Starting phenix.real_space_refine on Sat Jun 21 03:08:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d37_46526/06_2025/9d37_46526.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d37_46526/06_2025/9d37_46526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d37_46526/06_2025/9d37_46526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d37_46526/06_2025/9d37_46526.map" model { file = "/net/cci-nas-00/data/ceres_data/9d37_46526/06_2025/9d37_46526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d37_46526/06_2025/9d37_46526.cif" } resolution = 3.34 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= 0.015 sd= 0.062 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 15549 2.51 5 N 4077 2.21 5 O 4512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 24274 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 6163 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 754} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 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: 5880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 5880 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 28, 'TRANS': 747} Chain breaks: 3 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 207 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 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 14.48, per 1000 atoms: 0.60 Number of scatterers: 24274 At special positions: 0 Unit cell: (128.289, 149.814, 185.976, 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 4512 8.00 N 4077 7.00 C 15549 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=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 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: 5.85 Conformation dependent library (CDL) restraints added in 2.8 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: 120 helices and 27 sheets defined 43.2% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.719A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 removed outlier: 4.147A pdb=" N ALA A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 removed outlier: 3.633A 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 106 through 111 removed outlier: 3.502A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.554A pdb=" N SER A 129 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 Processing helix chain 'A' and resid 147 through 158 removed outlier: 3.763A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.329A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.981A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.792A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.195A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 255' Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.894A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 3.689A pdb=" N ARG A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.242A pdb=" N GLU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.815A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 468 " --> pdb=" O ILE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 removed outlier: 4.001A pdb=" N LEU A 505 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.726A pdb=" N GLN A 525 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.711A pdb=" N TRP A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 567 " --> pdb=" O TRP A 563 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.530A pdb=" N PHE A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 655 removed outlier: 3.577A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.904A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.605A pdb=" N ARG A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET A 706 " --> pdb=" O MET A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 744 removed outlier: 4.176A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A 742 " --> pdb=" O PHE A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 removed outlier: 3.620A pdb=" N LYS A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER A 779 " --> pdb=" O SER A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 removed outlier: 3.710A pdb=" N ASP A 787 " --> pdb=" O GLY A 783 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 788 " --> pdb=" O PHE A 784 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP A 789 " --> pdb=" O MET A 785 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP A 792 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 837 removed outlier: 3.530A pdb=" N MET A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 830 " --> pdb=" O ALA A 826 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 53 removed outlier: 3.518A pdb=" N ILE B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.548A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N MET B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER B 90 " --> pdb=" O CYS B 86 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 119 removed outlier: 4.160A pdb=" N ILE B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.980A pdb=" N SER B 130 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 165 removed outlier: 3.834A pdb=" N GLN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 3.812A pdb=" N PHE B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 233 through 248 removed outlier: 4.228A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 243 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.835A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 removed outlier: 3.586A pdb=" N ILE B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 309 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 4.286A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 472 removed outlier: 3.623A pdb=" N ILE B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 502 removed outlier: 3.902A pdb=" N VAL B 501 " --> pdb=" O MET B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.591A pdb=" N GLU B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 576 removed outlier: 3.926A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET B 565 " --> pdb=" O MET B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.577A pdb=" N LEU B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 654 removed outlier: 3.581A pdb=" N LYS B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 removed outlier: 4.054A pdb=" N ILE B 695 " --> pdb=" O THR B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 706 removed outlier: 3.839A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 724 removed outlier: 3.741A pdb=" N LEU B 719 " --> pdb=" O ASP B 715 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.611A pdb=" N ASN B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 747 removed outlier: 3.623A pdb=" N CYS B 746 " --> pdb=" O ASP B 743 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS B 747 " --> pdb=" O GLU B 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 743 through 747' Processing helix chain 'B' and resid 772 through 787 removed outlier: 3.568A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 4.002A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 840 removed outlier: 3.828A pdb=" N ALA B 828 " --> pdb=" O MET B 824 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA B 830 " --> pdb=" O GLY B 826 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU B 833 " --> pdb=" O MET B 829 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 38 Processing helix