Starting phenix.real_space_refine on Mon Sep 14 17:41:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6chs_7476/09_2026/6chs_7476.cif Found real_map, /net/cci-nas-00/data/ceres_data/6chs_7476/09_2026/6chs_7476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6chs_7476/09_2026/6chs_7476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6chs_7476/09_2026/6chs_7476.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6chs_7476/09_2026/6chs_7476.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6chs_7476/09_2026/6chs_7476.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6chs_7476/09_2026/6chs_7476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6chs_7476/09_2026/6chs_7476.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 3652 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 36 5.49 5 Mg 12 5.21 5 S 166 5.16 5 C 18418 2.51 5 N 5162 2.21 5 O 5706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29502 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3658 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 425} Chain breaks: 1 Chain: "H" Number of atoms: 4243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4243 Classifications: {'peptide': 550} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 519} Chain breaks: 1 Chain: "I" Number of atoms: 4243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4243 Classifications: {'peptide': 550} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 519} Chain breaks: 1 Chain: "J" Number of atoms: 4243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4243 Classifications: {'peptide': 550} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 519} Chain breaks: 1 Chain: "D" Number of atoms: 4243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4243 Classifications: {'peptide': 550} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 519} Chain breaks: 1 Chain: "E" Number of atoms: 4243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4243 Classifications: {'peptide': 550} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 519} Chain breaks: 1 Chain: "F" Number of atoms: 4243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4243 Classifications: {'peptide': 550} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 519} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 260 SG CYS A 160 87.390 105.805 78.146 1.00103.34 S ATOM 319 SG CYS A 168 85.449 102.556 77.626 1.00 93.04 S ATOM 345 SG CYS A 171 87.954 102.929 80.465 1.00 87.56 S ATOM 811 SG CYS A 227 89.185 49.733 85.067 1.00155.57 S ATOM 902 SG CYS A 239 86.469 48.956 82.436 1.00123.01 S ATOM 924 SG CYS A 242 90.257 49.346 81.295 1.00 95.98 S Time building chain proxies: 6.35, per 1000 atoms: 0.22 Number of scatterers: 29502 At special positions: 0 Unit cell: (162.5, 146.9, 136.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 166 16.00 P 36 15.00 Mg 12 11.99 O 5706 8.00 N 5162 7.00 C 18418 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 162 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 168 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 160 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 171 " pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" NE2 HIS A 231 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 242 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 227 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 239 " Number of angles added : 6 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6988 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 18 sheets defined 54.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 139 through 147 removed outlier: 4.265A pdb=" N LYS A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 192 through 200 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 239 through 243 removed outlier: 3.683A pdb=" N CYS A 242 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 243 " --> pdb=" O THR A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 243' Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.732A pdb=" N ILE A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.799A pdb=" N ASN A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 384 Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.559A pdb=" N VAL A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 490 removed outlier: 3.919A pdb=" N PHE A 490 " --> pdb=" O GLU A 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 487 through 490' Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 544 through 555 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 573 through 581 Processing helix chain 'A' and resid 583 through 593 removed outlier: 3.549A pdb=" N LEU A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 236 Processing helix chain 'H' and resid 236 through 242 removed outlier: 3.545A pdb=" N LEU H 240 " --> pdb=" O VAL H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 250 removed outlier: 4.589A pdb=" N PHE H 246 " --> pdb=" O HIS H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 276 removed outlier: 3.594A pdb=" N ALA H 271 " --> pdb=" O LYS H 267 