Starting phenix.real_space_refine on Tue Aug 26 21:19:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3j6q_5926/08_2025/3j6q_5926.cif Found real_map, /net/cci-nas-00/data/ceres_data/3j6q_5926/08_2025/3j6q_5926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/3j6q_5926/08_2025/3j6q_5926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3j6q_5926/08_2025/3j6q_5926.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3j6q_5926/08_2025/3j6q_5926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3j6q_5926/08_2025/3j6q_5926.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.202 sd= 10.389 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 235 5.16 5 C 26930 2.51 5 N 7375 2.21 5 O 8030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42575 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL%rna2p': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL%rna2p:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL%rna2p': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL%rna2p:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL%rna2p': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL%rna2p:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL%rna2p': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL%rna2p:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 8463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8463 Unusual residues: {'GPL%rna2p': 1} Classifications: {'peptide': 1057, 'undetermined': 1} Modifications used: {'rna2p': 1} Link IDs: {'CIS': 12, 'PCIS': 8, 'PTRANS': 44, 'TRANS': 993} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GPL%rna2p:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain breaks: 1 Time building chain proxies: 8.18, per 1000 atoms: 0.19 Number of scatterers: 42575 At special positions: 0 Unit cell: (179.4, 177.008, 111.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 235 16.00 P 5 15.00 O 8030 8.00 N 7375 7.00 C 26930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10200 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 50 sheets defined 33.5% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 12 through 16 removed outlier: 3.924A pdb=" N ASP A 16 " --> pdb=" O VAL A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 removed outlier: 4.472A pdb=" N GLY A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N HIS A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 77' Processing helix chain 'A' and resid 84 through 98 removed outlier: 3.834A pdb=" N LEU A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 124 removed outlier: 3.501A pdb=" N GLY A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 137 removed outlier: 4.416A pdb=" N VAL A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.968A pdb=" N SER A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.908A pdb=" N VAL A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 193 " --> pdb=" O MET A 189 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 226 Processing helix chain 'A' and resid 227 through 246 removed outlier: 3.901A pdb=" N ALA A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU A 243 " --> pdb=" O TRP A 239 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.834A pdb=" N ARG A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 307 removed outlier: 3.521A pdb=" N ASP A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 303 " --> pdb=" O GLN A 299 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.573A pdb=" N ASN A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 333 through 341 removed outlier: 3.525A pdb=" N LEU A 337 " --> pdb=" O GLN A 333 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.679A pdb=" N ASP A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.680A pdb=" N ASN A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN A 458 " --> pdb=" O GLY A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 458' Processing helix chain 'A' and resid 462 through 471 Proline residue: A 468 - end of helix Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 490 through 497 Processing helix chain 'A' and resid 526 through 544 removed outlier: 3.571A pdb=" N MET A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N MET A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 575 Processing helix chain 'A' and resid 624 through 637 removed outlier: 4.246A pdb=" N SER A 630 " --> pdb=" O GLU A 626 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 637 " --> pdb=" O ILE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 667 removed outlier: 3.575A pdb=" N ASN A 659 " --> pdb=" O GLU A 655 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 667 " --> pdb=" O GLU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 removed outlier: 4.049A pdb=" N ARG A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 760 removed outlier: 3.631A pdb=" N ALA A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 Processing helix chain 'A' and resid 788 through 796 removed outlier: 3.623A pdb=" N ALA A 793 " --> pdb=" O PRO A 789 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 809 removed outlier: 3.861A pdb=" N TYR A 808 " --> pdb=" O ALA A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 850 removed outlier: 3.951A pdb=" N LYS A 838 " --> pdb=" O THR A 834 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 847 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 893 removed outlier: 3.576A pdb=" N GLU A 893 " --> pdb=" O THR A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 951 removed outlier: 4.436A pdb=" N VAL A 946 " --> pdb=" O LYS A 942 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 971 Processing helix chain 'A' and resid 999 through 1006 removed outlier: 3.682A pdb=" N LEU A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1032 Processing helix chain 'A' and resid 1036 through 1038 No H-bonds generated for 'chain 'A' and resid 1036 through 1038' Processing helix chain 'A' and resid 1039 through 1047 removed outlier: 4.197A pdb=" N VAL A1045 " --> pdb=" O ALA A1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 16 removed outlier: 3.924A pdb=" N ASP B 16 " --> pdb=" O VAL B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 69 removed outlier: 4.473A pdb=" N GLY B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 69' Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU B 76 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 77' Processing helix chain 'B' and resid 84 through 98 removed outlier: 3.835A pdb=" N LEU B 88 " --> pdb=" O PRO B 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 124 removed outlier: 3.600A pdb=" N THR B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 137 removed outlier: 4.415A pdb=" N VAL B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.969A pdb=" N SER B 152 " --> pdb=" O ASP B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 196 removed outlier: 3.908A pdb=" N VAL B 192 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN B 193 " --> pdb=" O MET B 189 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 226 Processing helix chain 'B' and resid 227 through 246 removed outlier: 3.901A pdb=" N ALA B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU B 243 " --> pdb=" O TRP B 239 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.834A pdb=" N ARG B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.519A pdb=" N ASP B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 removed outlier: 3.574A pdb=" N ASN B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 333 through 341 removed outlier: 3.526A pdb=" N LEU B 337 " --> pdb=" O GLN B 333 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.678A pdb=" N ASP B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.680A pdb=" N ASN B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN B 458 " --> pdb=" O GLY B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 458' Processing helix chain 'B' and resid 462 through 471 Proline residue: B 468 - end of helix Processing helix chain 'B' and resid 472 through 478 Processing helix chain 'B' and resid 490 through 497 Processing helix chain 'B' and resid 526 through 544 removed outlier: 3.572A pdb=" N MET B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET B 532 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL B 537 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 544 " --> pdb=" O LYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 624 through 637 removed outlier: 4.247A pdb=" N SER B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 637 " --> pdb=" O ILE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.575A pdb=" N ASN B 659 " --> pdb=" O GLU B 655 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 667 " --> pdb=" O GLU B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 removed outlier: 4.049A pdb=" N ARG B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 760 removed outlier: 3.631A pdb=" N ALA B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 788 through 796 removed outlier: 3.624A pdb=" N ALA B 793 " --> pdb=" O PRO B 789 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU B 794 " --> pdb=" O ALA B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 809 removed outlier: 3.860A pdb=" N TYR B 808 " --> pdb=" O ALA B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 850 removed outlier: 3.951A pdb=" N LYS B 838 " --> pdb=" O THR B 834 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 845 " --> pdb=" O MET B 841 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU B 847 " --> pdb=" O ALA B 843 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 848 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 893 removed outlier: 3.579A pdb=" N GLU B 893 " --> pdb=" O THR B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 951 removed outlier: 4.436A pdb=" N VAL B 946 " --> pdb=" O LYS B 942 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 949 " --> pdb=" O ASN B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 971 Processing helix chain 'B' and resid 999 through 1006 removed outlier: 3.681A pdb=" N LEU B1005 " --> pdb=" O ALA B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1020 through 1032 Processing helix chain 'B' and resid 1036 through 1038 No H-bonds generated for 'chain 'B' and resid 1036 through 1038' Processing helix chain 'B' and resid 1039 through 1047 removed outlier: 4.199A pdb=" N VAL B1045 " --> pdb=" O ALA B1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 16 removed outlier: 3.925A pdb=" N ASP C 16 " --> pdb=" O VAL C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 69 removed outlier: 4.471A pdb=" N GLY C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS C 69 " --> pdb=" O THR C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 69' Processing helix chain 'C' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU C 76 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 77' Processing helix chain 'C' and resid 84 through 98 removed outlier: 3.834A pdb=" N LEU C 88 " --> pdb=" O PRO C 84 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.601A pdb=" N THR C 124 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 137 removed outlier: 4.416A pdb=" N VAL C 134 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN C 136 " --> pdb=" O GLN C 132 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 147 through 152 removed outlier: 3.969A pdb=" N SER C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 196 removed outlier: 3.907A pdb=" N VAL C 192 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN C 193 " --> pdb=" O MET C 189 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS C 194 " --> pdb=" O THR C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 226 Processing helix chain 'C' and resid 227 through 246 removed outlier: 3.901A pdb=" N ALA C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 243 " --> pdb=" O TRP C 239 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 277 removed outlier: 3.834A pdb=" N ARG C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 307 removed outlier: 3.520A pdb=" N ASP C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 321 removed outlier: 3.573A pdb=" N ASN C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 332 Processing helix chain 'C' and resid 333 through 341 removed outlier: 3.526A pdb=" N LEU C 337 " --> pdb=" O GLN C 333 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 435 through 447 removed outlier: 3.678A pdb=" N ASP C 446 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.679A pdb=" N ASN C 457 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASN C 458 " --> pdb=" O GLY C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 453 through 458' Processing helix