chain 'C' and resid 39 through 48 removed outlier: 3.613A pdb=" N GLU C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 78 removed outlier: 3.510A pdb=" N ALA C 75 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL C 78 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.088A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 4.025A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 129 " --> pdb=" O SER C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 129' Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.920A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 189 removed outlier: 3.658A pdb=" N ALA C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 210 removed outlier: 3.989A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 214 removed outlier: 3.875A pdb=" N LEU C 214 " --> pdb=" O ALA C 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 211 through 214' Processing helix chain 'C' and resid 226 through 237 removed outlier: 4.221A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 254 Processing helix chain 'C' and resid 255 through 259 removed outlier: 3.679A pdb=" N ALA C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 296 removed outlier: 3.517A pdb=" N GLY C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.568A pdb=" N GLY C 418 " --> pdb=" O LEU C 415 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 419 " --> pdb=" O SER C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 419' Processing helix chain 'C' and resid 457 through 471 removed outlier: 3.567A pdb=" N LYS C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 506 removed outlier: 3.695A pdb=" N LEU C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.533A pdb=" N GLN C 525 " --> pdb=" O ASN C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 584 removed outlier: 3.692A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 565 " --> pdb=" O THR C 561 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET C 576 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 577 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 579 " --> pdb=" O VAL C 575 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER C 584 " --> pdb=" O LEU C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 616 removed outlier: 3.702A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 652 removed outlier: 3.748A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA C 637 " --> pdb=" O GLY C 633 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET C 641 " --> pdb=" O ALA C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 693 removed outlier: 3.780A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 707 Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.676A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.526A pdb=" N GLU C 737 " --> pdb=" O SER C 733 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 769 Processing helix chain 'C' and resid 770 through 782 removed outlier: 3.541A pdb=" N ILE C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 793 removed outlier: 3.764A pdb=" N ASP C 789 " --> pdb=" O MET C 785 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS C 790 " --> pdb=" O GLU C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 822 removed outlier: 3.900A pdb=" N VAL C 820 " --> pdb=" O VAL C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 839 removed outlier: 3.623A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA C 836 " --> pdb=" O PHE C 832 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS C 838 " --> pdb=" O GLU C 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 62 through 67 removed outlier: 4.242A pdb=" N ALA D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 75 removed outlier: 4.049A pdb=" N ALA D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA D 75 " --> pdb=" O PRO D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 68 through 75' Processing helix chain 'D' and resid 97 through 111 removed outlier: 4.447A pdb=" N LEU D 103 " --> pdb=" O LEU D 99 " (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 137 removed outlier: 3.849A pdb=" N LEU D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.636A pdb=" N ALA D 149 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU D 150 " --> pdb=" O GLY D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 150' Processing helix chain 'D' and resid 167 through 182 removed outlier: 3.570A pdb=" N GLN D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D 174 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU D 177 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 203 removed outlier: 3.537A pdb=" N LEU D 201 " --> pdb=" O HIS D 197 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.845A pdb=" N LEU D 207 " --> pdb=" O TYR D 203 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR D 208 " --> pdb=" O ILE D 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 203 through 208' Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 249 through 264 removed outlier: 3.859A pdb=" N GLU D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Proline residue: D 255 - end of helix removed outlier: 3.586A pdb=" N GLU D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA D 263 " --> pdb=" O ALA D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 338 removed outlier: 3.587A pdb=" N VAL D 327 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU D 334 " --> pdb=" O GLY D 330 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 335 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 347 removed outlier: 3.942A pdb=" N ASP D 347 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 500 removed outlier: 3.518A pdb=" N ILE D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 530 removed outlier: 4.086A pdb=" N VAL D 528 " --> pdb=" O MET D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 549 removed outlier: 3.733A pdb=" N GLU D 548 " --> pdb=" O GLU D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.940A pdb=" N PHE D 577 " --> pdb=" O PRO D 574 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 578 " --> pdb=" O SER D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 588 removed outlier: 3.526A pdb=" N TRP D 586 " --> pdb=" O SER D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 603 removed outlier: 3.620A pdb=" N MET D 592 " --> pdb=" O MET D 588 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS D 593 " --> pdb=" O MET D 589 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR D 595 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA D 598 " --> pdb=" O LEU D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 606 No H-bonds generated for 'chain 'D' and resid 604 through 606' Processing helix chain 'D' and resid 629 through 641 removed outlier: 3.931A pdb=" N LEU D 635 " --> pdb=" O LYS D 631 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA D 638 " --> pdb=" O TRP D 634 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL D 640 " --> pdb=" O LEU D 636 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE D 641 " --> pdb=" O TRP D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 683 removed outlier: 3.618A pdb=" N MET D 658 " --> pdb=" O THR D 654 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL D 659 " --> pdb=" O SER D 655 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 668 " --> pdb=" O PHE D 664 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 675 " --> pdb=" O ALA