Starting phenix.real_space_refine on Fri May 30 07:14:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xnf_38502/05_2025/8xnf_38502.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xnf_38502/05_2025/8xnf_38502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xnf_38502/05_2025/8xnf_38502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xnf_38502/05_2025/8xnf_38502.map" model { file = "/net/cci-nas-00/data/ceres_data/8xnf_38502/05_2025/8xnf_38502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xnf_38502/05_2025/8xnf_38502.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4869 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 135 5.16 5 C 18737 2.51 5 N 4791 2.21 5 O 5637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29301 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} bond proxies already assigned to first conformer: 4990 Chain: "B" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7853 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 54, 'TRANS': 946} Chain breaks: 6 Chain: "C" Number of atoms: 7965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7965 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 55, 'TRANS': 959} Chain breaks: 6 Chain: "D" Number of atoms: 7972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7972 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 55, 'TRANS': 960} Chain breaks: 6 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 85 Unusual residues: {' ZN': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 18.76, per 1000 atoms: 0.64 Number of scatterers: 29301 At special positions: 0 Unit cell: (147.9, 135.15, 232.05, 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) Zn 1 29.99 S 135 16.00 O 5637 8.00 N 4791 7.00 C 18737 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=1.99 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 487 " distance=2.01 Simple disulfide: pdb=" SG CYS B 616 " - pdb=" SG CYS B 648 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 670 " distance=2.03 Simple disulfide: pdb=" SG CYS B 737 " - pdb=" SG CYS B 759 " distance=2.03 Simple disulfide: pdb=" SG CYS B 742 " - pdb=" SG CYS B 748 " distance=2.03 Simple disulfide: pdb=" SG CYS B1031 " - pdb=" SG CYS B1042 " distance=2.03 Simple disulfide: pdb=" SG CYS B1081 " - pdb=" SG CYS B1125 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 487 " distance=2.01 Simple disulfide: pdb=" SG CYS C 616 " - pdb=" SG CYS C 648 " distance=2.03 Simple disulfide: pdb=" SG CYS C 661 " - pdb=" SG CYS C 670 " distance=2.03 Simple disulfide: pdb=" SG CYS C 737 " - pdb=" SG CYS C 759 " distance=2.03 Simple disulfide: pdb=" SG CYS C 742 " - pdb=" SG CYS C 748 " distance=2.03 Simple disulfide: pdb=" SG CYS C1031 " - pdb=" SG CYS C1042 " distance=2.03 Simple disulfide: pdb=" SG CYS C1081 " - pdb=" SG CYS C1125 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.04 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.01 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 487 " distance=2.01 Simple disulfide: pdb=" SG CYS D 616 " - pdb=" SG CYS D 648 " distance=2.03 Simple disulfide: pdb=" SG CYS D 661 " - pdb=" SG CYS D 670 " distance=2.03 Simple disulfide: pdb=" SG CYS D 737 " - pdb=" SG CYS D 759 " distance=2.03 Simple disulfide: pdb=" SG CYS D 742 " - pdb=" SG CYS D 748 " distance=2.03 Simple disulfide: pdb=" SG CYS D1031 " - pdb=" SG CYS D1042 " distance=2.03 Simple disulfide: pdb=" SG CYS D1081 " - pdb=" SG CYS D1125 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 90 " " NAG A 704 " - " ASN A 322 " " NAG A 705 " - " ASN A 432 " " NAG A 706 " - " ASN A 546 " " NAG A 707 " - " ASN A 103 " " NAG B1201 " - " ASN B 282 " " NAG B1202 " - " ASN B 331 " " NAG B1203 " - " ASN B 615 " " NAG B1204 " - " ASN B 716 " " NAG B1205 " - " ASN B1133 " " NAG B1206 " - " ASN B 354 " " NAG B1207 " - " ASN B 343 " " NAG C1201 " - " ASN C 282 " " NAG C1202 " - " ASN C 615 " " NAG C1203 " - " ASN C 708 " " NAG C1204 " - " ASN C 716 " " NAG C1205 " - " ASN C1097 " " NAG C1206 " - " ASN C1133 " " NAG C1207 " - " ASN C 354 " " NAG C1208 " - " ASN C 343 " " NAG D1201 " - " ASN D 62 " " NAG D1202 " - " ASN D 165 " " NAG D1203 " - " ASN D 331 " " NAG D1204 " - " ASN D 615 " " NAG D1205 " - " ASN D 708 " " NAG D1206 " - " ASN D 716 " " NAG D1208 " - " ASN D 282 " " NAG D1209 " - " ASN D1073 " " NAG D1210 " - " ASN D 656 " " NAG D1211 " - " ASN D 354 " " NAG D1212 " - " ASN D 343 " " NAG E 1 " - " ASN B 708 " " NAG F 1 " - " ASN B 800 " " NAG G 1 " - " ASN B1097 " " NAG H 1 " - " ASN C 800 " " NAG I 1 " - " ASN D 800 " " NAG J 1 " - " ASN D1097 " Time building additional restraints: 6.96 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6812 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 50 sheets defined 32.2% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 4.147A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.565A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.776A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 158 through 173 removed outlier: 3.781A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.632A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.956A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.748A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.911A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.561A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.649A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.613A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.653A pdb=" N THR A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.816A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.588A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'B' and resid 295 through 304 removed outlier: 5.092A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.639A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.244A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.701A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 624 Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.716A pdb=" N GLY B 756 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 782 removed outlier: 3.801A pdb=" N GLN B 761 " --> pdb=" O SER B 757 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 774 " --> pdb=" O ALA B 770 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 777 " --> pdb=" O GLN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 823 Processing helix chain 'B' and resid 865 through 883 Processing helix chain 'B' and resid 885 through 889 removed outlier: 3.541A pdb=" N GLY B 888 " --> pdb=" O TRP B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 907 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.577A pdb=" N TYR B 916 " --> pdb=" O GLN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 940 removed outlier: 3.831A pdb=" N GLN B 934 " --> pdb=" O ILE B 930 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP B 935 " --> pdb=" O GLY B 931 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 940 " --> pdb=" O SER B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 964 removed outlier: 3.571A pdb=" N GLN B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 950 " --> pdb=" O LYS B 946 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 951 " --> pdb=" O LEU B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 967 No H-bonds generated for 'chain 'B' and resid 965 through 967' Processing helix chain 'B' and resid 975 through 981 Processing helix chain 'B' and resid 984 through 1032 Processing helix chain 'C' and resid 295 through 304 removed outlier: 5.260A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 372 removed outlier: 3.639A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.244A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.700A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 625 removed outlier: 5.710A pdb=" N ALA C 622 " --> pdb=" O GLU C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 741 Processing helix chain 'C' and resid 745 through 751 removed outlier: 3.693A pdb=" N ASN C 750 " --> pdb=" O THR C 746 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 751 " --> pdb=" O GLU C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 756 Processing helix chain 'C' and resid 757 through 782 removed outlier: 3.667A pdb=" N ASP C 774 " --> pdb=" O ALA C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 814 removed outlier: 3.690A pdb=" N LYS C 813 " --> pdb=" O LYS C 810 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG C 814 " --> pdb=" O PRO C 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 810 through 814' Processing helix chain 'C' and resid 815 through 823 Processing helix chain 'C' and resid 865 through 884 Processing helix chain 'C' and resid 885 through 889 removed outlier: 3.671A pdb=" N GLY C 888 " --> pdb=" O TRP C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 912 through 917 removed outlier: 3.693A pdb=" N TYR C 916 " --> pdb=" O GLN C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 940 removed outlier: 3.635A pdb=" N GLN C 934 " --> pdb=" O ILE C 930 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP C 935 " --> pdb=" O GLY C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 964 removed outlier: 3.725A pdb=" N VAL C 950 " --> pdb=" O LYS C 946 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 951 " --> pdb=" O LEU C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 981 Processing helix chain 'C' and resid 984 through 1032 removed outlier: 3.623A pdb=" N VAL C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C1016 " --> pdb=" O ILE C1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 304 removed outlier: 5.262A pdb=" N CYS D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 366 through 372 removed outlier: 3.639A pdb=" N ASN D 370 " --> pdb=" O SER D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 removed outlier: 4.244A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.701A pdb=" N SER D 443 " --> pdb=" O ASN D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 626 removed outlier: 3.598A pdb=" N VAL D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 639 No H-bonds generated for 'chain 'D' and resid 637 through 639' Processing helix chain 'D' and resid 736 through 742 Processing helix chain 'D' and resid 745 through 754 removed outlier: 3.734A pdb=" N SER D 749 " --> pdb=" O SER D 745 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN D 750 " --> pdb=" O THR D 746 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU D 751 " --> pdb=" O GLU D 747 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 782 removed outlier: 3.678A pdb=" N GLN D 761 " --> pdb=" O SER D 757 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP D 774 " --> pdb=" O ALA D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 814 removed outlier: 3.791A pdb=" N LYS D 813 " --> pdb=" O LYS D 810 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG D 814 " --> pdb=" O PRO D 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 810 through 814' Processing helix chain 'D' and resid 815 through 825 removed outlier: 3.630A pdb=" N VAL D 825 " --> pdb=" O LEU D 821 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 884 Processing helix chain 'D' and resid 896 through 909 Processing helix chain 'D' and resid 912 through 917 Processing helix chain 'D' and resid 918 through 940 removed outlier: 3.712A pdb=" N GLN D 934 " --> pdb=" O ILE D 930 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP D 935 " --> pdb=" O GLY D 931 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 940 " --> pdb=" O SER D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 964 removed outlier: 3.602A pdb=" N VAL D 950 " --> pdb=" O LYS D 946 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 951 " --> pdb=" O LEU D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 967 No H-bonds generated for 'chain 'D' and resid 965 through 967' Processing helix chain 'D' and resid 975 through 981 Processing helix chain 'D' and resid 984 through 1032 removed outlier: 3.725A pdb=" N VAL D 990 " --> pdb=" O PRO D 986 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU D1016 " --> pdb=" O ILE D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1115 through 1117 No H-bonds generated for 'chain 'D' and resid 1115 through 1117' Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.608A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 31 removed outlier: 7.375A pdb=" N ASN B 62 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TYR B 269 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL B 37 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 56 removed outlier: 4.227A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.680A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 313 Processing sheet with id=AA8, first strand: chain 'B' and resid 317 through 319 Processing sheet with id=AA9, first strand: chain 'B' and resid 324 through 327 removed outlier: 4.119A pdb=" N GLU B 324 " --> pdb=" O CYS B 537 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.226A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP B 398 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 511 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AB3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'B' and resid 564 through 565 removed outlier: 7.034A pdb=" N PHE B 564 " --> pdb=" O PHE D 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 653 through 654 removed outlier: 5.722A pdb=" N GLU B 653 " --> pdb=" O ALA B 693 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N THR B 695 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 669 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 701 through 703 removed outlier: 3.574A pdb=" N LYS D 789 " --> pdb=" O ASN B 702 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 