chain 'C' and resid 462 through 471 Proline residue: C 468 - end of helix Processing helix chain 'C' and resid 472 through 478 Processing helix chain 'C' and resid 490 through 497 Processing helix chain 'C' and resid 526 through 544 removed outlier: 3.571A pdb=" N MET C 530 " --> pdb=" O ASN C 526 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS C 531 " --> pdb=" O ASN C 527 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N MET C 532 " --> pdb=" O SER C 528 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL C 537 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 538 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN C 544 " --> pdb=" O LYS C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 575 Processing helix chain 'C' and resid 624 through 637 removed outlier: 4.245A pdb=" N SER C 630 " --> pdb=" O GLU C 626 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 634 " --> pdb=" O SER C 630 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 636 " --> pdb=" O THR C 632 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR C 637 " --> pdb=" O ILE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 667 removed outlier: 3.575A pdb=" N ASN C 659 " --> pdb=" O GLU C 655 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 665 " --> pdb=" O VAL C 661 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN C 667 " --> pdb=" O GLU C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 removed outlier: 4.048A pdb=" N ARG C 714 " --> pdb=" O ALA C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 760 removed outlier: 3.631A pdb=" N ALA C 758 " --> pdb=" O SER C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 765 Processing helix chain 'C' and resid 788 through 796 removed outlier: 3.622A pdb=" N ALA C 793 " --> pdb=" O PRO C 789 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU C 794 " --> pdb=" O ALA C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 809 removed outlier: 3.861A pdb=" N TYR C 808 " --> pdb=" O ALA C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 850 removed outlier: 3.952A pdb=" N LYS C 838 " --> pdb=" O THR C 834 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 845 " --> pdb=" O MET C 841 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU C 847 " --> pdb=" O ALA C 843 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN C 848 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 893 removed outlier: 3.578A pdb=" N GLU C 893 " --> pdb=" O THR C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 951 removed outlier: 4.436A pdb=" N VAL C 946 " --> pdb=" O LYS C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 971 Processing helix chain 'C' and resid 999 through 1006 removed outlier: 3.682A pdb=" N LEU C1005 " --> pdb=" O ALA C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1020 through 1032 Processing helix chain 'C' and resid 1036 through 1038 No H-bonds generated for 'chain 'C' and resid 1036 through 1038' Processing helix chain 'C' and resid 1039 through 1047 removed outlier: 4.199A pdb=" N VAL C1045 " --> pdb=" O ALA C1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 16 removed outlier: 3.925A pdb=" N ASP D 16 " --> pdb=" O VAL D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 removed outlier: 4.472A pdb=" N GLY D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS D 69 " --> pdb=" O THR D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 69' Processing helix chain 'D' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 72 through 77' Processing helix chain 'D' and resid 84 through 98 removed outlier: 3.834A pdb=" N LEU D 88 " --> pdb=" O PRO D 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 124 removed outlier: 3.601A pdb=" N THR D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 137 removed outlier: 4.416A pdb=" N VAL D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL D 135 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN D 136 " --> pdb=" O GLN D 132 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 147 through 152 removed outlier: 3.969A pdb=" N SER D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 196 removed outlier: 3.908A pdb=" N VAL D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN D 193 " --> pdb=" O MET D 189 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS D 194 " --> pdb=" O THR D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 226 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.900A pdb=" N ALA D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU D 243 " --> pdb=" O TRP D 239 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 245 " --> pdb=" O GLN D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 277 removed outlier: 3.833A pdb=" N ARG D 271 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 307 removed outlier: 3.520A pdb=" N ASP D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR D 303 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 321 removed outlier: 3.574A pdb=" N ASN D 321 " --> pdb=" O ARG D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 332 Processing helix chain 'D' and resid 333 through 341 removed outlier: 3.526A pdb=" N LEU D 337 " --> pdb=" O GLN D 333 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 417 Processing helix chain 'D' and resid 435 through 447 removed outlier: 3.678A pdb=" N ASP D 446 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR D 447 " --> pdb=" O ALA D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.680A pdb=" N ASN D 457 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN D 458 " --> pdb=" O GLY D 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 453 through 458' Processing helix chain 'D' and resid 462 through 471 Proline residue: D 468 - end of helix Processing helix chain 'D' and resid 472 through 478 Processing helix chain 'D' and resid 490 through 497 Processing helix chain 'D' and resid 526 through 544 removed outlier: 3.571A pdb=" N MET D 530 " --> pdb=" O ASN D 526 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N MET D 532 " --> pdb=" O SER D 528 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 537 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN D 544 " --> pdb=" O LYS D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 575 Processing helix chain 'D' and resid 624 through 637 removed outlier: 4.245A pdb=" N SER D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 631 " --> pdb=" O SER D 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D 634 " --> pdb=" O SER D 630 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 636 " --> pdb=" O THR D 632 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 667 removed outlier: 3.575A pdb=" N ASN D 659 " --> pdb=" O GLU D 655 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 665 " --> pdb=" O VAL D 661 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN D 667 " --> pdb=" O GLU D 663 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 714 removed outlier: 4.048A pdb=" N ARG D 714 " --> pdb=" O ALA D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 760 removed outlier: 3.630A pdb=" N ALA D 758 " --> pdb=" O SER D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 765 Processing helix chain 'D' and resid 788 through 796 removed outlier: 3.622A pdb=" N ALA D 793 " --> pdb=" O PRO D 789 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LEU D 794 " --> pdb=" O ALA D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 809 removed outlier: 3.862A pdb=" N TYR D 808 " --> pdb=" O ALA D 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 850 removed outlier: 3.951A pdb=" N LYS D 838 " --> pdb=" O THR D 834 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 845 " --> pdb=" O MET D 841 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU D 847 " --> pdb=" O ALA D 843 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN D 848 " --> pdb=" O LEU D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 893 removed outlier: 3.578A pdb=" N GLU D 893 " --> pdb=" O THR D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 951 removed outlier: 4.438A pdb=" N VAL D 946 " --> pdb=" O LYS D 942 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 949 " --> pdb=" O ASN D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 971 Processing helix chain 'D' and resid 999 through 1006 removed outlier: 3.681A pdb=" N LEU D1005 " --> pdb=" O ALA D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1020 through 1032 Processing helix chain 'D' and resid 1036 through 1038 No H-bonds generated for 'chain 'D' and resid 1036 through 1038' Processing helix chain 'D' and resid 1039 through 1047 removed outlier: 4.199A pdb=" N VAL D1045 " --> pdb=" O ALA D1041 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.925A pdb=" N ASP E 16 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 69 removed outlier: 4.472A pdb=" N GLY E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 64 through 69' Processing helix chain 'E' and resid 72 through 77 removed outlier: 3.724A pdb=" N LEU E 76 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 72 through 77' Processing helix chain 'E' and resid 84 through 98 removed outlier: 3.836A pdb=" N LEU E 88 " --> pdb=" O PRO E 84 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE E 89 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER E 98 " --> pdb=" O SER E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 124 removed outlier: 3.600A pdb=" N THR E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 137 removed outlier: 4.416A pdb=" N VAL E 134 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL E 135 " --> pdb=" O GLY E 131 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E 137 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 147 through 152 removed outlier: 3.970A pdb=" N SER E 152 " --> pdb=" O ASP E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 196 removed outlier: 3.909A pdb=" N VAL E 192 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN E 193 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 226 Processing helix chain 'E' and resid 227 through 246 removed outlier: 3.900A pdb=" N ALA E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU E 236 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU E 243 " --> pdb=" O TRP E 239 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 245 " --> pdb=" O GLN E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 277 removed outlier: 3.834A pdb=" N ARG E 271 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 275 " --> pdb=" O ARG E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 307 removed outlier: 3.520A pdb=" N ASP E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR E 303 " --> pdb=" O GLN E 299 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR E 305 " --> pdb=" O SER E 301 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 321 removed outlier: 3.574A pdb=" N ASN E 321 " --> pdb=" O ARG E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 332 Processing helix chain 'E' and resid 333 through 341 removed outlier: 3.526A pdb=" N LEU E 337 " --> pdb=" O GLN E 333 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR E 341 " --> pdb=" O LEU E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 417 Processing helix chain 'E' and resid 435 through 447 removed outlier: 3.679A pdb=" N ASP E 446 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR E 447 " --> pdb=" O ALA E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 458 removed outlier: 3.681A pdb=" N ASN E 457 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN E 458 " --> pdb=" O GLY E 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 453 through 458' Processing helix chain 'E' and resid 462 through 471 Proline residue: E 468 - end of helix Processing helix chain 'E' and resid 472 through 478 Processing helix chain 'E' and resid 490 through 497 Processing helix chain 'E' and resid 526 through 544 removed outlier: 3.573A pdb=" N MET E 530 " --> pdb=" O ASN E 526 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS E 531 " --> pdb=" O ASN E 527 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N MET E 532 " --> pdb=" O SER E 528 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E 537 " --> pdb=" O LEU E 533 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 543 " --> pdb=" O LEU E 539 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN E 544 " --> pdb=" O LYS E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 575 Processing helix chain 'E' and resid 624 through 637 removed outlier: 4.246A pdb=" N SER E 630 " --> pdb=" O GLU E 626 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU E 631 " --> pdb=" O SER E 627 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER E 634 " --> pdb=" O SER E 630 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL E 636 " --> pdb=" O THR E 632 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR E 637 " --> pdb=" O ILE E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 667 removed outlier: 3.575A pdb=" N ASN E 659 " --> pdb=" O GLU E 655 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 665 " --> pdb=" O VAL E 661 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN E 667 " --> pdb=" O GLU E 663 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 714 removed outlier: 4.050A pdb=" N ARG E 714 " --> pdb=" O ALA E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 754 through 760 removed outlier: 3.631A pdb=" N ALA E 758 " --> pdb=" O SER E 754 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 765 Processing helix chain 'E' and resid 788 through 796 removed outlier: 3.622A pdb=" N ALA E 793 " --> pdb=" O PRO E 789 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU E 794 " --> pdb=" O ALA E 790 " (cutoff:3.500A) Processing helix chain 'E' and resid 804 through 809 removed outlier: 3.860A pdb=" N TYR E 808 " --> pdb=" O ALA E 804 " (cutoff:3.500A) Processing helix chain 'E' and resid 833 through 850 removed outlier: 3.950A pdb=" N LYS E 838 " --> pdb=" O THR E 834 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE E 845 " --> pdb=" O MET E 841 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU E 847 " --> pdb=" O ALA E 843 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN E 848 " --> pdb=" O LEU E 844 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 893 removed outlier: 3.577A pdb=" N GLU E 893 " --> pdb=" O THR E 889 " (cutoff:3.500A) Processing helix chain 'E' and resid 940 through 951 removed outlier: 4.437A pdb=" N VAL E 946 " --> pdb=" O LYS E 942 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 971 Processing helix chain 'E' and resid 999 through 1006 removed outlier: 3.682A pdb=" N LEU E1005 " --> pdb=" O ALA E1001 " (cutoff:3.500A) Processing helix chain 'E' and resid 1020 through 1032 Processing helix chain 'E' and resid 1036 through 1038 No H-bonds generated for 'chain 'E' and resid 1036 through 1038' Processing helix chain 'E' and resid 1039 through 1047 removed outlier: 4.198A pdb=" N VAL E1045 " --> pdb=" O ALA E1041 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 39 through 43 removed outlier: 3.714A pdb=" N THR A 41 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 50 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 43 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=C, first strand: chain 'A' and resid 161 through 165 Processing sheet with id=D, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=E, first strand: chain 'A' and resid 745 through 751 removed outlier: 4.181A pdb=" N ARG A 786 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU A 768 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LYS A 374 " --> pdb=" O ARG E 597 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ILE E 596 " --> pdb=" O ILE E 584 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY E 586 " --> pdb=" O ILE E 596 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'A' and resid 401 through 403 removed outlier: 6.223A pdb=" N THR A 402 " --> pdb=" O GLU A 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=F Processing sheet with id=G, first strand: chain 'A' and resid 419 through 421 Processing sheet with id=H, first strand: chain 'A' and resid 505 through 506 removed outlier: 4.305A pdb=" N VAL A 506 " --> pdb=" O MET A 510 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=H Processing sheet with id=I, first strand: chain 'A' and resid 612 through 615 removed outlier: 8.778A pdb=" N ILE A 596 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY A 586 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 376 " --> pdb=" O ARG A 597 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU B 768 " --> pdb=" O ARG B 786 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG B 786 " --> pdb=" O GLU B 768 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'A' and resid 897 through 900 removed outlier: 6.858A pdb=" N TYR A 878 " --> pdb=" O GLU A 898 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLN A 900 " --> pdb=" O TYR A 878 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A 880 " --> pdb=" O GLN A 900 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR A 959 " --> pdb=" O SER A 917 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR A 919 " --> pdb=" O TYR A 959 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER A 961 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE A 921 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A1052 " --> pdb=" O ILE A1017 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'A' and resid 981 through 982 removed outlier: 3.663A pdb=" N ARG A 981 " --> pdb=" O LYS A 988 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'B' and resid 39 through 43 removed outlier: 3.714A pdb=" N THR B 41 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 50 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN B 43 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'B' and resid 112 through 113 Processing sheet with id=N, first strand: chain 'B' and resid 161 through 165 Processing sheet with id=O, first strand: chain 'B' and resid 326 through 328 Processing sheet with id=P, first strand: chain 'B' and resid 401 through 403 removed outlier: 6.223A pdb=" N THR B 402 " --> pdb=" O GLU B 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=P Processing sheet with id=Q, first strand: chain 'B' and resid 419 through 421 Processing sheet with id=R, first strand: chain 'B' and resid 505 through 506 removed outlier: 4.305A pdb=" N VAL B 506 " --> pdb=" O MET B 510 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=R Processing sheet with id=S, first strand: chain 'B' and resid 612 through 615 removed outlier: 8.780A pdb=" N ILE B 596 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY B 586 " --> pdb=" O ILE B 596 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER C 376 " --> pdb=" O ARG B 597 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLU C 768 " --> pdb=" O ARG C 786 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG C 786 " --> pdb=" O GLU C 768 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'B' and resid 897 through 900 removed outlier: 6.858A pdb=" N TYR B 878 " --> pdb=" O GLU B 898 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N GLN B 900 " --> pdb=" O TYR B 878 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B 880 " --> pdb=" O GLN B 900 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TYR B 959 " --> pdb=" O SER B 917 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR B 919 " --> pdb=" O TYR B 959 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER B 961 " --> pdb=" O TYR B 919 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE B 921 " --> pdb=" O SER B 961 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B1052 " --> pdb=" O ILE B1017 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain 'B' and resid 981 through 982 removed outlier: 3.662A pdb=" N ARG B 981 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'C' and resid 39 through 43 removed outlier: 3.714A pdb=" N THR C 41 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR C 50 " --> pdb=" O THR C 41 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN C 43 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing sheet with id=W, first strand: chain 'C' and resid 112 through 113 Processing sheet with id=X, first strand: chain 'C' and resid 161 through 165 Processing sheet with id=Y, first strand: chain 'C' and resid 326 through 328 Processing sheet with id=Z, first strand: chain 'C' and resid 401 through 403 removed outlier: 6.224A pdb=" N THR C 402 " --> pdb=" O GLU C 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=Z Processing sheet with id=AA, first strand: chain 'C' and resid 419 through 421 Processing sheet with id=AB, first strand: chain 'C' and resid 505 through 506 removed outlier: 4.304A pdb=" N VAL C 506 " --> pdb=" O MET C 510 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB Processing sheet with id=AC, first strand: chain 'C' and resid 612 through 615 removed outlier: 8.779A pdb=" N ILE C 596 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY C 586 " --> pdb=" O ILE C 596 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 376 " --> pdb=" O ARG C 597 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU D 768 " --> pdb=" O ARG D 786 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG D 786 " --> pdb=" O GLU D 768 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'C' and resid 897 through 900 removed outlier: 6.858A pdb=" N TYR C 878 " --> pdb=" O GLU C 898 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLN C 900 " --> pdb=" O TYR C 878 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL C 880 " --> pdb=" O GLN C 900 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TYR C 959 " --> pdb=" O SER C 917 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR C 919 " --> pdb=" O TYR C 959 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N SER C 961 " --> pdb=" O TYR C 919 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE C 921 " --> pdb=" O SER C 961 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C1052 " --> pdb=" O ILE C1017 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'C' and resid 981 through 982 removed outlier: 3.663A pdb=" N ARG C 981 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'D' and resid 39 through 43 removed outlier: 3.714A pdb=" N THR D 41 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR D 50 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN D 43 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AH, first strand: chain 'D' and resid 161 through 165 Processing sheet with id=AI, first strand: chain 'D' and resid 326 through 328 Processing sheet with id=AJ, first strand: chain 'D' and resid 401 through 403 removed outlier: 6.224A pdb=" N THR D 402 " --> pdb=" O GLU D 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ Processing sheet with id=AK, first strand: chain 'D' and resid 419 through 421 Processing sheet with id=AL, first strand: chain 'D' and resid 505 through 506 removed outlier: 4.305A pdb=" N VAL D 506 " --> pdb=" O MET D 510 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL Processing sheet with id=AM, first strand: chain 'D' and resid 612 through 615 removed outlier: 8.779A pdb=" N ILE D 596 " --> pdb=" O ILE D 584 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY D 586 " --> pdb=" O ILE D 596 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER E 376 " --> pdb=" O ARG D 597 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLU E 768 " --> pdb=" O ARG E 786 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG E 786 " --> pdb=" O GLU E 768 " (cutoff:3.500A) Processing sheet with id=AN, first strand: chain 'D' and resid 897 through 900 removed outlier: 6.858A pdb=" N TYR D 878 " --> pdb=" O GLU D 898 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLN D 900 " --> pdb=" O TYR D 878 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL D 880 " --> pdb=" O GLN D 900 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TYR D 959 " --> pdb=" O SER D 917 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR D 919 " --> pdb=" O TYR D 959 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER D 961 " --> pdb=" O TYR D 919 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE D 921 " --> pdb=" O SER D 961 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D1052 " --> pdb=" O ILE D1017 " (cutoff:3.500A) Processing sheet with id=AO, first strand: chain 'D' and resid 981 through 982 removed outlier: 3.663A pdb=" N ARG D 981 " --> pdb=" O LYS D 988 " (cutoff:3.500A) Processing sheet with id=AP, first strand: chain 'E' and resid 39 through 43 removed outlier: 3.713A pdb=" N THR E 41 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR E 50 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN E 43 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing sheet with id=AQ, first strand: chain 'E' and resid 112 through 113 Processing sheet with id=AR, first strand: chain 'E' and resid 161 through 165 Processing sheet with id=AS, first strand: chain 'E' and resid 326 through 328 Processing sheet with id=AT, first strand: chain 'E' and resid 401 through 403 removed outlier: 6.224A pdb=" N THR E 402 " --> pdb=" O GLU E 825 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT Processing sheet with id=AU, first strand: chain 'E' and resid 419 through 421 Processing