D 671 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA D 678 " --> pdb=" O THR D 674 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN D 683 " --> pdb=" O ALA D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 700 removed outlier: 3.666A pdb=" N GLN D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG D 700 " --> pdb=" O ARG D 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 695 through 700' Processing helix chain 'D' and resid 701 through 704 removed outlier: 3.635A 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: 3.945A pdb=" N LYS D 720 " --> pdb=" O GLY D 716 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE D 722 " --> pdb=" O THR D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 733 removed outlier: 3.865A pdb=" N TYR D 732 " --> pdb=" O ASP D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 751 removed outlier: 3.545A pdb=" N THR D 746 " --> pdb=" O GLU D 742 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 748 " --> pdb=" O ALA D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 769 removed outlier: 4.086A pdb=" N TYR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 799 through 813 Processing helix chain 'D' and resid 814 through 824 Processing helix chain 'D' and resid 840 through 872 removed outlier: 3.812A pdb=" N ASN D 844 " --> pdb=" O LEU D 840 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY D 847 " --> pdb=" O ASP D 843 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL D 848 " --> pdb=" O ASN D 844 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE D 849 " --> pdb=" O MET D 845 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR D 850 " --> pdb=" O ALA D 846 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET D 851 " --> pdb=" O GLY D 847 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU D 852 " --> pdb=" O VAL D 848 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 855 " --> pdb=" O MET D 851 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 860 " --> pdb=" O MET D 856 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 861 " --> pdb=" O GLY D 857 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP D 871 " --> pdb=" O HIS D 867 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG D 872 " --> pdb=" O LEU D 868 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.109A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 7.283A pdb=" N ILE A 163 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.791A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 478 removed outlier: 3.512A pdb=" N THR A 402 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.682A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.688A pdb=" N THR A 486 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.828A pdb=" N ALA A 682 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 730 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 68 through 72 removed outlier: 6.898A pdb=" N ILE B 37 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 124 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.715A pdb=" N PHE B 169 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 168 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU B 229 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 405 through 410 removed outlier: 3.606A pdb=" N ILE B 408 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 3.654A 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 488 through 490 Processing sheet with id=AB4, first strand: chain 'B' and resid 524 through 525 removed outlier: 3.565A pdb=" N ASP B 524 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.506A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 31 through 33 removed outlier: 3.583A pdb=" N VAL C 65 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 33 " --> pdb=" O VAL C 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 197 removed outlier: 4.308A pdb=" N SER C 168 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AB9, first strand: chain 'C' and resid 366 through 367 Processing sheet with id=AC1, first strand: chain 'C' and resid 476 through 478 removed outlier: 5.712A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 410 through 413 removed outlier: 3.633A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC4, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.690A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 54 through 57 removed outlier: 3.929A pdb=" N GLU D 118 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL D 115 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL D 144 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N PHE D 117 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE D 141 " --> pdb=" O LEU D 162 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 188 through 191 removed outlier: 6.876A pdb=" N VAL D 188 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N PHE D 247 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL D 190 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 244 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL D 307 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LEU D 304 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 444 through 447 removed outlier: 4.754A pdb=" N LEU D 505 " --> pdb=" O PRO D 461 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG D 463 " --> pdb=" O LEU D 505 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 507 " --> pdb=" O ARG D 463 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 515 through 516 Processing sheet with id=AC9, first strand: chain 'D' and resid 710 through 711 removed outlier: 6.598A pdb=" N GLY D 711 " --> pdb=" O ILE D 757 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N ASP D 759 " --> pdb=" O GLY D 711 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2154 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: 7.78 Time building geometry restraints manager: 7.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7848 1.35 - 1.46: 5882 1.46 - 1.58: 10851 1.58 - 1.70: 0 1.70 - 1.82: 233 Bond restraints: 24814 Sorted by residual: bond pdb=" CA PRO C 142 " pdb=" C PRO C 142 " ideal model delta sigma weight residual 1.517 1.503 0.014 6.70e-03 2.23e+04 4.50e+00 bond pdb=" CA PRO A 142 " pdb=" C PRO A 142 " ideal model delta sigma weight residual 1.517 1.529 -0.012 6.70e-03 2.23e+04 3.41e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C1 NAG C 902 " pdb=" O5 NAG C 902 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C1 NAG D 902 " pdb=" O5 NAG D 902 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.74e+00 ... (remaining 24809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 33172 1.47 - 2.93: 453 2.93 - 4.40: 63 4.40 - 5.86: 20 5.86 - 7.33: 2 Bond angle restraints: 33710 Sorted by residual: angle pdb=" C ASP A 130 " pdb=" N LYS A 131 " pdb=" CA LYS A 131 " ideal model delta sigma weight residual 121.54 126.62 -5.08 1.91e+00 2.74e-01 7.07e+00 angle pdb=" N VAL C 157 " pdb=" CA VAL C 157 " pdb=" C VAL C 157 " ideal model delta sigma weight residual 112.80 109.84 2.96 1.15e+00 7.56e-01 6.62e+00 angle pdb=" CA CYS D 828 " pdb=" CB CYS D 828 " pdb=" SG CYS D 828 " ideal model delta sigma weight residual 114.40 119.89 -5.49 2.30e+00 1.89e-01 5.69e+00 angle pdb=" C VAL C 218 " pdb=" N ILE C 219 " pdb=" CA ILE C 219 " ideal model delta sigma weight residual 120.69 123.97 -3.28 1.46e+00 4.69e-01 5.04e+00 angle pdb=" N VAL A 409 " pdb=" CA