710 through 727 removed outlier: 6.751A pdb=" N GLN B1070 " --> pdb=" O THR B 715 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE B 717 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE B 719 " --> pdb=" O TYR B1066 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TYR B1066 " --> pdb=" O ILE B 719 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 721 " --> pdb=" O VAL B1064 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B1064 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR B 723 " --> pdb=" O LEU B1062 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU B1062 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE B 725 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B1060 " --> pdb=" O ILE B 725 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY B1058 " --> pdb=" O PRO B 727 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY B1058 " --> pdb=" O SER B1054 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER B1054 " --> pdb=" O GLY B1058 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B1060 " --> pdb=" O PRO B1052 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B1062 " --> pdb=" O SER B1050 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER B1050 " --> pdb=" O LEU B1062 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B1064 " --> pdb=" O LEU B1048 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 710 through 727 removed outlier: 6.751A pdb=" N GLN B1070 " --> pdb=" O THR B 715 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE B 717 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE B 719 " --> pdb=" O TYR B1066 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TYR B1066 " --> pdb=" O ILE B 719 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 721 " --> pdb=" O VAL B1064 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL B1064 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR B 723 " --> pdb=" O LEU B1062 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU B1062 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE B 725 " --> pdb=" O VAL B1060 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B1060 " --> pdb=" O ILE B 725 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY B1058 " --> pdb=" O PRO B 727 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 732 through 735 removed outlier: 4.458A pdb=" N LYS B 732 " --> pdb=" O LEU B 860 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 787 through 788 removed outlier: 5.995A pdb=" N ILE B 787 " --> pdb=" O ASN C 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 1119 through 1124 removed outlier: 4.780A pdb=" N ALA B1086 " --> pdb=" O SER B1122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.568A pdb=" N ASN C 62 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TYR C 269 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.736A pdb=" N PHE C 44 " --> pdb=" O PHE D 564 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 48 through 56 removed outlier: 4.094A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.812A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 311 through 313 Processing sheet with id=AC8, first strand: chain 'C' and resid 311 through 313 removed outlier: 4.290A pdb=" N GLY C 593 " --> pdb=" O GLN C 612 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 324 through 327 removed outlier: 4.119A pdb=" N GLU C 324 " --> pdb=" O CYS C 537 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.226A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP C 398 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 511 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AD3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD4, first strand: chain 'C' and resid 653 through 654 removed outlier: 5.813A pdb=" N GLU C 653 " --> pdb=" O ALA C 693 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N THR C 695 " --> pdb=" O GLU C 653 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 710 through 727 removed outlier: 6.830A pdb=" N SER C 710 " --> pdb=" O THR C1075 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR C1075 " --> pdb=" O SER C 710 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA C 712 " --> pdb=" O ASN C1073 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN C1073 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU C1071 " --> pdb=" O PRO C 714 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR C1066 " --> pdb=" O HIS C1047 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N HIS C1047 " --> pdb=" O TYR C1066 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 710 through 727 removed outlier: 6.830A pdb=" N SER C 710 " --> pdb=" O THR C1075 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR C1075 " --> pdb=" O SER C 710 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA C 712 " --> pdb=" O ASN C1073 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN C1073 " --> pdb=" O ALA C 712 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU C1071 " --> pdb=" O PRO C 714 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 732 through 735 removed outlier: 4.603A pdb=" N LYS C 732 " --> pdb=" O LEU C 860 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 787 through 789 removed outlier: 5.936A pdb=" N ILE C 787 " --> pdb=" O ASN D 702 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 1119 through 1124 removed outlier: 5.462A pdb=" N VAL C1121 " --> pdb=" O PHE C1088 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE C1088 " --> pdb=" O VAL C1121 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY C1123 " --> pdb=" O ALA C1086 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 28 through 31 removed outlier: 7.350A pdb=" N ASN D 62 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR D 269 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 48 through 56 removed outlier: 4.143A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 84 through 85 removed outlier: 4.075A pdb=" N ILE D 105 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 311 through 313 removed outlier: 3.531A pdb=" N THR D 598 " --> pdb=" O GLY D 311 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 311 through 313 removed outlier: 3.531A pdb=" N THR D 598 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY D 593 " --> pdb=" O GLN D 612 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 324 through 327 removed outlier: 4.119A pdb=" N GLU D 324 " --> pdb=" O CYS D 537 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 354 through 358 removed outlier: 4.226A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL D 395 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP D 398 " --> pdb=" O VAL D 511 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 511 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 376 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AE9, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'D' and