sheet with id=AV, first strand: chain 'E' and resid 505 through 506 removed outlier: 4.304A pdb=" N VAL E 506 " --> pdb=" O MET E 510 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET E 510 " --> pdb=" O VAL E 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=AV Processing sheet with id=AW, first strand: chain 'E' and resid 897 through 900 removed outlier: 6.858A pdb=" N TYR E 878 " --> pdb=" O GLU E 898 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLN E 900 " --> pdb=" O TYR E 878 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL E 880 " --> pdb=" O GLN E 900 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TYR E 959 " --> pdb=" O SER E 917 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR E 919 " --> pdb=" O TYR E 959 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER E 961 " --> pdb=" O TYR E 919 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE E 921 " --> pdb=" O SER E 961 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL E1052 " --> pdb=" O ILE E1017 " (cutoff:3.500A) Processing sheet with id=AX, first strand: chain 'E' and resid 981 through 982 removed outlier: 3.661A pdb=" N ARG E 981 " --> pdb=" O LYS E 988 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.96 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8207 1.33 - 1.45: 10538 1.45 - 1.57: 24345 1.57 - 1.69: 10 1.69 - 1.81: 435 Bond restraints: 43535 Sorted by residual: bond pdb=" NZ GPL C 234 " pdb=" P GPL C 234 " ideal model delta sigma weight residual 1.569 1.751 -0.182 2.00e-02 2.50e+03 8.31e+01 bond pdb=" NZ GPL A 234 " pdb=" P GPL A 234 " ideal model delta sigma weight residual 1.569 1.751 -0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" NZ GPL E 234 " pdb=" P GPL E 234 " ideal model delta sigma weight residual 1.569 1.751 -0.182 2.00e-02 2.50e+03 8.26e+01 bond pdb=" NZ GPL B 234 " pdb=" P GPL B 234 " ideal model delta sigma weight residual 1.569 1.750 -0.181 2.00e-02 2.50e+03 8.23e+01 bond pdb=" NZ GPL D 234 " pdb=" P GPL D 234 " ideal model delta sigma weight residual 1.569 1.750 -0.181 2.00e-02 2.50e+03 8.18e+01 ... (remaining 43530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 57181 2.60 - 5.20: 1917 5.20 - 7.80: 141 7.80 - 10.40: 67 10.40 - 13.00: 24 Bond angle restraints: 59330 Sorted by residual: angle pdb=" N CYS D 639 " pdb=" CA CYS D 639 " pdb=" CB CYS D 639 " ideal model delta sigma weight residual 110.90 102.66 8.24 1.33e+00 5.65e-01 3.84e+01 angle pdb=" N CYS E 639 " pdb=" CA CYS E 639 " pdb=" CB CYS E 639 " ideal model delta sigma weight residual 110.90 102.71 8.19 1.33e+00 5.65e-01 3.79e+01 angle pdb=" N CYS B 639 " pdb=" CA CYS B 639 " pdb=" CB CYS B 639 " ideal model delta sigma weight residual 110.90 102.71 8.19 1.33e+00 5.65e-01 3.79e+01 angle pdb=" N CYS A 639 " pdb=" CA CYS A 639 " pdb=" CB CYS A 639 " ideal model delta sigma weight residual 110.90 102.74 8.16 1.33e+00 5.65e-01 3.77e+01 angle pdb=" N CYS C 639 " pdb=" CA CYS C 639 " pdb=" CB CYS C 639 " ideal model delta sigma weight residual 110.90 102.74 8.16 1.33e+00 5.65e-01 3.76e+01 ... (remaining 59325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.44: 25300 20.44 - 40.89: 710 40.89 - 61.33: 150 61.33 - 81.77: 20 81.77 - 102.21: 5 Dihedral angle restraints: 26185 sinusoidal: 10430 harmonic: 15755 Sorted by residual: dihedral pdb=" CA ALA E 308 " pdb=" C ALA E 308 " pdb=" N ASN E 309 " pdb=" CA ASN E 309 " ideal model delta harmonic sigma weight residual -180.00 -77.79 -102.21 0 5.00e+00 4.00e-02 4.18e+02 dihedral pdb=" CA ALA A 308 " pdb=" C ALA A 308 " pdb=" N ASN A 309 " pdb=" CA ASN A 309 " ideal model delta harmonic sigma weight residual -180.00 -77.80 -102.20 0 5.00e+00 4.00e-02 4.18e+02 dihedral pdb=" CA ALA C 308 " pdb=" C ALA C 308 " pdb=" N ASN C 309 " pdb=" CA ASN C 309 " ideal model delta harmonic sigma weight residual -180.00 -77.92 -102.08 0 5.00e+00 4.00e-02 4.17e+02 ... (remaining 26182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4589 0.043 - 0.087: 1697 0.087 - 0.130: 228 0.130 - 0.174: 296 0.174 - 0.217: 45 Chirality restraints: 6855 Sorted by residual: chirality pdb=" CA CYS A 749 " pdb=" N CYS A 749 " pdb=" C CYS A 749 " pdb=" CB CYS A 749 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA CYS C 749 " pdb=" N CYS C 749 " pdb=" C CYS C 749 " pdb=" CB CYS C 749 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA CYS D 639 " pdb=" N CYS D 639 " pdb=" C CYS D 639 " pdb=" CB CYS D 639 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 6852 not shown) Planarity restraints: 7560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 481 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" CG ASP C 481 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASP C 481 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP C 481 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 481 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" CG ASP E 481 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASP E 481 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP E 481 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 481 " -0.012 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" CG ASP B 481 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASP B 481 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP B 481 " -0.016 2.00e-02 2.50e+03 ... (remaining 7557 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.07: 20 2.07 - 2.78: 11217 2.78 - 3.49: 53132 3.49 - 4.19: 93990 4.19 - 4.90: 158938 Nonbonded interactions: 317297 Sorted by model distance: nonbonded pdb=" OE2 GLU A 566 " pdb=" OXT SAH A1101 " model vdw 1.368 3.040 nonbonded pdb=" OE2 GLU C 566 " pdb=" OXT SAH C1101 " model vdw 1.369 3.040 nonbonded pdb=" OE2 GLU D 566 " pdb=" OXT SAH D1101 " model vdw 1.369 3.040 nonbonded pdb=" OE2 GLU E 566 " pdb=" OXT SAH E1101 " model vdw 1.369 3.040 nonbonded pdb=" OE2 GLU B 566 " pdb=" OXT SAH B1101 " model vdw 1.370 3.040 ... (remaining 317292 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 35.540 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5751 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 : 0.015 0.779 43555 Z= 1.264 Angle : 1.167 13.000 59330 Z= 0.770 Chirality : 0.055 0.217 6855 Planarity : 0.008 0.047 7560 Dihedral : 10.655 102.215 15985 Min Nonbonded Distance : 1.368 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 4.20 % Allowed : 11.68 % Favored : 84.12 % Rotamer: Outliers : 0.64 % Allowed : 1.70 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.60 (0.09), residues: 5265 helix: -3.64 (0.08), residues: 1480 sheet: -1.00 (0.17), residues: 730 loop : -3.43 (0.10), residues: 3055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.003 ARG B 313 TYR 0.003 0.001 TYR C 38 PHE 0.003 0.001 PHE E 826 TRP 0.003 0.001 TRP E 95 HIS 0.002 0.000 HIS C 806 Details of bonding type rmsd covalent geometry : bond 0.01024 (43535) covalent geometry : angle 1.16691 (59330) hydrogen bonds : bond 0.26260 ( 996) hydrogen bonds : angle 9.85613 ( 2748) Misc. bond : bond 0.52273 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1468 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 1438 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ILE cc_start: 0.5189 (pt) cc_final: 0.4536 (pt) REVERT: A 481 ASP cc_start: 0.1677 (OUTLIER) cc_final: 0.1301 (t70) REVERT: A 1056 VAL cc_start: 0.7387 (p) cc_final: 0.7120 (p) REVERT: B 411 ILE cc_start: 0.5013 (pt) cc_final: 0.4515 (pt) REVERT: B 481 ASP cc_start: 0.1917 (OUTLIER) cc_final: 0.1568 (t70) REVERT: B 812 VAL cc_start: 0.7481 (t) cc_final: 0.7215 (m) REVERT: B 886 ARG cc_start: 0.4226 (mtt180) cc_final: 0.3862 (mtm-85) REVERT: C 411 ILE cc_start: 0.5425 (pt) cc_final: 0.5083 (pt) REVERT: C 481 ASP cc_start: 0.2183 (OUTLIER) cc_final: 0.1648 (t70) REVERT: C 812 VAL cc_start: 0.7774 (t) cc_final: 0.7490 (m) REVERT: C 1056 VAL cc_start: 0.7488 (p) cc_final: 0.7194 (p) REVERT: D 411 ILE cc_start: 0.5181 (pt) cc_final: 0.4106 (pt) REVERT: D 1056 VAL cc_start: 0.7278 (p) cc_final: 0.6936 (p) REVERT: E 411 ILE cc_start: 0.5347 (pt) cc_final: 0.5055 (pt) REVERT: E 481 ASP cc_start: 0.2766 (OUTLIER) cc_final: 0.2093 (t70) outliers start: 30 outliers final: 3 residues processed: 1463 average time/residue: 0.2494 time to fit residues: 579.6316 Evaluate side-chains 669 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 662 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain C residue 282 GLU Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain E residue 481 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 6.9990 chunk 497 optimal weight: 7.9990 chunk 414 optimal weight: 20.0000 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 0.0020 overall best weight: 5.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN A 281 ASN A 385 HIS ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN B 33 GLN B 49 HIS B 385 HIS B 544 ASN B 623 GLN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN C 434 GLN C 544 ASN C 623 GLN D 21 GLN D 33 GLN D 270 GLN D 281 ASN D 973 GLN E 33 GLN E 49 HIS E 93 HIS E 270 GLN E 281 ASN E 623 GLN E 651 ASN E 806 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.162941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.150014 restraints weight = 84405.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.151161 restraints weight = 59982.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.151855 restraints weight = 46262.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.152482 restraints weight = 38499.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.152479 restraints weight = 35997.907| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 43555 Z= 0.185 Angle : 0.828 10.757 59330 Z= 0.428 Chirality : 0.049 0.226 6855 Planarity : 0.007 0.081 7560 Dihedral : 7.441 89.735 5967 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 1.12 % Allowed : 12.23 % Favored : 86.65 % Rotamer: Outliers : 3.78 % Allowed : 10.59 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.72 (0.10), residues: 5265 helix: -2.55 (0.11), residues: 1400 sheet: -0.74 (0.18), residues: 755 loop : -3.03 (0.10), residues: 3110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 886 TYR 0.029 0.002 TYR A1031 PHE 0.019 0.002 PHE A1046 TRP 0.009 0.001 TRP C 772 HIS 0.010 0.002 HIS A 332 Details of bonding type rmsd covalent geometry : bond 0.00397 (43535) covalent geometry : angle 0.82821 (59330) hydrogen bonds : bond 0.04798 ( 996) hydrogen bonds : angle 5.85364 ( 2748) Misc. bond : bond 0.00246 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 725 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 MET cc_start: 0.6779 (ppp) cc_final: 0.6127 (ppp) REVERT: A 485 MET cc_start: 0.7140 (mmt) cc_final: 0.6914 (mmt) REVERT: A 799 ARG cc_start: 0.6858 (tpp80) cc_final: 0.6344 (tpp80) REVERT: A 938 MET cc_start: 0.7133 (mmm) cc_final: 0.6555 (tpt) REVERT: A 1056 VAL cc_start: 0.7999 (p) cc_final: 0.7436 (p) REVERT: B 100 HIS cc_start: 0.8182 (OUTLIER) cc_final: 0.7289 (p-80) REVERT: B 492 HIS cc_start: 0.5203 (p-80) cc_final: 0.4900 (p-80) REVERT: B 812 VAL cc_start: 0.7901 (t) cc_final: 0.7543 (m) REVERT: B 938 MET cc_start: 0.7178 (mmm) cc_final: 0.6613 (tpt) REVERT: B 1025 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7106 (tt) REVERT: C 455 MET cc_start: 0.6943 (tpp) cc_final: 0.6724 (tpp) REVERT: C 763 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7794 (ptmm) REVERT: C 812 VAL cc_start: 0.8043 (t) cc_final: 0.7626 (m) REVERT: C 938 MET cc_start: 0.7300 (mmm) cc_final: 0.6627 (tpt) REVERT: C 1056 VAL cc_start: 0.7953 (p) cc_final: 0.7313 (p) REVERT: D 783 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8517 (mt) REVERT: D 812 VAL cc_start: 0.7661 (t) cc_final: 0.7302 (m) REVERT: D 938 MET cc_start: 0.7310 (mmm) cc_final: 0.6468 (ptm) REVERT: D 1035 LEU cc_start: 0.6981 (tp) cc_final: 0.6727 (tt) REVERT: E 405 MET cc_start: 0.6739 (ppp) cc_final: 0.5648 (ppp) REVERT: E 938 MET cc_start: 0.7172 (mmm) cc_final: 0.6344 (ptm) outliers start: 178 outliers final: 110 residues processed: 853 average time/residue: 0.2363 time to fit residues: 336.8176 Evaluate side-chains 632 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 518 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1043 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1025 ILE Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 458 ASN Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 492 HIS Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 783 ILE Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 839 LEU Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 800 SER Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1028 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 205 optimal weight: 40.0000 chunk 235 optimal weight: 3.9990 chunk 369 optimal weight: 30.0000 chunk 491 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 chunk 417 optimal weight: 6.9990 chunk 375 optimal weight: 40.0000 chunk 305 optimal weight: 30.0000 chunk 50 optimal weight: 20.