VAL A 409 " pdb=" C VAL A 409 " ideal model delta sigma weight residual 106.61 110.45 -3.84 1.78e+00 3.16e-01 4.65e+00 ... (remaining 33705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 14034 21.54 - 43.08: 680 43.08 - 64.62: 102 64.62 - 86.16: 11 86.16 - 107.70: 10 Dihedral angle restraints: 14837 sinusoidal: 5789 harmonic: 9048 Sorted by residual: dihedral pdb=" CB CYS B 429 " pdb=" SG CYS B 429 " pdb=" SG CYS B 456 " pdb=" CB CYS B 456 " ideal model delta sinusoidal sigma weight residual 93.00 143.90 -50.90 1 1.00e+01 1.00e-02 3.55e+01 dihedral pdb=" CB CYS D 455 " pdb=" SG CYS D 455 " pdb=" SG CYS D 483 " pdb=" CB CYS D 483 " ideal model delta sinusoidal sigma weight residual 93.00 139.91 -46.91 1 1.00e+01 1.00e-02 3.04e+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 -155.44 -24.56 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 14834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2447 0.031 - 0.063: 953 0.063 - 0.094: 284 0.094 - 0.126: 163 0.126 - 0.157: 6 Chirality restraints: 3853 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.30e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 771 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CB ILE C 373 " pdb=" CA ILE C 373 " pdb=" CG1 ILE C 373 " pdb=" CG2 ILE C 373 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 3850 not shown) Planarity restraints: 4294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 318 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.17e+00 pdb=" N PRO C 319 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 319 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 319 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 262 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 263 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 263 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 263 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 623 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 624 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 624 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 624 " -0.021 5.00e-02 4.00e+02 ... (remaining 4291 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5841 2.79 - 3.32: 22334 3.32 - 3.85: 35903 3.85 - 4.37: 41381 4.37 - 4.90: 73023 Nonbonded interactions: 178482 Sorted by model distance: nonbonded pdb=" OG1 THR C 97 " pdb=" OD1 ASN C 99 " model vdw 2.266 3.040 nonbonded pdb=" O GLY C 307 " pdb=" ND2 ASN C 311 " model vdw 2.279 3.120 nonbonded pdb=" ND2 ASN A 70 " pdb=" OE1 GLN A 73 " model vdw 2.292 3.120 nonbonded pdb=" O SER B 599 " pdb=" NZ LYS B 604 " model vdw 2.293 3.120 nonbonded pdb=" O ASP B 113 " pdb=" OG SER B 116 " model vdw 2.297 3.040 ... (remaining 178477 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 810 or (resid 811 through 812 and (name N or name CA or name C or name O or n \ ame 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 52.890 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 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 : 0.002 0.039 24836 Z= 0.101 Angle : 0.459 7.326 33760 Z= 0.238 Chirality : 0.041 0.157 3853 Planarity : 0.003 0.067 4289 Dihedral : 12.556 107.700 8957 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.51 % Favored : 94.45 % Rotamer: Outliers : 1.44 % Allowed : 8.27 % Favored : 90.30 % 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: -1.98 (0.14), residues: 3101 helix: -0.86 (0.15), residues: 1120 sheet: -0.72 (0.28), residues: 391 loop : -1.80 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 379 HIS 0.004 0.001 HIS D 197 PHE 0.013 0.001 PHE C 472 TYR 0.011 0.001 TYR C 795 ARG 0.003 0.000 ARG D 329 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 5) link_NAG-ASN : angle 1.51869 ( 15) link_BETA1-4 : bond 0.00826 ( 1) link_BETA1-4 : angle 1.61618 ( 3) hydrogen bonds : bond 0.30719 ( 762) hydrogen bonds : angle 8.24276 ( 2154) SS BOND : bond 0.00187 ( 16) SS BOND : angle 0.81172 ( 32) covalent geometry : bond 0.00219 (24814) covalent geometry : angle 0.45751 (33710) *********************** 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 335 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 298 time to evaluate : 2.628 Fit side-chains revert: symmetry clash REVERT: A 209 MET cc_start: 0.8281 (tpp) cc_final: 0.7922 (tpt) REVERT: A 240 MET cc_start: 0.8433 (mtp) cc_final: 0.8011 (mtp) REVERT: A 523 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.6390 (mtt180) REVERT: A 651 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8240 (tt) REVERT: A 785 MET cc_start: 0.8347 (mtt) cc_final: 0.8073 (mtt) REVERT: C 74 MET cc_start: 0.5849 (tpp) cc_final: 0.5462 (tpp) REVERT: C 376 ASP cc_start: 0.8272 (m-30) cc_final: 0.8048 (m-30) REVERT: C 607 MET cc_start: 0.7910 (tpp) cc_final: 0.7619 (tpp) REVERT: D 581 TYR cc_start: 0.5305 (OUTLIER) cc_final: 0.3939 (m-10) outliers start: 37 outliers final: 12 residues processed: 330 average time/residue: 0.3455 time to fit residues: 182.2826 Evaluate side-chains 265 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 250 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 696 GLN Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain D residue 581 TYR 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: 3.9990 chunk 80 optimal weight: 30.0000 chunk 159 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 243 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 148 optimal weight: 0.6980 chunk 181 optimal weight: 7.9990 chunk 282 optimal weight: 3.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.126135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.090523 restraints weight = 61467.427| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.00 r_work: 0.3188 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 24836 Z= 0.304 Angle : 0.670 12.045 33760 Z= 0.351 Chirality : 0.049 0.174 3853 Planarity : 0.005 0.066 4289 Dihedral : 6.857 85.160 3507 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.22 % Favored : 92.71 % Rotamer: Outliers : 2.64 % Allowed : 11.68 % Favored : 85.68 % 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: -1.87 (0.14), residues: 3101 helix: -0.49 (0.15), residues: 1142 sheet: -0.96 (0.28), residues: 380 loop : -1.89 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 637 HIS 0.012 0.001 HIS C 477 PHE 0.045 0.003 PHE A 458 TYR 0.023 0.002 TYR D 506 ARG 0.006 0.001 ARG C 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00641 ( 5) link_NAG-ASN : angle 2.35499 ( 15) link_BETA1-4 : bond 0.00170 ( 1) link_BETA1-4 : angle 1.37334 ( 3) hydrogen bonds : bond 0.07512 ( 762) hydrogen bonds : angle 5.75504 ( 2154) SS BOND : bond 0.00688 ( 16) SS BOND : angle 1.17021 ( 32) covalent geometry : bond 0.00757 (24814) covalent geometry : angle 0.66734 (33710) *********************** 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 344 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 276 time to evaluate : 2.542 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.7157 (tmm) cc_final: 0.6947 (tmm) REVERT: A 209 MET cc_start: 0.8376 (tpp) cc_final: 0.7951 (tpt) REVERT: A 624 PRO cc_start: 0.7792 (Cg_exo) cc_final: 0.7520 (Cg_endo) REVERT: A 651 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8585 (tt) REVERT: C 74 MET cc_start: 0.5875 (tpp) cc_final: 0.5469 (tpp) REVERT: C 275 LYS cc_start: 0.7270 (mmmt) cc_final: 0.6988 (mmmt) REVERT: C 376 ASP cc_start: 0.8446 (m-30) cc_final: 