resid 653 through 654 removed outlier: 5.944A pdb=" N GLU D 653 " --> pdb=" O ALA D 693 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR D 695 " --> pdb=" O GLU D 653 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ALA D 671 " --> pdb=" O PRO D 664 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 710 through 727 removed outlier: 6.713A pdb=" N GLN D1070 " --> pdb=" O THR D 715 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE D 717 " --> pdb=" O PRO D1068 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE D 719 " --> pdb=" O TYR D1066 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR D1066 " --> pdb=" O ILE D 719 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL D 721 " --> pdb=" O VAL D1064 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL D1064 " --> pdb=" O VAL D 721 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR D 723 " --> pdb=" O LEU D1062 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU D1062 " --> pdb=" O THR D 723 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE D 725 " --> pdb=" O VAL D1060 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL D1060 " --> pdb=" O ILE D 725 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY D1058 " --> pdb=" O PRO D 727 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR D1066 " --> pdb=" O HIS D1047 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS D1047 " --> pdb=" O TYR D1066 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 732 through 735 removed outlier: 4.507A pdb=" N LYS D 732 " --> pdb=" O LEU D 860 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1080 through 1081 removed outlier: 4.692A pdb=" N ALA D1086 " --> pdb=" O SER D1122 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1093 through 1096 1177 hydrogen bonds defined for protein. 3234 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: 12.94 Time building geometry restraints manager: 8.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7943 1.33 - 1.46: 7358 1.46 - 1.58: 14540 1.58 - 1.71: 0 1.71 - 1.83: 182 Bond restraints: 30023 Sorted by residual: bond pdb=" C LYS C 528 " pdb=" N SER C 529 " ideal model delta sigma weight residual 1.330 1.220 0.111 1.45e-02 4.76e+03 5.81e+01 bond pdb=" C LYS B 528 " pdb=" N SER B 529 " ideal model delta sigma weight residual 1.330 1.220 0.110 1.45e-02 4.76e+03 5.74e+01 bond pdb=" C LYS D 528 " pdb=" N SER D 529 " ideal model delta sigma weight residual 1.330 1.220 0.110 1.45e-02 4.76e+03 5.73e+01 bond pdb=" CA SER B 815 " pdb=" CB SER B 815 " ideal model delta sigma weight residual 1.536 1.474 0.063 1.23e-02 6.61e+03 2.59e+01 bond pdb=" N VAL D1132 " pdb=" CA VAL D1132 " ideal model delta sigma weight residual 1.455 1.497 -0.042 1.18e-02 7.18e+03 1.26e+01 ... (remaining 30018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 39869 2.22 - 4.45: 868 4.45 - 6.67: 94 6.67 - 8.90: 22 8.90 - 11.12: 5 Bond angle restraints: 40858 Sorted by residual: angle pdb=" N HIS B 339 " pdb=" CA HIS B 339 " pdb=" C HIS B 339 " ideal model delta sigma weight residual 111.28 101.84 9.44 1.09e+00 8.42e-01 7.50e+01 angle pdb=" N HIS D 339 " pdb=" CA HIS D 339 " pdb=" C HIS D 339 " ideal model delta sigma weight residual 112.23 101.55 10.68 1.26e+00 6.30e-01 7.19e+01 angle pdb=" N HIS C 339 " pdb=" CA HIS C 339 " pdb=" C HIS C 339 " ideal model delta sigma weight residual 112.23 101.59 10.64 1.26e+00 6.30e-01 7.13e+01 angle pdb=" N ILE C 623 " pdb=" CA ILE C 623 " pdb=" C ILE C 623 " ideal model delta sigma weight residual 111.90 106.15 5.75 8.10e-01 1.52e+00 5.04e+01 angle pdb=" CA PHE D 318 " pdb=" CB PHE D 318 " pdb=" CG PHE D 318 " ideal model delta sigma weight residual 113.80 120.67 -6.87 1.00e+00 1.00e+00 4.72e+01 ... (remaining 40853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 17124 21.02 - 42.05: 1089 42.05 - 63.07: 135 63.07 - 84.10: 46 84.10 - 105.12: 11 Dihedral angle restraints: 18405 sinusoidal: 7816 harmonic: 10589 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 487 " pdb=" CB CYS C 487 " ideal model delta sinusoidal sigma weight residual 93.00 166.47 -73.47 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS D 480 " pdb=" SG CYS D 480 " pdb=" SG CYS D 487 " pdb=" CB CYS D 487 " ideal model delta sinusoidal sigma weight residual 93.00 166.47 -73.47 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 487 " pdb=" CB CYS B 487 " ideal model delta sinusoidal sigma weight residual 93.00 166.46 -73.46 1 1.00e+01 1.00e-02 6.87e+01 ... (remaining 18402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.222: 4657 0.222 - 0.443: 20 0.443 - 0.665: 4 0.665 - 0.886: 4 0.886 - 1.108: 1 Chirality restraints: 4686 Sorted by residual: chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.33e+01 chirality pdb=" C1 NAG C1207 " pdb=" ND2 ASN C 354 " pdb=" C2 NAG C1207 " pdb=" O5 NAG C1207 " both_signs ideal model delta sigma weight residual False -2.40 -1.29 -1.11 2.00e-01 2.50e+01 3.07e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 2.94e+01 ... (remaining 4683 not shown) Planarity restraints: 5248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1204 " 0.338 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG D1204 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG D1204 " 0.156 2.00e-02 2.50e+03 pdb=" N2 NAG D1204 " -0.514 2.00e-02 2.50e+03 pdb=" O7 NAG D1204 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1211 " -0.335 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG D1211 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG D1211 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG D1211 " 0.498 2.00e-02 2.50e+03 pdb=" O7 NAG D1211 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1207 " -0.328 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG C1207 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG C1207 " -0.047 2.00e-02 2.50e+03 pdb=" N2 NAG C1207 " 0.498 2.00e-02 2.50e+03 pdb=" O7 NAG C1207 " -0.200 2.00e-02 2.50e+03 ... (remaining 5245 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 248 2.60 - 3.17: 24305 3.17 - 3.75: 42131 3.75 - 4.32: 58488 4.32 - 4.90: 97476 Nonbonded interactions: 222648 Sorted by model distance: nonbonded pdb=" OD1 ASN D1133 " pdb=" C1 NAG D1207 " model vdw 2.021 3.470 nonbonded pdb=" OD1 ASN D1133 " pdb=" O5 NAG D1207 " model vdw 2.093 3.040 nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.100 2.230 nonbonded pdb=" OE1 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.118 2.230 nonbonded pdb=" OG SER B 469 " pdb=" OE1 GLU B 471 " model vdw 2.246 3.040 ... (remaining 222643 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 27 through 825 or resid 854 through 1139 or resid 1201 thr \ ough 1207)) selection = (chain 'C' and (resid 27 through 135 or resid 159 through 1139 or resid 1201 thr \ ough 1207)) selection = (chain 'D' and (resid 27 through 135 or resid 159 through 825 or resid 854 throu \ gh 1139 or resid 1201 through 1207)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 1.220 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 73.010 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 85.