond 0.03965 ( 723) hydrogen bonds : angle 4.85469 ( 2049) SS BOND : bond 0.00373 ( 16) SS BOND : angle 1.93771 ( 32) covalent geometry : bond 0.00280 (24811) covalent geometry : angle 0.56430 (33706) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 251 time to evaluate : 4.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.4842 (pmm) cc_final: 0.4529 (ttp) REVERT: A 317 THR cc_start: 0.4958 (OUTLIER) cc_final: 0.4652 (m) REVERT: B 408 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7951 (tt) REVERT: B 418 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7994 (mt) REVERT: B 567 LEU cc_start: 0.7624 (pp) cc_final: 0.6760 (mt) REVERT: D 821 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7335 (mtp85) outliers start: 77 outliers final: 60 residues processed: 318 average time/residue: 0.3429 time to fit residues: 181.5939 Evaluate side-chains 306 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 242 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 821 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 195 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 179 optimal weight: 0.0970 chunk 310 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.198132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.179468 restraints weight = 36416.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.177830 restraints weight = 63725.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.176111 restraints weight = 61967.447| |-----------------------------------------------------------------------------| r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24833 Z= 0.159 Angle : 0.591 11.493 33756 Z= 0.299 Chirality : 0.044 0.194 3852 Planarity : 0.004 0.060 4289 Dihedral : 5.321 59.475 3494 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.30 % Allowed : 13.56 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 3101 helix: 0.02 (0.16), residues: 1103 sheet: -1.23 (0.28), residues: 353 loop : -1.73 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 636 HIS 0.007 0.001 HIS A 171 PHE 0.029 0.002 PHE A 458 TYR 0.014 0.001 TYR B 479 ARG 0.004 0.000 ARG D 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 5) link_NAG-ASN : angle 2.18662 ( 15) link_BETA1-4 : bond 0.00470 ( 1) link_BETA1-4 : angle 1.62836 ( 3) hydrogen bonds : bond 0.04052 ( 723) hydrogen bonds : angle 4.85567 ( 2049) SS BOND : bond 0.00267 ( 16) SS BOND : angle 1.53623 ( 32) covalent geometry : bond 0.00378 (24811) covalent geometry : angle 0.58758 (33706) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 240 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.4860 (pmm) cc_final: 0.4509 (ttp) REVERT: A 317 THR cc_start: 0.4987 (OUTLIER) cc_final: 0.4671 (m) REVERT: B 99 PHE cc_start: 0.5969 (t80) cc_final: 0.5763 (t80) REVERT: B 307 MET cc_start: 0.3340 (tmm) cc_final: 0.1687 (ttt) REVERT: B 349 LEU cc_start: 0.7807 (tp) cc_final: 0.7605 (mm) REVERT: B 408 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8046 (tt) REVERT: B 567 LEU cc_start: 0.7514 (pp) cc_final: 0.6722 (mt) REVERT: B 681 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7873 (t80) REVERT: D 821 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7328 (mtp85) outliers start: 85 outliers final: 72 residues processed: 313 average time/residue: 0.3227 time to fit residues: 167.3049 Evaluate side-chains 311 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 235 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 731 TRP Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 797 SER Chi-restraints excluded: chain D residue 821 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 71 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 156 optimal weight: 7.9990 chunk 282 optimal weight: 0.7980 chunk 4 optimal weight: 30.0000 chunk 84 optimal weight: 1.9990 chunk 293 optimal weight: 0.0470 chunk 252 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.199496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.179473 restraints weight = 36586.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.177466 restraints weight = 60475.