0.7960 (m-30) REVERT: C 607 MET cc_start: 0.8337 (tpp) cc_final: 0.8078 (tpp) REVERT: C 813 MET cc_start: 0.7417 (mtt) cc_final: 0.7199 (mtt) REVERT: D 161 PHE cc_start: 0.6847 (t80) cc_final: 0.6354 (t80) REVERT: D 198 ARG cc_start: 0.7728 (mpt-90) cc_final: 0.7283 (mpt180) REVERT: D 588 MET cc_start: 0.6200 (ttp) cc_final: 0.5915 (ttp) outliers start: 68 outliers final: 50 residues processed: 325 average time/residue: 0.3475 time to fit residues: 184.8891 Evaluate side-chains 311 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 260 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 581 TYR Chi-restraints excluded: chain D residue 604 PHE Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 705 TYR Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 863 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 296 optimal weight: 0.5980 chunk 279 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 298 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 284 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.128710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.093818 restraints weight = 61583.030| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.14 r_work: 0.3253 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24836 Z= 0.114 Angle : 0.519 8.954 33760 Z= 0.266 Chirality : 0.043 0.182 3853 Planarity : 0.004 0.063 4289 Dihedral : 5.628 60.932 3496 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.97 % Favored : 94.97 % Rotamer: Outliers : 2.45 % Allowed : 13.63 % Favored : 83.93 % 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: -1.54 (0.15), residues: 3101 helix: -0.08 (0.15), residues: 1147 sheet: -0.84 (0.28), residues: 369 loop : -1.80 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 637 HIS 0.008 0.001 HIS D 497 PHE 0.020 0.001 PHE C 458 TYR 0.013 0.001 TYR D 506 ARG 0.004 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 5) link_NAG-ASN : angle 1.86739 ( 15) link_BETA1-4 : bond 0.00364 ( 1) link_BETA1-4 : angle 1.40590 ( 3) hydrogen bonds : bond 0.04928 ( 762) hydrogen bonds : angle 4.97076 ( 2154) SS BOND : bond 0.00277 ( 16) SS BOND : angle 0.75498 ( 32) covalent geometry : bond 0.00261 (24814) covalent geometry : angle 0.51684 (33710) *********************** 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 338 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 275 time to evaluate : 3.074 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.7135 (tmm) cc_final: 0.6901 (tmm) REVERT: A 171 HIS cc_start: 0.7478 (t-90) cc_final: 0.6832 (m-70) REVERT: A 209 MET cc_start: 0.8337 (tpp) cc_final: 0.8000 (tpt) REVERT: A 651 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8520 (tt) REVERT: A 780 HIS cc_start: 0.8816 (OUTLIER) cc_final: 0.7116 (m-70) REVERT: B 307 MET cc_start: 0.5968 (ttt) cc_final: 0.5598 (tmm) REVERT: B 565 MET cc_start: 0.5355 (tpp) cc_final: 0.4787 (tpp) REVERT: B 568 ILE cc_start: 0.8747 (mm) cc_final: 0.8540 (mt) REVERT: B 795 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8393 (tt) REVERT: C 74 MET cc_start: 0.5892 (tpp) cc_final: 0.5519 (tpp) REVERT: C 210 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7397 (pm20) REVERT: C 275 LYS cc_start: 0.7069 (mmmt) cc_final: 0.6863 (mmmt) REVERT: C 607 MET cc_start: 0.8185 (tpp) cc_final: 0.7923 (tpp) REVERT: C 632 LEU cc_start: 0.8653 (tp) cc_final: 0.8342 (tt) REVERT: D 102 GLN cc_start: 0.7672 (tp40) cc_final: 0.7338 (tt0) REVERT: D 161 PHE cc_start: 0.6789 (t80) cc_final: 0.6348 (t80) REVERT: D 198 ARG cc_start: 0.7839 (mpt-90) cc_final: 0.7401 (mpt180) REVERT: D 588 MET cc_start: 0.6114 (ttp) cc_final: 0.5752 (ttp) REVERT: D 589 MET cc_start: 0.6697 (tpt) cc_final: 0.6270 (tpt) outliers start: 63 outliers final: 42 residues processed: 323 average time/residue: 0.3290 time to fit residues: 173.4999 Evaluate side-chains 307 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 THR 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 568 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 787 ASP Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain D residue 705 TYR Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain D residue 863 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 241 optimal weight: 20.0000 chunk 199 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 chunk 248 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS B 622 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.128738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.093921 restraints weight = 61926.579| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.13 r_work: 0.3246 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24836 Z= 0.113 Angle : 0.512 12.576 33760 Z= 0.260 Chirality : 0.042 0.166 3853 Planarity : 0.003 0.062 4289 Dihedral : 5.168 58.935 3494 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.80 % Favored : 94.13 % Rotamer: Outliers : 2.60 % Allowed : 14.52 % Favored : 82.88 % 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: -1.38 (0.15), residues: 3101 helix: 0.11 (0.16), residues: 1156 sheet: -0.74 (0.28), residues: 378 loop : -1.78 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 637 HIS 0.008 0.001 HIS D 497 PHE 0.021 0.001 PHE C 458 TYR 0.015 0.001 TYR D 506 ARG 0.003 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 5) link_NAG-ASN : angle 1.85547 ( 15) link_BETA1-4 : bond 0.00137 ( 1) link_BETA1-4 : angle 1.19602 ( 3) hydrogen bonds : bond 0.04308 ( 762) hydrogen bonds : angle 4.70160 ( 2154) SS BOND : bond 0.00188 ( 16) SS BOND : angle 0.71985 ( 32) covalent geometry : bond 0.00263 (24814) covalent geometry : angle 0.51055 (33710) *********************** 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 327 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 260 time to evaluate : 2.533 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.7110 (tmm) cc_final: 0.6868 (tmm) REVERT: A 171 HIS cc_start: 0.7394 (t-90) cc_final: 0.6820 (m-70) REVERT: A 209 MET cc_start: 0.8341 (tpp) cc_final: 0.7965 (tpt) REVERT: A 651 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8460 (tt) REVERT: A 780 HIS cc_start: 0.8815 (OUTLIER) cc_final: 0.6258 (m-70) REVERT: B 307 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5566 (tmm) REVERT: B 361 LYS cc_start: 0.7592 (mmtm) cc_final: 0.7348 (mmtm) REVERT: B 565 MET cc_start: 0.5327 (tpp) cc_final: 0.4796 (tpp) REVERT: B 568 ILE cc_start: 0.8764 (mm) cc_final: 0.8552 (mt) REVERT: B 795 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8418 (tt) REVERT: B 829 MET cc_start: 0.7006 (mmp) cc_final: 0.6778 (mmm) REVERT: C 74 MET cc_start: 0.5841 (tpp) cc_final: 0.5483 (tpp) REVERT: C 210 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: C 339 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6666 (mp0) REVERT: C 376 ASP cc_start: 0.8576 (m-30) cc_final: 0.8318 (m-30) REVERT: C 607 MET cc_start: 0.8158 (tpp) cc_final: 0.7867 (tpp) REVERT: C 632 LEU cc_start: 0.8609 (tp) cc_final: 0.8358 (tt) REVERT: D 102 GLN cc_start: 0.7791 (tp40) cc_final: 0.7423 (tt0) REVERT: D 161 PHE cc_start: 0.6780 (t80) cc_final: 0.6323 (t80) REVERT: D 197 HIS cc_start: 0.7199 (p90) cc_final: 0.6650 (p90) REVERT: D 581 TYR cc_start: 0.5148 (OUTLIER) cc_final: 0.3751 (m-10) REVERT: D 588 MET cc_start: 0.6145 (ttp) cc_final: 0.5780 (ttp) outliers start: 67 outliers final: 44 residues processed: 313 average time/residue: 0.3132 time to fit residues: 