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 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 : 0.005 0.209 30106 Z= 0.298 Angle : 0.800 15.874 41065 Z= 0.461 Chirality : 0.062 1.108 4686 Planarity : 0.015 0.290 5210 Dihedral : 13.695 105.119 11485 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.15 % Favored : 91.46 % Rotamer: Outliers : 0.13 % Allowed : 1.13 % Favored : 98.75 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3585 helix: 1.63 (0.18), residues: 957 sheet: -0.09 (0.20), residues: 578 loop : -2.07 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 203 HIS 0.008 0.001 HIS A 374 PHE 0.043 0.001 PHE D 318 TYR 0.022 0.002 TYR C 635 ARG 0.004 0.000 ARG B 814 Details of bonding type rmsd link_NAG-ASN : bond 0.00933 ( 38) link_NAG-ASN : angle 5.04427 ( 114) link_BETA1-4 : bond 0.03946 ( 7) link_BETA1-4 : angle 6.01357 ( 21) hydrogen bonds : bond 0.15262 ( 1153) hydrogen bonds : angle 6.76716 ( 3234) metal coordination : bond 0.20344 ( 2) SS BOND : bond 0.01030 ( 36) SS BOND : angle 2.57549 ( 72) covalent geometry : bond 0.00513 (30023) covalent geometry : angle 0.73638 (40858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 202 time to evaluate : 3.123 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 332 MET cc_start: -0.0564 (ptm) cc_final: -0.0815 (ppp) outliers start: 4 outliers final: 0 residues processed: 205 average time/residue: 0.4132 time to fit residues: 134.9833 Evaluate side-chains 86 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 304 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 327 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 221 GLN A 401 HIS A 535 HIS B 207 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1082 HIS ** D 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 627 GLN D 823 ASN D 900 GLN D1134 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.098490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.057365 restraints weight = 171796.036| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 8.14 r_work: 0.2760 rms_B_bonded: 8.13 restraints_weight: 2.0000 r_work: 0.2877 rms_B_bonded: 6.07 restraints_weight: 4.0000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30106 Z= 0.186 Angle : 0.670 10.743 41065 Z= 0.330 Chirality : 0.045 0.459 4686 Planarity : 0.004 0.062 5210 Dihedral : 7.115 61.024 4855 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.31 % Favored : 93.67 % Rotamer: Outliers : 0.53 % Allowed : 5.64 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3585 helix: 1.76 (0.17), residues: 1004 sheet: -0.15 (0.22), residues: 505 loop : -1.85 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 632 HIS 0.004 0.001 HIS C 339 PHE 0.023 0.001 PHE C 338 TYR 0.019 0.001 TYR A 510 ARG 0.006 0.000 ARG B 633 Details of bonding type rmsd link_NAG-ASN : bond 0.00517 ( 38) link_NAG-ASN : angle 3.69936 ( 114) link_BETA1-4 : bond 0.01297 ( 7) link_BETA1-4 : angle 2.58454 ( 21) hydrogen bonds : bond 0.04641 ( 1153) hydrogen bonds : angle 5.50366 ( 3234) metal coordination : bond 0.00630 ( 2) SS BOND : bond 0.00341 ( 36) SS BOND : angle 1.16703 ( 72) covalent geometry : bond 0.00416 (30023) covalent geometry : angle 0.63768 (40858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.4437 (mtt) cc_final: 0.3617 (mmm) REVERT: A 297 MET cc_start: 0.0176 (mmt) cc_final: -0.0030 (tpt) REVERT: A 332 MET cc_start: 0.5691 (ptm) cc_final: 0.4756 (ppp) REVERT: A 360 MET cc_start: 0.4130 (tmm) cc_final: 0.3684 (tmm) REVERT: B 724 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8668 (tt0) REVERT: C 739 MET cc_start: 0.9563 (tpp) cc_final: 0.9240 (mmm) REVERT: D 739 MET cc_start: 0.9541 (tpp) cc_final: 0.9241 (tpp) outliers start: 17 outliers final: 9 residues processed: 100 average time/residue: 0.3817 time to fit residues: 66.4656 Evaluate side-chains 85 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 564 PHE Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain D residue 577 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 354 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 167 optimal weight: 0.0570 chunk 128 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 331 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 133 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 709 ASN D 439 ASN D1134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.098986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.058572 restraints weight = 158681.948| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 7.95 r_work: 0.2799 rms_B_bonded: 7.05 restraints_weight: 2.0000 r_work: 0.2913 rms_B_bonded: 5.44 restraints_weight: 4.0000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30106 Z= 0.113 Angle : 0.569 11.071 41065 Z= 0.283 Chirality : 0.044 0.441 4686 Planarity : 0.004 0.063 5210 Dihedral : 6.317 58.844 4855 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.11 % Rotamer: Outliers : 0.72 % Allowed : 7.27 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3585 helix: 1.97 (0.17), residues: 1002 sheet: -0.09 (0.20), residues: 572 loop : -1.74 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 632 HIS 0.005 0.000 HIS A 401 PHE 0.043 0.001 PHE B 371 TYR 0.016 0.001 TYR C1066 ARG 0.005 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 38) link_NAG-ASN : angle 3.15261 ( 114) link_BETA1-4 : bond 0.00761 ( 7) link_BETA1-4 : angle 2.44208 ( 21) hydrogen bonds : bond 0.04123 ( 1153) hydrogen bonds : angle 5.15829 ( 3234) metal coordination : bond 0.00153 ( 2) SS BOND : bond 0.00349 ( 36) SS BOND : angle 1.16338 ( 72) covalent geometry : bond 0.00246 (30023) covalent geometry : angle 0.54070 (40858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.4390 (mtt) cc_final: 0.3849 (mmt) REVERT: A 332 MET cc_start: 0.5835 (ptm) cc_final: 0.5323 (ppp) REVERT: B 724 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8607 (tt0) REVERT: C 229 LEU cc_start: 0.9140 (tp) cc_final: 0.8887 (tt) REVERT: C 983 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9131 (pp) REVERT: D 739 MET cc_start: 0.9472 (tpp) cc_final: 0.9190 (tpp) REVERT: D 868 MET cc_start: 0.9493 (mtt) cc_final: 0.9235 (mtp) outliers start: 23 outliers final: 10 residues processed: 97 average time/residue: 0.3696 time to fit residues: 63.1432 Evaluate side-chains 88 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 564 PHE Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 577 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 48 optimal weight: 7.9990 chunk 357 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 329 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 287 optimal weight: 30.0000 chunk 56 optimal weight: 40.0000 chunk 21 