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG H 272 " --> pdb=" O THR H 268 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 293 removed outlier: 3.627A pdb=" N LYS H 293 " --> pdb=" O GLU H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 312 removed outlier: 3.745A pdb=" N LEU H 302 " --> pdb=" O SER H 298 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU H 308 " --> pdb=" O LYS H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 326 removed outlier: 4.158A pdb=" N ILE H 325 " --> pdb=" O GLU H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 350 removed outlier: 3.659A pdb=" N ASP H 349 " --> pdb=" O LEU H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 402 Processing helix chain 'H' and resid 411 through 419 Processing helix chain 'H' and resid 423 through 443 Processing helix chain 'H' and resid 444 through 446 No H-bonds generated for 'chain 'H' and resid 444 through 446' Processing helix chain 'H' and resid 454 through 460 removed outlier: 3.921A pdb=" N LEU H 458 " --> pdb=" O ASP H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 473 removed outlier: 3.698A pdb=" N PHE H 468 " --> pdb=" O THR H 464 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY H 473 " --> pdb=" O ARG H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 510 Processing helix chain 'H' and resid 510 through 516 removed outlier: 3.639A pdb=" N VAL H 514 " --> pdb=" O VAL H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 517 through 524 removed outlier: 3.549A pdb=" N LEU H 521 " --> pdb=" O PRO H 517 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 552 removed outlier: 3.507A pdb=" N LEU H 544 " --> pdb=" O GLY H 540 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA H 545 " --> pdb=" O LYS H 541 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS H 546 " --> pdb=" O THR H 542 " (cutoff:3.500A) Processing helix chain 'H' and resid 560 through 570 removed outlier: 3.682A pdb=" N LEU H 564 " --> pdb=" O LYS H 560 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU H 565 " --> pdb=" O GLY H 561 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY H 570 " --> pdb=" O SER H 566 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 586 removed outlier: 3.691A pdb=" N PHE H 580 " --> pdb=" O ILE H 576 " (cutoff:3.500A) Processing helix chain 'H' and resid 595 through 602 removed outlier: 3.921A pdb=" N ILE H 599 " --> pdb=" O GLU H 595 " (cutoff:3.500A) Processing helix chain 'H' and resid 615 through 627 removed outlier: 3.663A pdb=" N THR H 623 " --> pdb=" O ASN H 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 642 through 646 removed outlier: 3.530A pdb=" N LEU H 646 " --> pdb=" O PRO H 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 666 through 678 Processing helix chain 'H' and resid 679 through 681 No H-bonds generated for 'chain 'H' and resid 679 through 681' Processing helix chain 'H' and resid 688 through 696 Processing helix chain 'H' and resid 700 through 725 removed outlier: 4.760A pdb=" N ALA H 721 " --> pdb=" O LYS H 717 " (cutoff:3.500A) Processing helix chain 'H' and resid 750 through 760 removed outlier: 3.540A pdb=" N GLU H 756 " --> pdb=" O ARG H 752 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA H 757 " --> pdb=" O HIS H 753 " (cutoff:3.500A) Processing helix chain 'H' and resid 766 through 779 Processing helix chain 'I' and resid 225 through 236 Processing helix chain 'I' and resid 236 through 242 removed outlier: 3.545A pdb=" N LEU I 240 " --> pdb=" O VAL I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 250 removed outlier: 4.589A pdb=" N PHE I 246 " --> pdb=" O HIS I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 276 removed outlier: 3.594A pdb=" N ALA I 271 " --> pdb=" O LYS I 267 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG I 272 " --> pdb=" O THR I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 293 removed outlier: 3.627A pdb=" N LYS I 293 " --> pdb=" O GLU I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 312 removed outlier: 3.745A pdb=" N LEU I 302 " --> pdb=" O SER I 298 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU I 308 " --> pdb=" O LYS I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 326 removed outlier: 4.158A pdb=" N ILE I 325 " --> pdb=" O GLU I 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 350 removed outlier: 3.659A pdb=" N ASP I 349 " --> pdb=" O LEU I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 389 through 402 Processing helix chain 'I' and resid 411 through 419 Processing helix chain 'I' and resid 423 through 443 Processing helix chain 'I' and resid 444 through 446 No H-bonds generated for 'chain 'I' and resid 444 through 446' Processing helix chain 'I' and resid 454 through 460 removed outlier: 3.922A pdb=" N LEU I 458 " --> pdb=" O ASP I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 464 through 473 removed outlier: 3.698A pdb=" N PHE I 468 " --> pdb=" O THR I 464 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY I 473 " --> pdb=" O ARG I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 499 through 510 Processing