161.2934 Evaluate side-chains 297 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 787 ASP Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 581 TYR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain D residue 705 TYR Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 863 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 74 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 223 optimal weight: 0.9980 chunk 259 optimal weight: 0.0980 chunk 62 optimal weight: 7.9990 chunk 227 optimal weight: 0.6980 chunk 243 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.129543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.094683 restraints weight = 62085.461| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.04 r_work: 0.3272 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24836 Z= 0.101 Angle : 0.499 10.392 33760 Z= 0.252 Chirality : 0.042 0.161 3853 Planarity : 0.003 0.061 4289 Dihedral : 4.815 58.722 3491 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.00 % Rotamer: Outliers : 2.68 % Allowed : 15.30 % Favored : 82.03 % 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: -1.25 (0.15), residues: 3101 helix: 0.27 (0.16), residues: 1152 sheet: -0.65 (0.28), residues: 374 loop : -1.74 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D 637 HIS 0.007 0.001 HIS D 497 PHE 0.020 0.001 PHE D 680 TYR 0.013 0.001 TYR D 506 ARG 0.003 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00305 ( 5) link_NAG-ASN : angle 1.82944 ( 15) link_BETA1-4 : bond 0.00263 ( 1) link_BETA1-4 : angle 1.13125 ( 3) hydrogen bonds : bond 0.03809 ( 762) hydrogen bonds : angle 4.50890 ( 2154) SS BOND : bond 0.00301 ( 16) SS BOND : angle 1.15749 ( 32) covalent geometry : bond 0.00230 (24814) covalent geometry : angle 0.49633 (33710) *********************** 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 326 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 257 time to evaluate : 3.334 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.7117 (tmm) cc_final: 0.6864 (tmm) REVERT: A 74 MET cc_start: 0.7660 (mmt) cc_final: 0.7303 (mmp) REVERT: A 171 HIS cc_start: 0.7349 (t-90) cc_final: 0.6842 (m-70) REVERT: A 209 MET cc_start: 0.8349 (tpp) cc_final: 0.7956 (tpt) REVERT: A 359 ARG cc_start: 0.7869 (mmm160) cc_final: 0.7287 (tpp80) REVERT: A 780 HIS cc_start: 0.8769 (OUTLIER) cc_final: 0.6080 (m-70) REVERT: B 307 MET cc_start: 0.5957 (ttt) cc_final: 0.5635 (tmm) REVERT: B 565 MET cc_start: 0.5225 (tpp) cc_final: 0.4643 (tpp) REVERT: B 568 ILE cc_start: 0.8746 (mm) cc_final: 0.8539 (mt) REVERT: B 795 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8428 (tt) REVERT: C 74 MET cc_start: 0.5874 (tpp) cc_final: 0.5507 (tpp) REVERT: C 210 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7396 (pm20) REVERT: C 339 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6670 (mp0) REVERT: C 607 MET cc_start: 0.8085 (tpp) cc_final: 0.7735 (tpp) REVERT: D 102 GLN cc_start: 0.7826 (tp40) cc_final: 0.7467 (tt0) REVERT: D 197 HIS cc_start: 0.7164 (p90) cc_final: 0.6263 (p90) REVERT: D 198 ARG cc_start: 0.7807 (mpt-90) cc_final: 0.7285 (mpt180) REVERT: D 581 TYR cc_start: 0.5049 (OUTLIER) cc_final: 0.3624 (m-10) REVERT: D 588 MET cc_start: 0.6184 (ttp) cc_final: 0.5797 (ttp) REVERT: D 589 MET cc_start: 0.6628 (tpt) cc_final: 0.6280 (tpt) outliers start: 69 outliers final: 50 residues processed: 312 average time/residue: 0.3594 time to fit residues: 184.8072 Evaluate side-chains 302 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 248 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 787 ASP Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 581 TYR Chi-restraints excluded: chain D residue 705 TYR Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 863 PHE Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 45 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 266 optimal weight: 20.0000 chunk 257 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS C 742 GLN C 770 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.126419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.091715 restraints weight = 61484.266| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.17 r_work: 0.3199 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 24836 Z= 0.285 Angle : 0.649 12.911 33760 Z= 0.330 Chirality : 0.048 0.202 3853 Planarity : 0.004 0.060 4289 Dihedral : 5.358 59.552 3487 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.45 % Favored : 92.49 % Rotamer: Outliers : 3.42 % Allowed : 15.26 % Favored : 81.33 % 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: -0.07 (0.15), residues: 1154 sheet: -0.60 (0.29), residues: 356 loop : -1.90 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 637 HIS 0.012 0.001 HIS C 477 PHE 0.040 0.002 PHE A 458 TYR 0.023 0.002 TYR B 479 ARG 0.005 0.001 ARG A 673 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 5) link_NAG-ASN : angle 2.56703 ( 15) link_BETA1-4 : bond 0.00558 ( 1) link_BETA1-4 : angle 1.38242 ( 3) hydrogen bonds : bond 0.05675 ( 762) hydrogen bonds : angle 4.88724 ( 2154) SS BOND : bond 0.00507 ( 16) SS BOND : angle 1.55362 ( 32) covalent geometry : bond 0.00718 (24814) covalent geometry : angle 0.64557 (33710) *********************** 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 349 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 261 time to evaluate : 2.553 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.7216 (tmm) cc_final: 0.6943 (tmm) REVERT: A 74 MET cc_start: 0.7712 (mmt) cc_final: 0.7407 (mmp) REVERT: A 171 HIS cc_start: 0.7574 (t-90) cc_final: 0.6968 (m-70) REVERT: A 209 MET cc_start: 0.8401 (tpp) cc_final: 0.7960 (tpt) REVERT: A 359 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7299 (tpp80) REVERT: A 555 MET cc_start: 0.6440 (mtm) cc_final: 0.6206 (mmm) REVERT: B 307 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5643 (tmm) REVERT: B 795 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8493 (tt) REVERT: B 824 MET cc_start: 0.7899 (ttp) cc_final: 0.7609 (ttp) REVERT: C 74 MET cc_start: 0.5751 (tpp) cc_final: 0.5363 (tpp) REVERT: C 607 MET cc_start: 0.8223 (tpp) cc_final: 0.7915 (tpp) REVERT: C 634 MET cc_start: 0.7458 (tmm) cc_final: 0.7149 (tmm) REVERT: D 102 GLN cc_start: 0.7799 (tp40) cc_final: 0.7478 (tt0) REVERT: D 161 PHE cc_start: 0.6841 (t80) cc_final: 0.6232 (t80) REVERT: D 197 HIS cc_start: 0.7207 (p90) cc_final: 0.6587 (p90) REVERT: D 588 MET cc_start: 0.6235 (ttp) cc_final: 0.5862 (ttp) REVERT: D 658 MET cc_start: 0.7373 (mmm) cc_final: 0.7112 (mmm) outliers start: 88 outliers final: 72 residues processed: 334 average time/residue: 0.3182 time to fit residues: 175.3534 Evaluate side-chains 326 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 252 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 581 TYR Chi-restraints excluded: chain D residue 604 PHE Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 705 TYR Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 34 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 309 optimal weight: 0.7980 chunk 232 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 151 optimal weight: 0.1980 chunk 209 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.127752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092187 restraints weight = 61426.882| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.05 r_work: 0.3243 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24836 