optimal weight: 9.9990 chunk 6 optimal weight: 0.0030 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS D 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.096699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.056857 restraints weight = 149896.732| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 6.05 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 30106 Z= 0.227 Angle : 0.624 10.271 41065 Z= 0.312 Chirality : 0.044 0.434 4686 Planarity : 0.004 0.059 5210 Dihedral : 5.971 57.637 4855 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.86 % Favored : 93.11 % Rotamer: Outliers : 1.25 % Allowed : 8.24 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.14), residues: 3585 helix: 1.83 (0.17), residues: 1012 sheet: -0.31 (0.20), residues: 595 loop : -1.75 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 632 HIS 0.004 0.001 HIS A 401 PHE 0.017 0.001 PHE C 905 TYR 0.019 0.001 TYR C1066 ARG 0.007 0.000 ARG B 904 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 38) link_NAG-ASN : angle 2.89384 ( 114) link_BETA1-4 : bond 0.00477 ( 7) link_BETA1-4 : angle 2.22022 ( 21) hydrogen bonds : bond 0.04408 ( 1153) hydrogen bonds : angle 5.18913 ( 3234) metal coordination : bond 0.00076 ( 2) SS BOND : bond 0.00264 ( 36) SS BOND : angle 1.08093 ( 72) covalent geometry : bond 0.00515 (30023) covalent geometry : angle 0.60274 (40858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 75 time to evaluate : 3.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8611 (ptt) cc_final: 0.7755 (ppp) REVERT: A 152 MET cc_start: -0.5076 (tpt) cc_final: -0.5364 (tpp) REVERT: A 249 MET cc_start: 0.1369 (mtt) cc_final: 0.0567 (mmm) REVERT: A 297 MET cc_start: -0.2208 (mmt) cc_final: -0.2409 (mmt) REVERT: A 332 MET cc_start: 0.3306 (ptm) cc_final: 0.2753 (ppp) REVERT: A 408 MET cc_start: 0.5179 (mmt) cc_final: 0.4372 (mmm) REVERT: B 724 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: C 618 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8675 (pm20) REVERT: D 739 MET cc_start: 0.9319 (tpp) cc_final: 0.9057 (tpp) outliers start: 40 outliers final: 17 residues processed: 112 average time/residue: 0.3493 time to fit residues: 68.6315 Evaluate side-chains 88 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 564 PHE Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 618 GLU Chi-restraints excluded: chain C residue 785 LYS Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 1103 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 208 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 243 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 358 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 310 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.097367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.056047 restraints weight = 179334.077| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 8.40 r_work: 0.2736 rms_B_bonded: 8.17 restraints_weight: 2.0000 r_work: 0.2858 rms_B_bonded: 6.76 restraints_weight: 4.0000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30106 Z= 0.129 Angle : 0.546 10.295 41065 Z= 0.274 Chirality : 0.043 0.412 4686 Planarity : 0.004 0.059 5210 Dihedral : 5.793 56.351 4855 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.83 % Favored : 94.14 % Rotamer: Outliers : 0.94 % Allowed : 8.99 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3585 helix: 1.89 (0.17), residues: 1022 sheet: -0.36 (0.20), residues: 578 loop : -1.60 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 632 HIS 0.004 0.001 HIS A 401 PHE 0.041 0.001 PHE B 371 TYR 0.016 0.001 TYR C1066 ARG 0.003 0.000 ARG A 161 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 38) link_NAG-ASN : angle 2.67487 ( 114) link_BETA1-4 : bond 0.00738 ( 7) link_BETA1-4 : angle 2.16972 ( 21) hydrogen bonds : bond 0.03905 ( 1153) hydrogen bonds : angle 4.95979 ( 3234) metal coordination : bond 0.00054 ( 2) SS BOND : bond 0.00227 ( 36) SS BOND : angle 0.83875 ( 72) covalent geometry : bond 0.00292 (30023) covalent geometry : angle 0.52487 (40858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 3.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7464 (tpt) cc_final: 0.7105 (tpp) REVERT: A 249 MET cc_start: 0.4767 (mtt) cc_final: 0.3895 (mmm) REVERT: A 297 MET cc_start: 0.1298 (mmt) cc_final: 0.0838 (mmt) REVERT: A 332 MET cc_start: 0.6396 (ptm) cc_final: 0.5877 (ppp) REVERT: A 408 MET cc_start: 0.4643 (mmt) cc_final: 0.4064 (mmt) REVERT: B 724 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: C 589 CYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8290 (m) REVERT: C 618 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8769 (pm20) REVERT: C 983 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9036 (pp) REVERT: D 739 MET cc_start: 0.9492 (tpp) cc_final: 0.9230 (tpp) outliers start: 30 outliers final: 16 residues processed: 102 average time/residue: 0.3481 time to fit residues: 63.7423 Evaluate side-chains 87 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 564 PHE Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 618 GLU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 564 PHE Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 659 TYR Chi-restraints excluded: chain D residue 1103 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 0 optimal weight: 30.0000 chunk 166 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 315 optimal weight: 3.9990 chunk 143 optimal weight: 0.0270 chunk 347 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 195 optimal weight: 50.0000 chunk 46 optimal weight: 0.0270 chunk 91 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.097971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.058005 restraints weight = 154618.243| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 7.27 r_work: 0.2770 rms_B_bonded: 6.92 restraints_weight: 2.0000 r_work: 0.2878 rms_B_bonded: 5.65 restraints_weight: 4.0000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30106 Z= 0.094 Angle : 0.524 11.705 41065 Z= 0.264 Chirality : 0.043 0.395 4686 Planarity : 0.004 0.059 5210 Dihedral : 5.551 55.958 4855 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.53 % Rotamer: Outliers : 0.91 % Allowed : 9.50 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3585 helix: 1.99 (0.17), residues: 1018 sheet: -0.10 (0.20), residues: 621 loop : -1.56 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 632 HIS 0.004 0.000 HIS A 401 PHE 0.015 0.001 PHE A 315 TYR 0.018 0.001 TYR A 217 ARG 0.005 0.000 ARG B1018 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 38) link_NAG-ASN : angle 2.49898 ( 114) link_BETA1-4 : bond 0.00775 ( 7) link_BETA1-4 : angle 2.13747 ( 21) hydrogen bonds : bond 0.03569 ( 1153) hydrogen bonds : angle 4.76632 ( 3234) metal coordination : bond 0.00070 ( 2) SS BOND : bond 0.00242 ( 36) SS BOND : angle 0.73524 ( 72) covalent geometry : bond 0.00201 (30023) covalent