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.176303 restraints weight = 60676.492| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24833 Z= 0.112 Angle : 0.568 13.806 33756 Z= 0.283 Chirality : 0.043 0.271 3852 Planarity : 0.004 0.060 4289 Dihedral : 5.065 57.186 3494 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.91 % Allowed : 14.14 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.15), residues: 3101 helix: 0.11 (0.16), residues: 1106 sheet: -1.27 (0.27), residues: 375 loop : -1.64 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 636 HIS 0.007 0.001 HIS A 171 PHE 0.025 0.001 PHE D 257 TYR 0.015 0.001 TYR D 203 ARG 0.003 0.000 ARG D 410 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 5) link_NAG-ASN : angle 2.10239 ( 15) link_BETA1-4 : bond 0.00378 ( 1) link_BETA1-4 : angle 1.42586 ( 3) hydrogen bonds : bond 0.03629 ( 723) hydrogen bonds : angle 4.71093 ( 2049) SS BOND : bond 0.00227 ( 16) SS BOND : angle 1.18040 ( 32) covalent geometry : bond 0.00255 (24811) covalent geometry : angle 0.56585 (33706) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 252 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.4877 (pmm) cc_final: 0.4581 (ttp) REVERT: A 317 THR cc_start: 0.4909 (OUTLIER) cc_final: 0.4616 (m) REVERT: A 818 MET cc_start: 0.3208 (ppp) cc_final: 0.0579 (mmt) REVERT: B 408 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.7990 (tt) REVERT: B 418 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7987 (mt) REVERT: B 567 LEU cc_start: 0.7524 (pp) cc_final: 0.6772 (mt) outliers start: 75 outliers final: 62 residues processed: 313 average time/residue: 0.3139 time to fit residues: 164.1983 Evaluate side-chains 302 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 237 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 797 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 252 optimal weight: 8.9990 chunk 305 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 223 optimal weight: 0.4980 chunk 251 optimal weight: 30.0000 chunk 210 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 155 optimal weight: 30.0000 chunk 151 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.196259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.177725 restraints weight = 36432.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.175544 restraints weight = 59716.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.173524 restraints weight = 65013.683| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 24833 Z= 0.233 Angle : 0.665 13.189 33756 Z= 0.337 Chirality : 0.046 0.237 3852 Planarity : 0.004 0.059 4289 Dihedral : 5.415 55.721 3492 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 3.30 % Allowed : 14.26 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.15), residues: 3101 helix: 0.01 (0.16), residues: 1097 sheet: -1.45 (0.28), residues: 350 loop : -1.78 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 636 HIS 0.009 0.001 HIS B 802 PHE 0.039 0.002 PHE A 458 TYR 0.019 0.002 TYR B 479 ARG 0.004 0.000 ARG D 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 5) link_NAG-ASN : angle 2.33148 ( 15) link_BETA1-4 : bond 0.00292 ( 1) link_BETA1-4 : angle 1.83730 ( 3) hydrogen bonds : bond 0.04322 ( 723) hydrogen bonds : angle 4.98522 ( 2049) SS BOND : bond 0.00345 ( 16) SS BOND : angle 1.14584 ( 32) covalent geometry : bond 0.00565 (24811) covalent geometry : angle 0.66273 (33706) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 239 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.4977 (pmm) cc_final: 0.4552 (ttp) REVERT: A 317 THR cc_start: 0.5059 (OUTLIER) cc_final: 0.4752 (m) REVERT: A 818 MET cc_start: 0.3299 (ppp) cc_final: 0.0681 (mmt) REVERT: B 307 MET cc_start: 0.3231 (tmm) cc_final: 0.1463 (ttt) REVERT: B 567 LEU cc_start: 0.7562 (pp) cc_final: 0.6719 (mt) REVERT: B 681 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7996 (t80) outliers start: 85 outliers final: 73 residues processed: 310 average time/residue: 0.3088 time to fit residues: 159.0293 Evaluate side-chains 311 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 236 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 787 ASP Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 590 PHE Chi-restraints excluded: chain D residue 672 SER Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 797 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 282 optimal weight: 0.9990 chunk 221 optimal weight: 0.6980 chunk 208 optimal weight: 0.6980 chunk 194 optimal weight: 4.9990 chunk 303 optimal weight: 0.7980 chunk 94 optimal weight: 0.4980 chunk 291 optimal weight: 5.9990 chunk 287 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.199395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.183107 restraints weight = 36704.