Z= 0.143 Angle : 0.549 13.095 33760 Z= 0.277 Chirality : 0.043 0.165 3853 Planarity : 0.004 0.060 4289 Dihedral : 4.962 56.543 3485 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 3.14 % Allowed : 16.15 % Favored : 80.71 % 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: -1.42 (0.15), residues: 3101 helix: 0.14 (0.16), residues: 1143 sheet: -0.88 (0.27), residues: 388 loop : -1.81 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 637 HIS 0.010 0.001 HIS D 497 PHE 0.024 0.001 PHE A 458 TYR 0.016 0.001 TYR D 506 ARG 0.003 0.000 ARG D 740 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 5) link_NAG-ASN : angle 2.18055 ( 15) link_BETA1-4 : bond 0.00260 ( 1) link_BETA1-4 : angle 1.31832 ( 3) hydrogen bonds : bond 0.04444 ( 762) hydrogen bonds : angle 4.64804 ( 2154) SS BOND : bond 0.00307 ( 16) SS BOND : angle 1.07928 ( 32) covalent geometry : bond 0.00350 (24814) covalent geometry : angle 0.54648 (33710) *********************** 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 334 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 253 time to evaluate : 2.995 Fit side-chains REVERT: A 41 MET cc_start: 0.7127 (tmm) cc_final: 0.6863 (tmm) REVERT: A 74 MET cc_start: 0.7633 (mmt) cc_final: 0.7331 (mmp) REVERT: A 171 HIS cc_start: 0.7415 (t-90) cc_final: 0.6865 (m-70) REVERT: A 209 MET cc_start: 0.8364 (tpp) cc_final: 0.7936 (tpt) REVERT: A 359 ARG cc_start: 0.7847 (mmm160) cc_final: 0.7284 (tpp80) REVERT: A 780 HIS cc_start: 0.8854 (OUTLIER) cc_final: 0.6401 (m-70) REVERT: B 307 MET cc_start: 0.6002 (OUTLIER) cc_final: 0.5696 (tmm) REVERT: B 565 MET cc_start: 0.5504 (tpp) cc_final: 0.5034 (tpp) REVERT: B 795 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8455 (tt) REVERT: B 824 MET cc_start: 0.7804 (ttp) cc_final: 0.7422 (ttp) REVERT: C 74 MET cc_start: 0.5825 (tpp) cc_final: 0.5454 (tpp) REVERT: C 339 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6712 (mp0) REVERT: C 607 MET cc_start: 0.8163 (tpp) cc_final: 0.7858 (tpp) REVERT: C 634 MET cc_start: 0.7465 (tmm) cc_final: 0.7237 (tmm) REVERT: D 102 GLN cc_start: 0.7790 (tp40) cc_final: 0.7418 (tt0) REVERT: D 198 ARG cc_start: 0.7640 (mpt-90) cc_final: 0.7351 (mpt180) REVERT: D 581 TYR cc_start: 0.5040 (OUTLIER) cc_final: 0.3579 (m-10) REVERT: D 588 MET cc_start: 0.6257 (ttp) cc_final: 0.5900 (ttp) REVERT: D 589 MET cc_start: 0.6678 (tpt) cc_final: 0.6301 (tpt) REVERT: D 658 MET cc_start: 0.7140 (mmm) cc_final: 0.6913 (mmm) outliers start: 81 outliers final: 66 residues processed: 320 average time/residue: 0.4347 time to fit residues: 230.4978 Evaluate side-chains 319 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 249 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 581 TYR Chi-restraints excluded: chain D residue 604 PHE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 705 TYR Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 863 PHE Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 163 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 308 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 221 optimal weight: 0.9990 chunk 305 optimal weight: 3.9990 chunk 261 optimal weight: 0.0370 chunk 54 optimal weight: 0.6980 chunk 96 optimal weight: 20.0000 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.129054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.094423 restraints weight = 61663.087| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 3.17 r_work: 0.3271 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24836 Z= 0.099 Angle : 0.514 12.338 33760 Z= 0.258 Chirality : 0.042 0.218 3853 Planarity : 0.003 0.061 4289 Dihedral : 4.604 58.084 3485 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.42 % Favored : 94.52 % Rotamer: Outliers : 2.83 % Allowed : 16.77 % Favored : 80.40 % 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: -1.26 (0.15), residues: 3101 helix: 0.29 (0.16), residues: 1156 sheet: -0.59 (0.28), residues: 365 loop : -1.80 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 637 HIS 0.010 0.001 HIS D 497 PHE 0.034 0.001 PHE C 829 TYR 0.013 0.001 TYR D 506 ARG 0.003 0.000 ARG D 740 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 5) link_NAG-ASN : angle 1.95534 ( 15) link_BETA1-4 : bond 0.00377 ( 1) link_BETA1-4 : angle 1.24654 ( 3) hydrogen bonds : bond 0.03645 ( 762) hydrogen bonds : angle 4.40712 ( 2154) SS BOND : bond 0.00219 ( 16) SS BOND : angle 0.82273 ( 32) covalent geometry : bond 0.00226 (24814) covalent geometry : angle 0.51235 (33710) *********************** 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 328 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 255 time to evaluate : 2.846 Fit side-chains REVERT: A 41 MET cc_start: 0.7136 (tmm) cc_final: 0.6875 (tmm) REVERT: A 165 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7850 (tt) REVERT: A 171 HIS cc_start: 0.7303 (t-90) cc_final: 0.6820 (m-70) REVERT: A 209 MET cc_start: 0.8369 (tpp) cc_final: 0.7934 (tpt) REVERT: A 359 ARG cc_start: 0.7871 (mmm160) cc_final: 0.7246 (tpp80) REVERT: A 780 HIS cc_start: 0.8760 (OUTLIER) cc_final: 0.6089 (m-70) REVERT: B 307 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5694 (tmm) REVERT: B 565 MET cc_start: 0.5278 (tpp) cc_final: 0.4776 (tpp) REVERT: B 795 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8406 (tt) REVERT: C 74 MET cc_start: 0.5851 (tpp) cc_final: 0.5491 (tpp) REVERT: C 339 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6716 (mp0) REVERT: C 607 MET cc_start: 0.8103 (tpp) cc_final: 0.7764 (tpp) REVERT: C 634 MET cc_start: 0.7488 (tmm) cc_final: 0.7259 (tmm) REVERT: D 102 GLN cc_start: 0.7845 (tp40) cc_final: 0.7528 (tt0) REVERT: D 197 HIS cc_start: 0.7211 (p90) cc_final: 0.6324 (p90) REVERT: D 198 ARG cc_start: 0.7692 (mpt-90) cc_final: 0.7390 (mpt180) REVERT: D 581 TYR cc_start: 0.5129 (OUTLIER) cc_final: 0.3732 (m-10) REVERT: D 588 MET cc_start: 0.6228 (ttp) cc_final: 0.5876 (ttp) REVERT: D 589 MET cc_start: 0.6646 (tpt) cc_final: 0.6279 (tpt) outliers start: 73 outliers final: 58 residues processed: 316 average time/residue: 0.3069 time to fit residues: 160.9417 Evaluate side-chains 311 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 248 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 581 TYR Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 863 PHE Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 227 optimal weight: 0.0980 chunk 15 optimal weight: 9.9990 chunk 294 optimal weight: 0.8980 chunk 257 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 237 optimal weight: 20.