geometry : angle 0.50570 (40858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.4840 (tpt) cc_final: 0.4032 (tpp) REVERT: A 249 MET cc_start: 0.3508 (mtt) cc_final: 0.2545 (mmm) REVERT: A 297 MET cc_start: -0.0189 (mmt) cc_final: -0.0569 (mmt) REVERT: A 332 MET cc_start: 0.5699 (ptm) cc_final: 0.5122 (ppp) REVERT: A 408 MET cc_start: 0.4993 (OUTLIER) cc_final: 0.4438 (mmt) REVERT: B 724 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: C 618 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: C 983 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9185 (pp) REVERT: D 739 MET cc_start: 0.9505 (tpp) cc_final: 0.9074 (tpp) outliers start: 29 outliers final: 17 residues processed: 98 average time/residue: 0.3349 time to fit residues: 59.7062 Evaluate side-chains 91 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 564 PHE Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 1049 MET Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 618 GLU Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 659 TYR Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1103 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 39 optimal weight: 50.0000 chunk 40 optimal weight: 8.9990 chunk 276 optimal weight: 4.9990 chunk 21 optimal weight: 20.0000 chunk 235 optimal weight: 0.0030 chunk 32 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 chunk 268 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 328 optimal weight: 3.9990 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.103373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.064568 restraints weight = 174497.688| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 9.08 r_work: 0.2778 rms_B_bonded: 7.28 restraints_weight: 2.0000 r_work: 0.2876 rms_B_bonded: 6.01 restraints_weight: 4.0000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30106 Z= 0.144 Angle : 0.542 10.169 41065 Z= 0.272 Chirality : 0.043 0.393 4686 Planarity : 0.004 0.056 5210 Dihedral : 5.483 56.408 4855 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.92 % Rotamer: Outliers : 1.10 % Allowed : 9.59 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3585 helix: 1.97 (0.17), residues: 1023 sheet: -0.24 (0.20), residues: 609 loop : -1.56 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 632 HIS 0.005 0.001 HIS B 518 PHE 0.017 0.001 PHE A 315 TYR 0.017 0.001 TYR C1066 ARG 0.004 0.000 ARG B1018 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 38) link_NAG-ASN : angle 2.46741 ( 114) link_BETA1-4 : bond 0.00680 ( 7) link_BETA1-4 : angle 2.06632 ( 21) hydrogen bonds : bond 0.03712 ( 1153) hydrogen bonds : angle 4.76116 ( 3234) metal coordination : bond 0.00059 ( 2) SS BOND : bond 0.00202 ( 36) SS BOND : angle 0.77534 ( 72) covalent geometry : bond 0.00329 (30023) covalent geometry : angle 0.52484 (40858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7280 (tpt) cc_final: 0.7030 (tpp) REVERT: A 249 MET cc_start: 0.5070 (mtt) cc_final: 0.4231 (mmm) REVERT: A 297 MET cc_start: 0.5799 (mmt) cc_final: 0.5302 (mmt) REVERT: A 332 MET cc_start: 0.7282 (ptm) cc_final: 0.6906 (ppp) REVERT: A 408 MET cc_start: 0.3978 (OUTLIER) cc_final: 0.3522 (mmt) REVERT: B 724 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8524 (tt0) REVERT: C 618 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8660 (pm20) REVERT: D 739 MET cc_start: 0.9481 (tpp) cc_final: 0.9167 (tpp) outliers start: 35 outliers final: 22 residues processed: 98 average time/residue: 0.3626 time to fit residues: 64.4854 Evaluate side-chains 90 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 3.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 564 PHE Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 1049 MET Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain C residue 618 GLU Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 564 PHE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 659 TYR Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1103 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 12 optimal weight: 7.9990 chunk 308 optimal weight: 0.2980 chunk 283 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 270 optimal weight: 7.9990 chunk 33 optimal weight: 40.0000 chunk 202 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 918 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.096548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.055463 restraints weight = 148264.144| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 7.43 r_work: 0.2739 rms_B_bonded: 7.23 restraints_weight: 2.0000 r_work: 0.2843 rms_B_bonded: 5.78 restraints_weight: 4.0000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30106 Z= 0.168 Angle : 0.553 9.963 41065 Z= 0.278 Chirality : 0.043 0.386 4686 Planarity : 0.004 0.067 5210 Dihedral : 5.527 56.500 4855 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.06 % Rotamer: Outliers : 0.91 % Allowed : 10.06 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3585 helix: 1.93 (0.17), residues: 1023 sheet: -0.27 (0.20), residues: 619 loop : -1.56 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 632 HIS 0.005 0.001 HIS A 401 PHE 0.015 0.001 PHE A 315 TYR 0.017 0.001 TYR D 635 ARG 0.008 0.000 ARG B 497 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 38) link_NAG-ASN : angle 2.47050 ( 114) link_BETA1-4 : bond 0.00748 ( 7) link_BETA1-4 : angle 2.10885 ( 21) hydrogen bonds : bond 0.03814 ( 1153) hydrogen bonds : angle 4.79791 ( 3234) metal coordination : bond 0.00057 ( 2) SS BOND : bond 0.00217 ( 36) SS BOND : angle 0.97193 ( 72) covalent geometry : bond 0.00384 (30023) covalent geometry : angle 0.53527 (40858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.6209 (tpt) cc_final: 0.5827 (tpp) REVERT: A 249 MET cc_start: 0.4142 (mtt) cc_final: 0.3204 (mmm) REVERT: A 270 MET cc_start: 0.5558 (ttm) cc_final: 0.5336 (ttp) REVERT: A 297 MET cc_start: 0.1252 (mmt) cc_final: 0.0777 (mmt) REVERT: A 332 MET cc_start: 0.6196 (ptm) cc_final: 0.5623 (ppp) REVERT: A 408 MET cc_start: 0.4563 (OUTLIER) cc_final: 0.4093 (mmt) REVERT: B 724 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8585 (tt0) REVERT: C 618 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8738 (pm20) REVERT: D 739 MET cc_start: 0.9523 (tpp) cc_final: 0.9298 (tpp) outliers start: 29 outliers final: 23 residues processed: 94 average time/residue: 0.3434 time to fit residues: 58.3103 Evaluate side-chains 92 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 564 PHE Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 1049 MET Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 618 GLU Chi-restraints excluded: chain C residue 779 GLU Chi-restraints excluded: chain C residue 785 LYS Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 858 THR Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 564 PHE Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 659 TYR Chi-restraints excluded: chain D