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 GLN A 49 HIS A 93 HIS A 212 HIS A 492 HIS A 945 ASN B 212 HIS ** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS C 212 HIS ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 ASN D 49 HIS D 212 HIS ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 HIS D 623 GLN D 651 ASN D 848 GLN D1048 HIS ** E 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 HIS E 385 HIS ** E 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.150982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.138277 restraints weight = 84360.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.138403 restraints weight = 66835.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.139134 restraints weight = 57882.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.139519 restraints weight = 47554.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.139592 restraints weight = 45094.875| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 43555 Z= 0.233 Angle : 0.840 10.126 59330 Z= 0.437 Chirality : 0.050 0.323 6855 Planarity : 0.007 0.090 7560 Dihedral : 7.169 175.558 5950 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.80 % Allowed : 12.44 % Favored : 86.76 % Rotamer: Outliers : 4.78 % Allowed : 12.40 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.39 (0.11), residues: 5265 helix: -2.00 (0.12), residues: 1510 sheet: -0.46 (0.19), residues: 725 loop : -2.98 (0.10), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG C 886 TYR 0.024 0.002 TYR D 78 PHE 0.022 0.003 PHE B 826 TRP 0.014 0.002 TRP D 213 HIS 0.023 0.002 HIS A 3 Details of bonding type rmsd covalent geometry : bond 0.00520 (43535) covalent geometry : angle 0.83976 (59330) hydrogen bonds : bond 0.05596 ( 996) hydrogen bonds : angle 5.39716 ( 2748) Misc. bond : bond 0.00410 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 571 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7168 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: A 95 TRP cc_start: 0.8715 (OUTLIER) cc_final: 0.7789 (t-100) REVERT: A 300 LEU cc_start: 0.8569 (tp) cc_final: 0.8167 (tt) REVERT: A 314 ARG cc_start: 0.7426 (mtt180) cc_final: 0.7174 (mtt90) REVERT: A 405 MET cc_start: 0.6379 (ppp) cc_final: 0.5612 (ppp) REVERT: A 481 ASP cc_start: 0.3452 (OUTLIER) cc_final: 0.2312 (t70) REVERT: A 485 MET cc_start: 0.7472 (mmt) cc_final: 0.7159 (mmm) REVERT: A 828 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.6548 (m-10) REVERT: A 938 MET cc_start: 0.6983 (mmm) cc_final: 0.6729 (tpt) REVERT: B 100 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7350 (p-80) REVERT: B 294 SER cc_start: 0.9228 (OUTLIER) cc_final: 0.8531 (t) REVERT: B 310 ASP cc_start: 0.6239 (OUTLIER) cc_final: 0.5360 (t0) REVERT: B 362 MET cc_start: 0.4953 (OUTLIER) cc_final: 0.4430 (tmm) REVERT: B 481 ASP cc_start: 0.3924 (OUTLIER) cc_final: 0.2389 (t70) REVERT: B 623 GLN cc_start: 0.4880 (pt0) cc_final: 0.4594 (tt0) REVERT: B 724 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.5950 (pmm) REVERT: B 812 VAL cc_start: 0.7854 (t) cc_final: 0.7470 (m) REVERT: B 828 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6720 (m-10) REVERT: B 938 MET cc_start: 0.7257 (mmm) cc_final: 0.6613 (tpt) REVERT: C 78 TYR cc_start: 0.6811 (OUTLIER) cc_final: 0.5081 (m-80) REVERT: C 86 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7546 (t70) REVERT: C 372 ARG cc_start: 0.7896 (ttp-110) cc_final: 0.7670 (ptp-170) REVERT: C 481 ASP cc_start: 0.2931 (OUTLIER) cc_final: 0.2199 (t70) REVERT: C 540 LYS cc_start: 0.7714 (mmtm) cc_final: 0.7221 (mmtt) REVERT: C 828 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6268 (m-10) REVERT: C 844 LEU cc_start: 0.8170 (tp) cc_final: 0.7948 (tt) REVERT: C 938 MET cc_start: 0.7364 (mmm) cc_final: 0.6757 (tpt) REVERT: C 992 TYR cc_start: 0.5048 (OUTLIER) cc_final: 0.4108 (m-80) REVERT: D 78 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.5877 (m-10) REVERT: D 416 MET cc_start: 0.7516 (mtm) cc_final: 0.7284 (mtm) REVERT: D 828 TYR cc_start: 0.6845 (OUTLIER) cc_final: 0.6033 (m-10) REVERT: D 938 MET cc_start: 0.7122 (mmm) cc_final: 0.6439 (tpt) REVERT: E 73 ARG cc_start: 0.7718 (ttp-170) cc_final: 0.7355 (ptm160) REVERT: E 78 TYR cc_start: 0.6604 (OUTLIER) cc_final: 0.6107 (m-80) REVERT: E 132 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6939 (tp40) REVERT: E 405 MET cc_start: 0.6564 (ppp) cc_final: 0.6048 (ppp) REVERT: E 411 ILE cc_start: 0.6252 (OUTLIER) cc_final: 0.5938 (pt) REVERT: E 481 ASP cc_start: 0.3990 (OUTLIER) cc_final: 0.2194 (t70) REVERT: E 485 MET cc_start: 0.7353 (mmt) cc_final: 0.7030 (mmm) REVERT: E 828 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6324 (m-10) REVERT: E 829 MET cc_start: 0.7295 (mtp) cc_final: 0.7053 (ttm) outliers start: 225 outliers final: 145 residues processed: 733 average time/residue: 0.2051 time to fit residues: 256.0395 Evaluate side-chains 622 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 454 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1024 LEU Chi-restraints excluded: chain B residue 1025 ILE Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 458 ASN Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 829 MET Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1025 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 492 HIS Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 549 SER Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 132 GLN Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 604 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 623 GLN Chi-restraints excluded: chain E residue 719 VAL Chi-restraints excluded: chain E residue 759 LEU Chi-restraints excluded: chain E residue 788 ASP Chi-restraints excluded: chain E residue 800 SER Chi-restraints excluded: chain E residue 828 TYR Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 998 LEU Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 60 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 423 optimal weight: 0.0060 chunk 78 optimal weight: 20.0000 chunk 258 optimal weight: 50.0000 chunk 447 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 465 optimal weight: 9.9990 chunk 293 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 ASN B 492 HIS B 945 ASN C 49 HIS C 945 ASN D 281 ASN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN ** E 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.153589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.140310 restraints weight = 84209.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.141474 restraints weight = 73411.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.142592 restraints weight = 51831.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.142654 restraints weight = 41548.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.142852 restraints weight = 37341.533| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43555 Z= 0.136 Angle : 0.705 9.682 59330 Z= 0.363 Chirality : 0.045 0.167 6855 Planarity : 0.006 0.093 7560 Dihedral : 6.987 172.176 5950 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.41 % Favored : 88.76 % Rotamer: Outliers : 3.48 % Allowed : 14.90 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.11), residues: 5265 helix: -1.64 (0.12), residues: 1520 sheet: -0.47 (0.19), residues: 730 loop : -2.81 (0.11), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG B 886 TYR 0.023 0.001 TYR B 688 PHE 0.014 0.001 PHE A 42 TRP 0.022 0.001 TRP D 213 HIS 0.014 0.001 HIS B 3 Details of bonding type rmsd covalent geometry : bond 0.00284 (43535) covalent geometry : angle 0.70493 (59330) hydrogen bonds : bond 0.03864 ( 996) hydrogen bonds : angle 4.93153 ( 2748) Misc. bond : bond 0.00279 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 503 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.6963 (OUTLIER) cc_final: 0.6692 (m-80) REVERT: A 372 ARG cc_start: 0.7612 (ttp-110) cc_final: 0.7411 (ttp-170) REVERT: A 405 MET cc_start: 0.6275 (ppp) cc_final: 0.5505 (ppp) REVERT: A 481 ASP cc_start: 0.3076 (OUTLIER) cc_final: 0.2187 (t70) REVERT: A 485 MET cc_start: 0.7225 (mmt) cc_final: 0.6941 (mmm) REVERT: A 623 GLN cc_start: 0.5391 (pm20) cc_final: 0.5008 (pp30) REVERT: A 950 MET cc_start: 0.5157 (mmm) cc_final: 0.4920 (mmm) REVERT: B 95 TRP cc_start: 0.8605 (OUTLIER) cc_final: 0.7688 (t-100) REVERT: B 100 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7160 (p-80) REVERT: B 102 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8067 (mm) REVERT: B 938 MET cc_start: 0.7173 (mmm) cc_final: 0.6682 (tpt) REVERT: B 1006 MET cc_start: 0.7186 (ptm) cc_final: 0.6971 (ptm) REVERT: C 362 MET cc_start: 0.5385 (OUTLIER) cc_final: 0.4774 (tmt) REVERT: C 479 LYS cc_start: 0.5256 (OUTLIER) cc_final: 0.4324 (ptpp) REVERT: C 540 LYS cc_start: 0.7543 (mmtm) cc_final: 0.6977 (mmtt) REVERT: C 620 TYR cc_start: 0.5852 (OUTLIER) cc_final: 0.5381 (t80) REVERT: C 938 MET cc_start: 0.7362 (mmm) cc_final: 0.6797 (tpt) REVERT: D 73 ARG cc_start: 0.5492 (OUTLIER) cc_final: 0.4200 (ptt-90) REVERT: D 479 LYS cc_start: 0.5509 (OUTLIER) cc_final: 0.4457 (pttt) REVERT: D 683 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: D 898 GLU cc_start: 0.7216 (mp0) cc_final: 0.6717 (mp0) REVERT: D 938 MET cc_start: 0.7087 (mmm) cc_final: 0.6497 (tpt) REVERT: E 73 ARG cc_start: 0.7728 (ttp-170) cc_final: 0.7312 (ptm160) REVERT: E 78 TYR cc_start: 0.6603 (OUTLIER) cc_final: 0.6069 (m-80) REVERT: E 300 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8327 (tp) REVERT: E 530 MET cc_start: 0.6392 (mmm) cc_final: 0.6145 (mmm) REVERT: E 732 THR cc_start: 0.7396 (p) cc_final: 0.6980 (p) REVERT: E 938 MET cc_start: 0.7210 (mmm) cc_final: 0.6262 (ptt) outliers start: 164 outliers final: 111 residues processed: 619 average time/residue: 0.2203 time to fit residues: 233.1173 Evaluate side-chains 568 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 444 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 956 CYS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 SER Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 829 MET Chi-restraints excluded: chain C residue 956 CYS Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 467 SER Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 479 LYS Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 683 GLN Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 956 CYS Chi-restraints excluded: chain D residue 978 LYS Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 869 ILE Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 257 optimal weight: 10.0000 chunk 196 optimal weight: 40.0000 chunk 75 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 410 optimal weight: 40.0000 chunk 295 optimal weight: 40.0000 chunk 504 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 485 optimal weight: 20.0000 chunk 461 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 945 ASN B 61 ASN B 779 ASN C 49 HIS D 212 HIS ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 ASN E 607 ASN ** E 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 945 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.148384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.135352 restraints weight = 84467.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.136324 restraints weight = 73309.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.137616 restraints weight = 54249.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.137681 restraints weight = 42123.