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.126898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.091224 restraints weight = 61721.778| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.96 r_work: 0.3210 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 24836 Z= 0.237 Angle : 0.613 12.657 33760 Z= 0.311 Chirality : 0.046 0.200 3853 Planarity : 0.004 0.060 4289 Dihedral : 5.059 59.048 3485 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.45 % Favored : 92.49 % Rotamer: Outliers : 2.99 % Allowed : 17.00 % Favored : 80.01 % 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: -1.46 (0.15), residues: 3101 helix: 0.08 (0.16), residues: 1144 sheet: -0.75 (0.29), residues: 366 loop : -1.85 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 637 HIS 0.009 0.001 HIS C 477 PHE 0.035 0.002 PHE A 458 TYR 0.019 0.002 TYR B 479 ARG 0.004 0.000 ARG A 673 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 5) link_NAG-ASN : angle 2.43909 ( 15) link_BETA1-4 : bond 0.00046 ( 1) link_BETA1-4 : angle 1.26638 ( 3) hydrogen bonds : bond 0.05128 ( 762) hydrogen bonds : angle 4.68911 ( 2154) SS BOND : bond 0.00414 ( 16) SS BOND : angle 1.22279 ( 32) covalent geometry : bond 0.00594 (24814) covalent geometry : angle 0.60989 (33710) *********************** 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 328 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 251 time to evaluate : 4.478 Fit side-chains revert: symmetry clash REVERT: A 41 MET cc_start: 0.7216 (tmm) cc_final: 0.6935 (tmm) REVERT: A 165 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7921 (tt) REVERT: A 171 HIS cc_start: 0.7492 (t-90) cc_final: 0.6947 (m-70) REVERT: A 209 MET cc_start: 0.8439 (tpp) cc_final: 0.7994 (tpt) REVERT: A 359 ARG cc_start: 0.7872 (mmm160) cc_final: 0.7224 (mmm-85) REVERT: A 780 HIS cc_start: 0.8887 (OUTLIER) cc_final: 0.6680 (m-70) REVERT: B 142 MET cc_start: 0.7524 (ptp) cc_final: 0.6800 (ppp) REVERT: B 307 MET cc_start: 0.6014 (OUTLIER) cc_final: 0.5670 (tmm) REVERT: B 795 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8466 (tt) REVERT: C 576 MET cc_start: 0.8605 (ppp) cc_final: 0.8174 (ptt) REVERT: C 607 MET cc_start: 0.8180 (tpp) cc_final: 0.7872 (tpp) REVERT: D 102 GLN cc_start: 0.7762 (tp40) cc_final: 0.7397 (tt0) REVERT: D 197 HIS cc_start: 0.7252 (p90) cc_final: 0.6349 (p90) REVERT: D 198 ARG cc_start: 0.7698 (mpt-90) cc_final: 0.7382 (mpt180) REVERT: D 415 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6299 (pt) REVERT: D 588 MET cc_start: 0.6352 (ttp) cc_final: 0.5977 (ttp) REVERT: D 589 MET cc_start: 0.6727 (tpt) cc_final: 0.6394 (tpt) REVERT: D 658 MET cc_start: 0.7191 (mmm) cc_final: 0.6978 (mmm) outliers start: 77 outliers final: 67 residues processed: 318 average time/residue: 0.4223 time to fit residues: 227.3230 Evaluate side-chains 321 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 249 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain D residue 559 THR Chi-restraints excluded: chain D residue 581 TYR Chi-restraints excluded: chain D residue 604 PHE Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 66 optimal weight: 2.9990 chunk 308 optimal weight: 0.0770 chunk 217 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 209 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 227 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 300 optimal weight: 0.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.129016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.094372 restraints weight = 61504.966| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.98 r_work: 0.3275 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24836 Z= 0.103 Angle : 0.527 12.651 33760 Z= 0.263 Chirality : 0.042 0.190 3853 Planarity : 0.003 0.061 4289 Dihedral : 4.599 55.994 3485 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.78 % Rotamer: Outliers : 2.52 % Allowed : 17.51 % Favored : 79.97 % 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: -1.26 (0.15), residues: 3101 helix: 0.32 (0.16), residues: 1140 sheet: -0.73 (0.28), residues: 376 loop : -1.76 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 608 HIS 0.011 0.001 HIS D 497 PHE 0.037 0.001 PHE C 829 TYR 0.014 0.001 TYR D 506 ARG 0.003 0.000 ARG D 740 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 5) link_NAG-ASN : angle 1.94196 ( 15) link_BETA1-4 : bond 0.00349 ( 1) link_BETA1-4 : angle 1.37886 ( 3) hydrogen bonds : bond 0.03650 ( 762) hydrogen bonds : angle 4.39965 ( 2154) SS BOND : bond 0.00212 ( 16) SS BOND : angle 0.85359 ( 32) covalent geometry : bond 0.00237 (24814) covalent geometry : angle 0.52498 (33710) ********************** 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 316 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 251 time to evaluate : 2.716 Fit side-chains REVERT: A 41 MET cc_start: 0.7139 (tmm) cc_final: 0.6875 (tmm) REVERT: A 165 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7889 (tt) REVERT: A 171 HIS cc_start: 0.7355 (t-90) cc_final: 0.6883 (m-70) REVERT: A 209 MET cc_start: 0.8358 (tpp) cc_final: 0.7905 (tpt) REVERT: A 359 ARG cc_start: 0.7903 (mmm160) cc_final: 0.7273 (mmm-85) REVERT: A 780 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.6147 (m-70) REVERT: B 142 MET cc_start: 0.7553 (ptp) cc_final: 0.6794 (ppp) REVERT: B 307 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5745 (tmm) REVERT: B 565 MET cc_start: 0.5294 (tpp) cc_final: 0.4828 (tpp) REVERT: B 795 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8461 (tt) REVERT: C 74 MET cc_start: 0.5963 (tpp) cc_final: 0.5628 (tpp) REVERT: C 339 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6740 (mp0) REVERT: C 576 MET cc_start: 0.8535 (ppp) cc_final: 0.8206 (ptm) REVERT: C 607 MET cc_start: 0.8115 (tpp) cc_final: 0.7815 (tpp) REVERT: D 102 GLN cc_start: 0.7852 (tp40) cc_final: 0.7523 (tt0) REVERT: D 197 HIS cc_start: 0.7247 (p90) cc_final: 0.6380 (p90) REVERT: D 198 ARG cc_start: 0.7712 (mpt-90) cc_final: 0.7406 (mpt180) REVERT: D 581 TYR cc_start: 0.5078 (OUTLIER) cc_final: 0.3588 (m-10) REVERT: D 588 MET cc_start: 0.6410 (ttp) cc_final: 0.6039 (ttp) REVERT: D 589 MET cc_start: 0.6681 (tpt) cc_final: 0.6385 (tpt) REVERT: D 740 ARG cc_start: 0.7838 (mtm110) cc_final: 0.7621 (mtm110) outliers start: 65 outliers final: 59 residues processed: 307 average time/residue: 0.3116 time to fit residues: 157.4807 Evaluate side-chains 316 residues out of total 2686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 252 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 561 MET Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 417 SER Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 581 TYR Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 682 ILE Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 184 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 193 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 277 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.127943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.093272 restraints weight = 61489.847| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.19 r_work: 0.3238 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24836 Z= 0.157 Angle : 0.555 12.906 33760 Z= 0.279 Chirality : 0.044 0.209 3853 Planarity : 0.004 0.060 4289 Dihedral : 4.731 56.176 3485 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.64 % Favored : 93.29 % Rotamer: Outliers : 2.95 % Allowed : 17.31 % Favored : 79.74 % 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: -1.28 (0.15), residues: 3101 helix: 0.32 (0.16), residues: 1138 sheet: -0.83 (0.27), residues: 384 loop : -1.77 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 637 HIS 0.010 0.001 HIS D 497 PHE 0.036 0.002 PHE C 829 TYR 0.015 0.001 TYR D 506 ARG 0.005 0.000 ARG C 630 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 5) link_NAG-ASN : angle 2.13028 ( 15) link_BETA1-4 : bond 0.00479 ( 1) link_BETA1-4 : angle 1.31040 ( 3) hydrogen bonds : bond 0.04293 ( 762) hydrogen bonds : angle 4.46151 ( 2154) SS BOND : bond 0.00302 ( 16) SS BOND : angle 1.00383 ( 32) covalent geometry : bond 0.00388 (24814) covalent geometry : angle 0.55282 (33710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15200.70 seconds wall clock time: 270 minutes 11.20 seconds (16211.20 seconds total)