residue 983 LEU Chi-restraints excluded: chain D residue 1103 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 207 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 80 optimal weight: 0.3980 chunk 277 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 243 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.104078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.065912 restraints weight = 184008.383| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 9.10 r_work: 0.2780 rms_B_bonded: 7.94 restraints_weight: 2.0000 r_work: 0.2884 rms_B_bonded: 6.33 restraints_weight: 4.0000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30106 Z= 0.095 Angle : 0.517 9.949 41065 Z= 0.260 Chirality : 0.042 0.373 4686 Planarity : 0.004 0.056 5210 Dihedral : 5.380 55.836 4855 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.53 % Rotamer: Outliers : 0.75 % Allowed : 10.25 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3585 helix: 1.98 (0.17), residues: 1025 sheet: -0.00 (0.20), residues: 631 loop : -1.50 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 632 HIS 0.004 0.001 HIS A 401 PHE 0.014 0.001 PHE A 315 TYR 0.018 0.001 TYR A 50 ARG 0.004 0.000 ARG B1018 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 38) link_NAG-ASN : angle 2.33929 ( 114) link_BETA1-4 : bond 0.00674 ( 7) link_BETA1-4 : angle 1.99388 ( 21) hydrogen bonds : bond 0.03397 ( 1153) hydrogen bonds : angle 4.61629 ( 3234) metal coordination : bond 0.00035 ( 2) SS BOND : bond 0.00208 ( 36) SS BOND : angle 0.86221 ( 72) covalent geometry : bond 0.00207 (30023) covalent geometry : angle 0.50040 (40858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.4946 (mtt) cc_final: 0.4726 (mmt) REVERT: A 297 MET cc_start: 0.5100 (mmt) cc_final: 0.4711 (mmm) REVERT: A 332 MET cc_start: 0.6948 (ptm) cc_final: 0.6520 (ppp) REVERT: A 408 MET cc_start: 0.4143 (OUTLIER) cc_final: 0.3689 (mmt) REVERT: B 724 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: C 618 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8719 (pm20) REVERT: D 739 MET cc_start: 0.9492 (tpp) cc_final: 0.9192 (tpp) outliers start: 24 outliers final: 17 residues processed: 92 average time/residue: 0.3481 time to fit residues: 58.0114 Evaluate side-chains 87 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 564 PHE Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 618 GLU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 659 TYR Chi-restraints excluded: chain D residue 1103 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 241 optimal weight: 0.6980 chunk 220 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 chunk 360 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 689 GLN D 964 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.095553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.053602 restraints weight = 160823.920| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 7.96 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 30106 Z= 0.246 Angle : 0.623 14.487 41065 Z= 0.310 Chirality : 0.044 0.381 4686 Planarity : 0.004 0.069 5210 Dihedral : 5.579 56.821 4855 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.61 % Favored : 93.36 % Rotamer: Outliers : 0.85 % Allowed : 10.31 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3585 helix: 1.69 (0.17), residues: 1044 sheet: -0.25 (0.20), residues: 608 loop : -1.59 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 632 HIS 0.005 0.001 HIS A 401 PHE 0.024 0.001 PHE B 897 TYR 0.020 0.001 TYR C1066 ARG 0.005 0.000 ARG B 904 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 38) link_NAG-ASN : angle 2.50293 ( 114) link_BETA1-4 : bond 0.00506 ( 7) link_BETA1-4 : angle 2.17101 ( 21) hydrogen bonds : bond 0.04204 ( 1153) hydrogen bonds : angle 4.91305 ( 3234) metal coordination : bond 0.00050 ( 2) SS BOND : bond 0.00248 ( 36) SS BOND : angle 1.10862 ( 72) covalent geometry : bond 0.00560 (30023) covalent geometry : angle 0.60680 (40858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.0271 (mmt) cc_final: 0.0048 (mmm) REVERT: A 297 MET cc_start: 0.4555 (mmt) cc_final: 0.3890 (mmm) REVERT: A 332 MET cc_start: 0.6387 (ptm) cc_final: 0.5826 (ppp) REVERT: A 408 MET cc_start: 0.4676 (OUTLIER) cc_final: 0.4144 (mmt) REVERT: A 557 MET cc_start: 0.6889 (ppp) cc_final: 0.6588 (ppp) REVERT: B 486 ASN cc_start: 0.4614 (OUTLIER) cc_final: 0.3891 (p0) REVERT: B 724 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: C 618 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8695 (pm20) REVERT: C 724 GLU cc_start: 0.8541 (tt0) cc_final: 0.8251 (tt0) REVERT: D 739 MET cc_start: 0.9253 (tpp) cc_final: 0.9007 (tpp) outliers start: 27 outliers final: 19 residues processed: 91 average time/residue: 0.3538 time to fit residues: 58.8073 Evaluate side-chains 90 residues out of total 3189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 486 ASN Chi-restraints excluded: chain B residue 564 PHE Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 1103 VAL Chi-restraints excluded: chain C residue 577 ASP Chi-restraints excluded: chain C residue 618 GLU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 868 MET Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 587 THR Chi-restraints excluded: chain D residue 659 TYR Chi-restraints excluded: chain D residue 1103 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 218 optimal weight: 0.9990 chunk 18 optimal weight: 40.0000 chunk 264 optimal weight: 0.5980 chunk 293 optimal weight: 50.0000 chunk 64 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.095654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.054715 restraints weight = 152047.483| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 7.70 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.175 30106 Z= 0.238 Angle : 0.731 59.196 41065 Z= 0.392 Chirality : 0.045 0.835 4686 Planarity : 0.004 0.066 5210 Dihedral : 5.588 56.763 4855 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.67 % Favored : 93.28 % Rotamer: Outliers : 0.85 % Allowed : 10.37 % Favored : 88.78 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3585 helix: 1.66 (0.17), residues: 1044 sheet: -0.27 (0.20), residues: 608 loop : -1.60 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 632 HIS 0.005 0.001 HIS A 401 PHE 0.023 0.001 PHE B 897 TYR 0.019 0.001 TYR C1066 ARG 0.004 0.000 ARG A 245 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 38) link_NAG-ASN : angle 2.50152 ( 114) link_BETA1-4 : bond 0.00696 ( 7) link_BETA1-4 : angle 2.76790 ( 21) hydrogen bonds : bond 0.04160 ( 1153) hydrogen bonds : angle 4.90968 ( 3234) metal coordination : bond 0.00056 ( 2) SS BOND : bond 0.00264 ( 36) SS BOND : angle 1.09545 ( 72) covalent geometry : bond 0.00532 (30023) covalent geometry : angle 0.71676 (40858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32921.88 seconds wall clock time: 564 minutes 7.87 seconds (33847.87 seconds total)