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.137785 restraints weight = 39369.938| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.6552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 43555 Z= 0.183 Angle : 0.747 10.821 59330 Z= 0.385 Chirality : 0.047 0.221 6855 Planarity : 0.006 0.081 7560 Dihedral : 6.623 173.492 5950 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.74 % Allowed : 11.78 % Favored : 87.48 % Rotamer: Outliers : 4.59 % Allowed : 15.27 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.04 (0.11), residues: 5265 helix: -1.54 (0.12), residues: 1560 sheet: -0.30 (0.19), residues: 710 loop : -2.85 (0.11), residues: 2995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 886 TYR 0.026 0.002 TYR A 688 PHE 0.015 0.002 PHE A 835 TRP 0.021 0.001 TRP D 213 HIS 0.055 0.002 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00406 (43535) covalent geometry : angle 0.74735 (59330) hydrogen bonds : bond 0.04545 ( 996) hydrogen bonds : angle 5.06456 ( 2748) Misc. bond : bond 0.00380 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 451 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.4851 (mtm-85) REVERT: A 372 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7478 (ttp-170) REVERT: A 481 ASP cc_start: 0.3297 (OUTLIER) cc_final: 0.2431 (t70) REVERT: A 828 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6486 (m-10) REVERT: A 839 LEU cc_start: 0.8378 (mm) cc_final: 0.8085 (mm) REVERT: A 1006 MET cc_start: 0.6445 (ptm) cc_final: 0.6243 (ptm) REVERT: B 95 TRP cc_start: 0.8779 (OUTLIER) cc_final: 0.8033 (t-100) REVERT: B 100 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7209 (p-80) REVERT: B 362 MET cc_start: 0.5273 (OUTLIER) cc_final: 0.4669 (tmm) REVERT: B 471 SER cc_start: 0.8335 (m) cc_final: 0.8045 (p) REVERT: B 481 ASP cc_start: 0.3587 (OUTLIER) cc_final: 0.2989 (t70) REVERT: B 492 HIS cc_start: 0.6867 (OUTLIER) cc_final: 0.6558 (p-80) REVERT: B 683 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: B 724 MET cc_start: 0.6073 (pmm) cc_final: 0.5795 (pmm) REVERT: B 828 TYR cc_start: 0.7407 (OUTLIER) cc_final: 0.6609 (m-10) REVERT: B 838 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8097 (mmtm) REVERT: B 938 MET cc_start: 0.7297 (mmm) cc_final: 0.6707 (tpt) REVERT: C 73 ARG cc_start: 0.5421 (OUTLIER) cc_final: 0.4027 (ptt-90) REVERT: C 78 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.5054 (m-80) REVERT: C 86 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7439 (t70) REVERT: C 267 THR cc_start: 0.8529 (p) cc_final: 0.8317 (t) REVERT: C 294 SER cc_start: 0.9387 (OUTLIER) cc_final: 0.9064 (t) REVERT: C 362 MET cc_start: 0.5544 (OUTLIER) cc_final: 0.4759 (tmt) REVERT: C 455 MET cc_start: 0.7712 (tpp) cc_final: 0.7031 (mtp) REVERT: C 481 ASP cc_start: 0.3027 (OUTLIER) cc_final: 0.2343 (t70) REVERT: C 485 MET cc_start: 0.7831 (tpt) cc_final: 0.7322 (tpp) REVERT: C 540 LYS cc_start: 0.7773 (mmtm) cc_final: 0.7173 (mmtt) REVERT: C 620 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.5358 (t80) REVERT: C 683 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: C 828 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6468 (m-10) REVERT: C 938 MET cc_start: 0.7369 (mmm) cc_final: 0.6857 (tpt) REVERT: C 992 TYR cc_start: 0.4873 (OUTLIER) cc_final: 0.4070 (m-10) REVERT: D 73 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.4497 (ptt-90) REVERT: D 78 TYR cc_start: 0.6842 (OUTLIER) cc_final: 0.4956 (m-80) REVERT: D 479 LYS cc_start: 0.5374 (OUTLIER) cc_final: 0.4491 (pttt) REVERT: D 623 GLN cc_start: 0.5091 (OUTLIER) cc_final: 0.4888 (tt0) REVERT: D 683 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: D 828 TYR cc_start: 0.6892 (OUTLIER) cc_final: 0.6027 (m-10) REVERT: D 938 MET cc_start: 0.7249 (mmm) cc_final: 0.6648 (tpt) REVERT: E 78 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.6121 (m-80) REVERT: E 95 TRP cc_start: 0.8684 (OUTLIER) cc_final: 0.7754 (t-100) REVERT: E 455 MET cc_start: 0.7220 (tpt) cc_final: 0.6609 (tpt) REVERT: E 481 ASP cc_start: 0.3520 (OUTLIER) cc_final: 0.2488 (t70) REVERT: E 485 MET cc_start: 0.7400 (tpp) cc_final: 0.7161 (mmp) REVERT: E 828 TYR cc_start: 0.7214 (OUTLIER) cc_final: 0.6418 (m-10) REVERT: E 938 MET cc_start: 0.7293 (mmm) cc_final: 0.6611 (ptm) outliers start: 216 outliers final: 130 residues processed: 614 average time/residue: 0.2124 time to fit residues: 224.5233 Evaluate side-chains 575 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 414 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 492 HIS Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 683 GLN Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 683 GLN Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 458 ASN Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 479 LYS Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 623 GLN Chi-restraints excluded: chain D residue 683 GLN Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 95 TRP Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 604 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 623 GLN Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 828 TYR Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain E residue 956 CYS Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 332 optimal weight: 20.0000 chunk 383 optimal weight: 8.9990 chunk 350 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 440 optimal weight: 9.9990 chunk 318 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 708 ASN A1048 HIS B1048 HIS C 492 HIS C 607 ASN C 865 ASN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 607 ASN ** E 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN E 753 GLN E 916 ASN E1048 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.147909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.135688 restraints weight = 85012.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.135932 restraints weight = 69309.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.136562 restraints weight = 56992.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.136970 restraints weight = 49199.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.137102 restraints weight = 43675.078| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 43555 Z= 0.167 Angle : 0.728 10.004 59330 Z= 0.371 Chirality : 0.046 0.240 6855 Planarity : 0.006 0.100 7560 Dihedral : 6.452 168.700 5950 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.63 % Allowed : 11.24 % Favored : 88.13 % Rotamer: Outliers : 4.46 % Allowed : 15.86 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.94 (0.11), residues: 5265 helix: -1.34 (0.13), residues: 1550 sheet: -0.34 (0.19), residues: 720 loop : -2.84 (0.10), residues: 2995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 886 TYR 0.022 0.001 TYR A 688 PHE 0.024 0.002 PHE A 602 TRP 0.019 0.001 TRP B 213 HIS 0.012 0.001 HIS A 3 Details of bonding type rmsd covalent geometry : bond 0.00374 (43535) covalent geometry : angle 0.72788 (59330) hydrogen bonds : bond 0.04189 ( 996) hydrogen bonds : angle 4.97132 ( 2748) Misc. bond : bond 0.00316 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 439 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.4756 (mtm-85) REVERT: A 73 ARG cc_start: 0.6290 (OUTLIER) cc_final: 0.4283 (ptt-90) REVERT: A 95 TRP cc_start: 0.8809 (OUTLIER) cc_final: 0.7873 (t-100) REVERT: A 372 ARG cc_start: 0.7855 (ttp-110) cc_final: 0.7519 (ttp-170) REVERT: A 481 ASP cc_start: 0.3422 (OUTLIER) cc_final: 0.2719 (t70) REVERT: A 828 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6454 (m-10) REVERT: A 839 LEU cc_start: 0.8485 (mm) cc_final: 0.8101 (mm) REVERT: B 95 TRP cc_start: 0.8759 (OUTLIER) cc_final: 0.8044 (t-100) REVERT: B 100 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7179 (p-80) REVERT: B 102 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8182 (mm) REVERT: B 362 MET cc_start: 0.5615 (OUTLIER) cc_final: 0.5082 (tmm) REVERT: B 455 MET cc_start: 0.7910 (tpp) cc_final: 0.7620 (ttp) REVERT: B 481 ASP cc_start: 0.3538 (OUTLIER) cc_final: 0.3075 (t70) REVERT: B 724 MET cc_start: 0.5988 (OUTLIER) cc_final: 0.5752 (pmm) REVERT: B 828 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6612 (m-10) REVERT: B 838 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8065 (mmtm) REVERT: B 866 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8161 (pp) REVERT: B 938 MET cc_start: 0.7284 (mmm) cc_final: 0.6911 (tpp) REVERT: C 73 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.4628 (ptt-90) REVERT: C 78 TYR cc_start: 0.6754 (OUTLIER) cc_final: 0.5046 (m-80) REVERT: C 86 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7199 (t70) REVERT: C 267 THR cc_start: 0.8477 (p) cc_final: 0.8245 (t) REVERT: C 362 MET cc_start: 0.5536 (OUTLIER) cc_final: 0.4643 (tmt) REVERT: C 455 MET cc_start: 0.7835 (tpp) cc_final: 0.7289 (mtp) REVERT: C 481 ASP cc_start: 0.3206 (OUTLIER) cc_final: 0.2522 (t70) REVERT: C 540 LYS cc_start: 0.7770 (mmtm) cc_final: 0.7443 (mmmt) REVERT: C 620 TYR cc_start: 0.5930 (OUTLIER) cc_final: 0.5332 (t80) REVERT: C 828 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.6235 (m-10) REVERT: D 39 LEU cc_start: 0.7736 (mt) cc_final: 0.7491 (mp) REVERT: D 73 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.4680 (ptt-90) REVERT: D 78 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.5035 (m-80) REVERT: D 475 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.5491 (ttm-80) REVERT: D 479 LYS cc_start: 0.5360 (OUTLIER) cc_final: 0.4415 (pttt) REVERT: D 623 GLN cc_start: 0.4937 (OUTLIER) cc_final: 0.4713 (tt0) REVERT: D 683 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8005 (tm-30) REVERT: D 828 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.6030 (m-10) REVERT: D 938 MET cc_start: 0.7276 (mmm) cc_final: 0.6661 (tpt) REVERT: E 78 TYR cc_start: 0.6785 (OUTLIER) cc_final: 0.6128 (m-80) REVERT: E 95 TRP cc_start: 0.8660 (OUTLIER) cc_final: 0.7740 (t-100) REVERT: E 455 MET cc_start: 0.6937 (tpt) cc_final: 0.6431 (tpt) REVERT: E 481 ASP cc_start: 0.3435 (OUTLIER) cc_final: 0.2435 (t70) REVERT: E 683 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8223 (tm-30) REVERT: E 828 TYR cc_start: 0.7245 (OUTLIER) cc_final: 0.6450 (m-10) outliers start: 210 outliers final: 145 residues processed: 599 average time/residue: 0.2352 time to fit residues: 243.1239 Evaluate side-chains 589 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 411 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 839 LEU Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 956 CYS Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1010 ILE Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 475 ARG Chi-restraints excluded: chain D residue 479 LYS Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 604 ILE Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 623 GLN Chi-restraints excluded: chain D residue 683 GLN Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 95 TRP Chi-restraints excluded: chain E residue 100 HIS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 604 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 683 GLN Chi-restraints excluded: chain E residue 732 THR Chi-restraints excluded: chain E residue 828 TYR Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain E residue 869 ILE Chi-restraints excluded: chain E residue 880 VAL Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 87 optimal weight: 30.0000 chunk 55 optimal weight: 6.9990 chunk 286 optimal weight: 9.9990 chunk 250 optimal weight: 8.9990 chunk 237 optimal weight: 1.9990 chunk 479 optimal weight: 20.0000 chunk 453 optimal weight: 6.9990 chunk 465 optimal weight: 8.9990 chunk 125 optimal weight: 0.9990 chunk 411 optimal weight: 1.9990 chunk 32 optimal weight: 0.0570 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 ASN B 492 HIS B 753 GLN C 492 HIS C1048 HIS ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 618 ASN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 779 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.150765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.138084 restraints weight = 83866.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.139553 restraints weight = 68289.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.140343 restraints weight = 46970.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.140342 restraints weight = 40152.