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.181089 restraints weight = 55664.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.178363 restraints weight = 55753.774| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24833 Z= 0.110 Angle : 0.590 13.766 33756 Z= 0.292 Chirality : 0.043 0.236 3852 Planarity : 0.004 0.061 4289 Dihedral : 5.019 58.100 3492 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.76 % Allowed : 14.69 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.15), residues: 3101 helix: 0.14 (0.16), residues: 1098 sheet: -1.18 (0.28), residues: 352 loop : -1.74 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 636 HIS 0.007 0.001 HIS B 802 PHE 0.023 0.001 PHE D 200 TYR 0.018 0.001 TYR D 203 ARG 0.003 0.000 ARG D 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 5) link_NAG-ASN : angle 2.16283 ( 15) link_BETA1-4 : bond 0.00283 ( 1) link_BETA1-4 : angle 1.47309 ( 3) hydrogen bonds : bond 0.03572 ( 723) hydrogen bonds : angle 4.72031 ( 2049) SS BOND : bond 0.00274 ( 16) SS BOND : angle 1.73368 ( 32) covalent geometry : bond 0.00247 (24811) covalent geometry : angle 0.58620 (33706) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6202 Ramachandran restraints generated. 3101 Oldfield, 0 Emsley, 3101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 247 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 MET cc_start: 0.4874 (pmm) cc_final: 0.4608 (ttp) REVERT: A 317 THR cc_start: 0.4899 (OUTLIER) cc_final: 0.4620 (m) REVERT: A 818 MET cc_start: 0.3178 (ppp) cc_final: 0.0565 (mmt) REVERT: B 307 MET cc_start: 0.3268 (tmm) cc_final: 0.1487 (ttt) REVERT: B 418 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7957 (mt) REVERT: B 567 LEU cc_start: 0.7469 (pp) cc_final: 0.6692 (mt) REVERT: B 681 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7936 (t80) outliers start: 71 outliers final: 64 residues processed: 306 average time/residue: 0.3107 time to fit residues: 158.1627 Evaluate side-chains 305 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 238 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 581 ASP Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain B residue 801 CYS Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 528 VAL Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 554 VAL Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 105 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 228 optimal weight: 0.9990 chunk 252 optimal weight: 30.0000 chunk 171 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 197 optimal weight: 0.0370 chunk 146 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 overall best weight: 2.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.195413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.178204 restraints weight = 37203.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.177070 restraints weight = 63887.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.175009 restraints weight = 59756.950| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24833 Z= 0.227 Angle : 0.674 13.637 33756 Z= 0.342 Chirality : 0.046 0.233 3852 Planarity : 0.004 0.060 4289 Dihedral : 5.406 55.883 3492 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.07 % Allowed : 14.92 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.15), residues: 3101 helix: 0.01 (0.16), residues: 1100 sheet: -1.30 (0.28), residues: 347 loop : -1.85 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 636 HIS 0.008 0.001 HIS B 802 PHE 0.039 0.002 PHE A 458 TYR 0.018 0.002 TYR B 479 ARG 0.003 0.000 ARG C 468 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 5) link_NAG-ASN : angle 2.32957 ( 15) link_BETA1-4 : bond 0.00401 ( 1) link_BETA1-4 : angle 1.90097 ( 3) hydrogen bonds : bond 0.04217 ( 723) hydrogen bonds : angle 4.97761 ( 2049) SS BOND : bond 0.00368 ( 16) SS BOND : angle 1.63527 ( 32) covalent geometry : bond 0.00549 (24811) covalent geometry : angle 0.67058 (33706) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7061.74 seconds wall clock time: 126 minutes 47.77 seconds (7607.77 seconds total)