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.140477 restraints weight = 37021.842| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.7015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43555 Z= 0.124 Angle : 0.691 12.259 59330 Z= 0.347 Chirality : 0.045 0.175 6855 Planarity : 0.005 0.072 7560 Dihedral : 6.082 171.847 5950 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.86 % Favored : 88.57 % Rotamer: Outliers : 3.38 % Allowed : 17.52 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.79 (0.11), residues: 5265 helix: -1.23 (0.13), residues: 1615 sheet: -0.13 (0.19), residues: 715 loop : -2.79 (0.11), residues: 2935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 574 TYR 0.021 0.001 TYR A 688 PHE 0.022 0.001 PHE A 602 TRP 0.010 0.001 TRP B 213 HIS 0.011 0.001 HIS B 3 Details of bonding type rmsd covalent geometry : bond 0.00256 (43535) covalent geometry : angle 0.69130 (59330) hydrogen bonds : bond 0.03501 ( 996) hydrogen bonds : angle 4.73403 ( 2748) Misc. bond : bond 0.00231 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 462 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.4335 (ptt-90) REVERT: A 372 ARG cc_start: 0.7790 (ttp-110) cc_final: 0.7506 (ttp-170) REVERT: A 481 ASP cc_start: 0.3200 (OUTLIER) cc_final: 0.2500 (t70) REVERT: A 828 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6304 (m-10) REVERT: A 839 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7970 (mm) REVERT: B 95 TRP cc_start: 0.8700 (OUTLIER) cc_final: 0.7771 (t-100) REVERT: B 362 MET cc_start: 0.5585 (OUTLIER) cc_final: 0.4947 (tmm) REVERT: B 481 ASP cc_start: 0.3367 (OUTLIER) cc_final: 0.2775 (t70) REVERT: B 584 ILE cc_start: 0.7873 (mm) cc_final: 0.7648 (tp) REVERT: B 683 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: B 828 TYR cc_start: 0.7196 (OUTLIER) cc_final: 0.6631 (m-10) REVERT: B 838 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8039 (mmtm) REVERT: B 938 MET cc_start: 0.7330 (mmm) cc_final: 0.6955 (tpp) REVERT: C 73 ARG cc_start: 0.6183 (OUTLIER) cc_final: 0.4734 (ptt-90) REVERT: C 78 TYR cc_start: 0.6484 (OUTLIER) cc_final: 0.4824 (m-80) REVERT: C 86 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.6806 (t70) REVERT: C 267 THR cc_start: 0.8596 (p) cc_final: 0.8359 (t) REVERT: C 362 MET cc_start: 0.5418 (OUTLIER) cc_final: 0.4566 (tmt) REVERT: C 479 LYS cc_start: 0.5316 (OUTLIER) cc_final: 0.4542 (ptpp) REVERT: C 481 ASP cc_start: 0.3231 (OUTLIER) cc_final: 0.2585 (t70) REVERT: C 485 MET cc_start: 0.7845 (tpt) cc_final: 0.7644 (tpp) REVERT: C 540 LYS cc_start: 0.7677 (mmtm) cc_final: 0.7381 (mmmt) REVERT: C 620 TYR cc_start: 0.5710 (OUTLIER) cc_final: 0.5173 (t80) REVERT: C 623 GLN cc_start: 0.6500 (pp30) cc_final: 0.5994 (pp30) REVERT: C 683 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: C 828 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6312 (m-10) REVERT: C 938 MET cc_start: 0.7254 (mmm) cc_final: 0.6836 (tpt) REVERT: D 39 LEU cc_start: 0.7781 (mt) cc_final: 0.7529 (mp) REVERT: D 73 ARG cc_start: 0.6081 (OUTLIER) cc_final: 0.4702 (ptt-90) REVERT: D 78 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.4911 (m-80) REVERT: D 479 LYS cc_start: 0.5443 (OUTLIER) cc_final: 0.4516 (pttt) REVERT: D 623 GLN cc_start: 0.4903 (OUTLIER) cc_final: 0.4658 (tt0) REVERT: D 683 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8353 (tm-30) REVERT: D 828 TYR cc_start: 0.6599 (OUTLIER) cc_final: 0.5768 (m-10) REVERT: D 938 MET cc_start: 0.7165 (mmm) cc_final: 0.6658 (tpt) REVERT: D 981 ARG cc_start: 0.6474 (OUTLIER) cc_final: 0.5916 (ptt-90) REVERT: E 78 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.5840 (m-80) REVERT: E 282 GLU cc_start: 0.4290 (OUTLIER) cc_final: 0.3880 (pp20) REVERT: E 455 MET cc_start: 0.6906 (tpt) cc_final: 0.6194 (tpt) REVERT: E 481 ASP cc_start: 0.3129 (OUTLIER) cc_final: 0.1813 (t70) REVERT: E 828 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6342 (m-10) REVERT: E 938 MET cc_start: 0.7180 (mmm) cc_final: 0.6176 (ptm) outliers start: 159 outliers final: 98 residues processed: 583 average time/residue: 0.2361 time to fit residues: 237.8577 Evaluate side-chains 528 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 400 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 683 GLN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 683 GLN Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 479 LYS Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 623 GLN Chi-restraints excluded: chain D residue 683 GLN Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 828 TYR Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Chi-restraints excluded: chain E residue 1056 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 168 optimal weight: 0.0000 chunk 267 optimal weight: 8.9990 chunk 361 optimal weight: 6.9990 chunk 195 optimal weight: 30.0000 chunk 221 optimal weight: 10.0000 chunk 356 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 515 optimal weight: 0.9980 chunk 426 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 chunk 462 optimal weight: 0.0000 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 683 GLN B 487 GLN B 492 HIS B 683 GLN C 103 HIS C 683 GLN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 945 ASN ** E 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.150560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.138089 restraints weight = 84195.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.138708 restraints weight = 66934.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.138708 restraints weight = 53412.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.138708 restraints weight = 53412.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.138708 restraints weight = 53412.730| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.7162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 43555 Z= 0.126 Angle : 0.695 11.296 59330 Z= 0.347 Chirality : 0.045 0.186 6855 Planarity : 0.005 0.061 7560 Dihedral : 5.890 173.468 5950 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.35 % Favored : 89.12 % Rotamer: Outliers : 3.10 % Allowed : 17.86 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.11), residues: 5265 helix: -1.05 (0.13), residues: 1565 sheet: 0.00 (0.19), residues: 715 loop : -2.73 (0.10), residues: 2985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 799 TYR 0.022 0.001 TYR E 113 PHE 0.021 0.001 PHE B 42 TRP 0.007 0.001 TRP E 213 HIS 0.010 0.001 HIS B 3 Details of bonding type rmsd covalent geometry : bond 0.00260 (43535) covalent geometry : angle 0.69482 (59330) hydrogen bonds : bond 0.03446 ( 996) hydrogen bonds : angle 4.62924 ( 2748) Misc. bond : bond 0.00267 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 433 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.4532 (mtm-85) REVERT: A 73 ARG cc_start: 0.6211 (OUTLIER) cc_final: 0.4549 (ptt-90) REVERT: A 372 ARG cc_start: 0.7835 (ttp-110) cc_final: 0.7517 (ttp-170) REVERT: A 481 ASP cc_start: 0.3139 (OUTLIER) cc_final: 0.2482 (t70) REVERT: A 545 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.6231 (t80) REVERT: A 683 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8418 (tm-30) REVERT: A 828 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.6258 (m-10) REVERT: A 839 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7869 (mm) REVERT: A 940 MET cc_start: 0.6052 (mtm) cc_final: 0.5704 (mtp) REVERT: B 95 TRP cc_start: 0.8716 (OUTLIER) cc_final: 0.7755 (t-100) REVERT: B 481 ASP cc_start: 0.3697 (OUTLIER) cc_final: 0.3008 (t70) REVERT: B 623 GLN cc_start: 0.5727 (pp30) cc_final: 0.5410 (pp30) REVERT: B 683 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: B 828 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6701 (m-10) REVERT: B 838 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7866 (mmtm) REVERT: B 938 MET cc_start: 0.7421 (mmm) cc_final: 0.7009 (tpp) REVERT: C 73 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.4810 (ptt-90) REVERT: C 78 TYR cc_start: 0.6566 (OUTLIER) cc_final: 0.4841 (m-80) REVERT: C 86 ASP cc_start: 0.6944 (OUTLIER) cc_final: 0.6725 (t70) REVERT: C 267 THR cc_start: 0.8541 (p) cc_final: 0.8278 (t) REVERT: C 362 MET cc_start: 0.5302 (OUTLIER) cc_final: 0.4506 (tmt) REVERT: C 455 MET cc_start: 0.7712 (tpp) cc_final: 0.7115 (mtp) REVERT: C 479 LYS cc_start: 0.5343 (OUTLIER) cc_final: 0.4503 (ptpp) REVERT: C 481 ASP cc_start: 0.2987 (OUTLIER) cc_final: 0.2534 (t70) REVERT: C 683 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: C 828 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6315 (m-10) REVERT: C 938 MET cc_start: 0.7390 (mmm) cc_final: 0.6840 (tpt) REVERT: D 39 LEU cc_start: 0.7831 (mt) cc_final: 0.7593 (mp) REVERT: D 73 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.4628 (ptt-90) REVERT: D 78 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.4923 (m-80) REVERT: D 479 LYS cc_start: 0.5674 (OUTLIER) cc_final: 0.4766 (pttt) REVERT: D 623 GLN cc_start: 0.4828 (OUTLIER) cc_final: 0.4605 (tt0) REVERT: D 828 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.5568 (m-10) REVERT: D 938 MET cc_start: 0.7242 (mmm) cc_final: 0.6935 (tpt) REVERT: D 981 ARG cc_start: 0.6537 (OUTLIER) cc_final: 0.5972 (ptt-90) REVERT: E 78 TYR cc_start: 0.6570 (OUTLIER) cc_final: 0.6040 (m-80) REVERT: E 282 GLU cc_start: 0.4043 (OUTLIER) cc_final: 0.3743 (pp20) REVERT: E 456 PHE cc_start: 0.6104 (m-80) cc_final: 0.5859 (m-10) REVERT: E 481 ASP cc_start: 0.3030 (OUTLIER) cc_final: 0.1766 (t70) REVERT: E 683 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8239 (tm-30) REVERT: E 828 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6358 (m-10) REVERT: E 839 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8405 (mm) REVERT: E 938 MET cc_start: 0.7288 (mmm) cc_final: 0.6556 (ptm) outliers start: 146 outliers final: 100 residues processed: 550 average time/residue: 0.2330 time to fit residues: 220.8379 Evaluate side-chains 542 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 410 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 683 GLN Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 683 GLN Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 683 GLN Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 956 CYS Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 393 LEU Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 479 LYS Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 623 GLN Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 945 ASN Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 495 LEU Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 683 GLN Chi-restraints excluded: chain E residue 828 TYR Chi-restraints excluded: chain E residue 839 LEU Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 188 optimal weight: 6.9990 chunk 339 optimal weight: 20.0000 chunk 489 optimal weight: 7.9990 chunk 490 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 248 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 476 optimal weight: 50.0000 chunk 175 optimal weight: 0.0050 overall best weight: 3.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 GLN B 492 HIS B 607 ASN C 708 ASN C 905 GLN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.150116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.137718 restraints weight = 83936.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.138118 restraints weight = 69554.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.138602 restraints weight = 55512.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.138985 restraints weight = 48113.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.139192 restraints weight = 42492.662| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.7263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 43555 Z= 0.127 Angle : 0.706 12.449 59330 Z= 0.351 Chirality : 0.045 0.181 6855 Planarity : 0.005 0.060 7560 Dihedral : 5.823 173.986 5950 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.73 % Favored : 88.72 % Rotamer: Outliers : 3.01 % Allowed : 18.22 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.11), residues: 5265 helix: -0.94 (0.13), residues: 1615 sheet: 0.02 (0.19), residues: 720 loop : -2.75 (0.11), residues: 2930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 799 TYR 0.023 0.001 TYR E 113 PHE 0.023 0.001 PHE A 42 TRP 0.007 0.001 TRP C 211 HIS 0.010 0.001 HIS B 3 Details of bonding type rmsd covalent geometry : bond 0.00271 (43535) covalent geometry : angle 0.70606 (59330) hydrogen bonds : bond 0.03459 ( 996) hydrogen bonds : angle 4.61518 ( 2748) Misc. bond : bond 0.00283 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 433 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.4581 (mtm-85) REVERT: A 73 ARG cc_start: 0.6359 (OUTLIER) cc_final: 0.4743 (ptt-90) REVERT: A 282 GLU cc_start: 0.5002 (OUTLIER) cc_final: 0.4501 (pp20) REVERT: A 372 ARG cc_start: 0.7874 (ttp-110) cc_final: 0.7568 (ttp-170) REVERT: A 481 ASP cc_start: 0.3076 (OUTLIER) cc_final: 0.2491 (t70) REVERT: A 545 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.6221 (t80) REVERT: A 828 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6291 (m-10) REVERT: A 839 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7947 (mm) REVERT: A 940 MET cc_start: 0.6091 (mtm) cc_final: 0.5723 (mtp) REVERT: B 95 TRP cc_start: 0.8725 (OUTLIER) cc_final: 0.7850 (t-100) REVERT: B 481 ASP cc_start: 0.3734 (OUTLIER) cc_final: 0.3035 (t70) REVERT: B 607 ASN cc_start: 0.6940 (OUTLIER) cc_final: 0.6681 (m-40) REVERT: B 828 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6547 (m-10) REVERT: B 838 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7936 (mmtm) REVERT: B 938 MET cc_start: 0.7468 (mmm) cc_final: 0.6994 (tpp) REVERT: C 73 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.4898 (ptt-90) REVERT: C 78 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.4857 (m-80) REVERT: C 267 THR cc_start: 0.8565 (p) cc_final: 0.8356 (t) REVERT: C 362 MET cc_start: 0.5290 (OUTLIER) cc_final: 0.4490 (tmt) REVERT: C 455 MET cc_start: 0.7764 (tpp) cc_final: 0.7380 (ttm) REVERT: C 479 LYS cc_start: 0.5347 (OUTLIER) cc_final: 0.4521 (ptpp) REVERT: C 481 ASP cc_start: 0.3018 (OUTLIER) cc_final: 0.1944 (t70) REVERT: C 623 GLN cc_start: 0.6411 (pp30) cc_final: 0.5629 (pp30) REVERT: C 627 SER cc_start: 0.7822 (m) cc_final: 0.7180 (t) REVERT: C 763 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7900 (ptmm) REVERT: C 828 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6226 (m-10) REVERT: C 938 MET cc_start: 0.7346 (mmm) cc_final: 0.6811 (tpt) REVERT: D 39 LEU cc_start: 0.7878 (mt) cc_final: 0.7650 (mp) REVERT: D 73 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.4441 (ptt-90) REVERT: D 78 TYR cc_start: 0.6639 (OUTLIER) cc_final: 0.4932 (m-80) REVERT: D 479 LYS cc_start: 0.5733 (OUTLIER) cc_final: 0.4766 (pttt) REVERT: D 623 GLN cc_start: 0.4824 (OUTLIER) cc_final: 0.4593 (tt0) REVERT: D 683 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8350 (tm-30) REVERT: D 828 TYR cc_start: 0.6665 (OUTLIER) cc_final: 0.5679 (m-10) REVERT: D 829 MET cc_start: 0.6798 (ttm) cc_final: 0.6492 (mtp) REVERT: D 855 MET cc_start: 0.6736 (mmp) cc_final: 0.6417 (mmp) REVERT: D 981 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.6012 (ptt-90) REVERT: E 78 TYR cc_start: 0.6576 (OUTLIER) cc_final: 0.6042 (m-80) REVERT: E 481 ASP cc_start: 0.3070 (OUTLIER) cc_final: 0.1786 (t70) REVERT: E 828 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6367 (m-10) REVERT: E 938 MET cc_start: 0.7317 (mmm) cc_final: 0.6562 (ptm) outliers start: 142 outliers final: 108 residues processed: 539 average time/residue: 0.2124 time to fit residues: 197.8098 Evaluate side-chains 553 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 416 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 763 LYS Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 956 CYS Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 479 LYS Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 623 GLN Chi-restraints excluded: chain D residue 683 GLN Chi-restraints excluded: chain D residue 732 THR Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 596 ILE Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 828 TYR Chi-restraints excluded: chain E residue 855 MET Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 176 optimal weight: 5.9990 chunk 337 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 404 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 256 optimal weight: 3.9990 chunk 378 optimal weight: 30.0000 chunk 268 optimal weight: 6.9990 chunk 316 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 487 GLN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 GLN A 905 GLN B 61 ASN B 492 HIS B 607 ASN C 607 ASN C 683 GLN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 753 GLN D 905 GLN ** E 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN E 607 ASN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.155869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.143143 restraints weight = 84397.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.143445 restraints weight = 71516.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.144250 restraints weight = 57572.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.144656 restraints weight = 48062.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.144866 restraints weight = 42963.149| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.7559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 43555 Z= 0.161 Angle : 0.750 13.423 59330 Z= 0.374 Chirality : 0.047 0.183 6855 Planarity : 0.007 0.403 7560 Dihedral : 5.777 121.406 5950 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.57 % Allowed : 11.36 % Favored : 88.07 % Rotamer: Outliers : 3.31 % Allowed : 18.15 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.11), residues: 5265 helix: -0.99 (0.13), residues: 1625 sheet: -0.05 (0.19), residues: 730 loop : -2.73 (0.11), residues: 2910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 886 TYR 0.025 0.002 TYR A 417 PHE 0.018 0.002 PHE B 505 TRP 0.008 0.001 TRP A 95 HIS 0.011 0.001 HIS B 3 Details of bonding type rmsd covalent geometry : bond 0.00358 (43535) covalent geometry : angle 0.74954 (59330) hydrogen bonds : bond 0.04111 ( 996) hydrogen bonds : angle 4.75592 ( 2748) Misc. bond : bond 0.00329 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10530 Ramachandran restraints generated. 5265 Oldfield, 0 Emsley, 5265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 442 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.4671 (mtm-85) REVERT: A 73 ARG cc_start: 0.6631 (OUTLIER) cc_final: 0.4711 (ptt-90) REVERT: A 95 TRP cc_start: 0.8733 (OUTLIER) cc_final: 0.7743 (t-100) REVERT: A 372 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7641 (ttp-170) REVERT: A 481 ASP cc_start: 0.3414 (OUTLIER) cc_final: 0.2652 (t70) REVERT: A 545 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.6307 (t80) REVERT: A 828 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6454 (m-10) REVERT: A 839 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7936 (mm) REVERT: A 940 MET cc_start: 0.6009 (mtm) cc_final: 0.5731 (mtp) REVERT: A 1006 MET cc_start: 0.6959 (ptm) cc_final: 0.6553 (ptm) REVERT: B 95 TRP cc_start: 0.8790 (OUTLIER) cc_final: 0.8025 (t-100) REVERT: B 362 MET cc_start: 0.5919 (OUTLIER) cc_final: 0.5264 (tmm) REVERT: B 481 ASP cc_start: 0.3723 (OUTLIER) cc_final: 0.3079 (t70) REVERT: B 623 GLN cc_start: 0.5646 (pp30) cc_final: 0.5403 (pp30) REVERT: B 697 ILE cc_start: 0.3934 (pp) cc_final: 0.3480 (tp) REVERT: B 828 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.6762 (m-10) REVERT: B 838 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8028 (mmtm) REVERT: B 938 MET cc_start: 0.7394 (mmm) cc_final: 0.6926 (tpp) REVERT: C 73 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.5077 (ptt-90) REVERT: C 78 TYR cc_start: 0.6792 (OUTLIER) cc_final: 0.5087 (m-80) REVERT: C 267 THR cc_start: 0.8634 (p) cc_final: 0.8361 (t) REVERT: C 362 MET cc_start: 0.5265 (OUTLIER) cc_final: 0.4396 (tmt) REVERT: C 455 MET cc_start: 0.7828 (tpp) cc_final: 0.7601 (ttm) REVERT: C 481 ASP cc_start: 0.3094 (OUTLIER) cc_final: 0.2000 (t70) REVERT: C 623 GLN cc_start: 0.6497 (pp30) cc_final: 0.5756 (pp30) REVERT: C 627 SER cc_start: 0.8132 (m) cc_final: 0.7514 (t) REVERT: C 828 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.6524 (m-10) REVERT: C 938 MET cc_start: 0.7166 (mmm) cc_final: 0.6794 (tpt) REVERT: D 39 LEU cc_start: 0.8083 (mt) cc_final: 0.7851 (mp) REVERT: D 73 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.4493 (ptt-90) REVERT: D 78 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.5073 (m-80) REVERT: D 455 MET cc_start: 0.6878 (tpt) cc_final: 0.6379 (tpt) REVERT: D 479 LYS cc_start: 0.5689 (OUTLIER) cc_final: 0.5313 (pmtt) REVERT: D 623 GLN cc_start: 0.4883 (OUTLIER) cc_final: 0.4640 (tt0) REVERT: D 683 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8397 (tm-30) REVERT: D 828 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6117 (m-10) REVERT: D 829 MET cc_start: 0.6661 (ttm) cc_final: 0.6297 (mtp) REVERT: D 855 MET cc_start: 0.6780 (mmp) cc_final: 0.6488 (tpt) REVERT: D 981 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.5987 (ptt-90) REVERT: E 78 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.5945 (m-80) REVERT: E 282 GLU cc_start: 0.4265 (OUTLIER) cc_final: 0.3866 (pp20) REVERT: E 455 MET cc_start: 0.7542 (tpt) cc_final: 0.7015 (tpt) REVERT: E 481 ASP cc_start: 0.3519 (OUTLIER) cc_final: 0.2663 (t70) REVERT: E 683 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: E 828 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6538 (m-10) REVERT: E 938 MET cc_start: 0.7367 (mmm) cc_final: 0.6518 (ptm) outliers start: 156 outliers final: 114 residues processed: 561 average time/residue: 0.2232 time to fit residues: 215.2376 Evaluate side-chains 561 residues out of total 4710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 418 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 467 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1042 VAL Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 483 MET Chi-restraints excluded: chain B residue 585 ILE Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 838 LYS Chi-restraints excluded: chain B residue 839 LEU Chi-restraints excluded: chain B residue 977 HIS Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 992 TYR Chi-restraints excluded: chain B residue 999 VAL Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1056 VAL Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 432 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 479 LYS Chi-restraints excluded: chain C residue 481 ASP Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 549 SER Chi-restraints excluded: chain C residue 585 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 683 GLN Chi-restraints excluded: chain C residue 828 TYR Chi-restraints excluded: chain C residue 956 CYS Chi-restraints excluded: chain C residue 967 ILE Chi-restraints excluded: chain C residue 992 TYR Chi-restraints excluded: chain C residue 999 VAL Chi-restraints excluded: chain C residue 1042 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 47 ARG Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 401 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 479 LYS Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 623 GLN Chi-restraints excluded: chain D residue 683 GLN Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 828 TYR Chi-restraints excluded: chain D residue 981 ARG Chi-restraints excluded: chain D residue 989 VAL Chi-restraints excluded: chain D residue 992 TYR Chi-restraints excluded: chain D residue 999 VAL Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1056 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 78 TYR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 411 ILE Chi-restraints excluded: chain E residue 432 ASP Chi-restraints excluded: chain E residue 469 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 600 VAL Chi-restraints excluded: chain E residue 604 ILE Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 683 GLN Chi-restraints excluded: chain E residue 828 TYR Chi-restraints excluded: chain E residue 855 MET Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 992 TYR Chi-restraints excluded: chain E residue 999 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 525 random chunks: chunk 204 optimal weight: 7.9990 chunk 495 optimal weight: 30.0000 chunk 196 optimal weight: 40.0000 chunk 487 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 267 optimal weight: 30.0000 chunk 58 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 146 optimal weight: 20.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 487 GLN ** A 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 HIS ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN C 607 ASN C 683 GLN ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 683 GLN ** E 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.155404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.142470 restraints weight = 84714.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.143073 restraints weight = 69876.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.143577 restraints weight = 55319.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.143791 restraints weight = 47631.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.143947 restraints weight = 46845.131| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.7604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.160 43555 Z= 0.225 Angle : 0.865 59.190 59330 Z= 0.459 Chirality : 0.051 1.100 6855 Planarity : 0.008 0.389 7560 Dihedral : 5.808 124.246 5950 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.57 % Allowed : 11.47 % Favored : 87.96 % Rotamer: Outliers : 3.33 % Allowed : 18.24 % Favored : 78.43 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.11), residues: 5265 helix: -0.99 (0.13), residues: 1625 sheet: -0.06 (0.19), residues: 730 loop : -2.73 (0.11), residues: 2910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG C 886 TYR 0.022 0.002 TYR A 417 PHE 0.059 0.002 PHE A 505 TRP 0.008 0.001 TRP A 95 HIS 0.010 0.001 HIS B 3 Details of bonding type rmsd covalent geometry : bond 0.00489 (43535) covalent geometry : angle 0.86488 (59330) hydrogen bonds : bond 0.04165 ( 996) hydrogen bonds : angle 4.76023 ( 2748) Misc. bond : bond 0.00324 ( 20) =============================================================================== Job complete usr+sys time: 6616.48 seconds wall clock time: 115 minutes 26.36 seconds (6926.36 seconds total)