helix chain 'I' and resid 510 through 516 removed outlier: 3.638A pdb=" N VAL I 514 " --> pdb=" O VAL I 510 " (cutoff:3.500A) Processing helix chain 'I' and resid 517 through 524 removed outlier: 3.548A pdb=" N LEU I 521 " --> pdb=" O PRO I 517 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 552 removed outlier: 3.508A pdb=" N LEU I 544 " --> pdb=" O GLY I 540 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA I 545 " --> pdb=" O LYS I 541 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS I 546 " --> pdb=" O THR I 542 " (cutoff:3.500A) Processing helix chain 'I' and resid 560 through 570 removed outlier: 3.681A pdb=" N LEU I 564 " --> pdb=" O LYS I 560 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU I 565 " --> pdb=" O GLY I 561 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY I 570 " --> pdb=" O SER I 566 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 586 removed outlier: 3.691A pdb=" N PHE I 580 " --> pdb=" O ILE I 576 " (cutoff:3.500A) Processing helix chain 'I' and resid 595 through 602 removed outlier: 3.921A pdb=" N ILE I 599 " --> pdb=" O GLU I 595 " (cutoff:3.500A) Processing helix chain 'I' and resid 615 through 627 removed outlier: 3.663A pdb=" N THR I 623 " --> pdb=" O ASN I 619 " (cutoff:3.500A) Processing helix chain 'I' and resid 642 through 646 removed outlier: 3.530A pdb=" N LEU I 646 " --> pdb=" O PRO I 643 " (cutoff:3.500A) Processing helix chain 'I' and resid 666 through 678 Processing helix chain 'I' and resid 679 through 681 No H-bonds generated for 'chain 'I' and resid 679 through 681' Processing helix chain 'I' and resid 688 through 696 Processing helix chain 'I' and resid 700 through 724 removed outlier: 4.758A pdb=" N ALA I 721 " --> pdb=" O LYS I 717 " (cutoff:3.500A) Processing helix chain 'I' and resid 750 through 760 removed outlier: 3.540A pdb=" N GLU I 756 " --> pdb=" O ARG I 752 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA I 757 " --> pdb=" O HIS I 753 " (cutoff:3.500A) Processing helix chain 'I' and resid 766 through 779 Processing helix chain 'J' and resid 225 through 236 Processing helix chain 'J' and resid 236 through 242 removed outlier: 3.545A pdb=" N LEU J 240 " --> pdb=" O VAL J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 250 removed outlier: 4.589A pdb=" N PHE J 246 " --> pdb=" O HIS J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 276 removed outlier: 3.593A pdb=" N ALA J 271 " --> pdb=" O LYS J 267 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG J 272 " --> pdb=" O THR J 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 293 removed outlier: 3.626A pdb=" N LYS J 293 " --> pdb=" O GLU J 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 312 removed outlier: 3.746A pdb=" N LEU J 302 " --> pdb=" O SER J 298 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU J 308 " --> pdb=" O LYS J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 321 through 326 removed outlier: 4.158A pdb=" N ILE J 325 " --> pdb=" O GLU J 321 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 350 removed outlier: 3.659A pdb=" N ASP J 349 " --> pdb=" O LEU J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 389 through 402 Processing helix chain 'J' and resid 411 through 419 Processing helix chain 'J' and resid 423 through 443 Processing helix chain 'J' and resid 444 through 446 No H-bonds generated for 'chain 'J' and resid 444 through 446' Processing helix chain 'J' and resid 454 through 460 removed outlier: 3.922A pdb=" N LEU J 458 " --> pdb=" O ASP J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 464 through 472 removed outlier: 3.699A pdb=" N PHE J 468 " --> pdb=" O THR J 464 " (cutoff:3.500A) Processing helix chain 'J' and resid 499 through 510 Processing helix chain 'J' and resid 510 through 516 removed outlier: 3.639A pdb=" N VAL J 514 " --> pdb=" O VAL J 510 " (cutoff:3.500A) Processing helix chain 'J' and resid 517 through 524 removed outlier: 3.549A pdb=" N LEU J 521 " --> pdb=" O PRO J 517 " (cutoff:3.500A) Processing helix chain 'J' and resid 540 through 552 removed outlier: 3.507A pdb=" N LEU J 544 " --> pdb=" O GLY J 540 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA J 545 " --> pdb=" O LYS J 541 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS J 546 " --> pdb=" O THR J 542 " (cutoff:3.500A) Processing helix chain 'J' and resid 560 through 570 removed outlier: 3.683A pdb=" N LEU J 564 " --> pdb=" O LYS J 560 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU J 565 " --> pdb=" O GLY J 561 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY J 570 " --> pdb=" O SER J 566 " (cutoff:3.500A) Processing helix chain 'J' and resid 573 through 586 removed outlier: 3.692A pdb=" N PHE J 580 " --> pdb=" O ILE J 576 " (cutoff:3.500A) Processing helix chain 'J' and resid 595 through 602 removed outlier: 3.920A pdb=" N ILE J 599 " --> pdb=" O GLU J 595 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 627 removed outlier: 3.663A pdb=" N THR J 623 " --> pdb=" O ASN J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 642 through 646 removed outlier: 3.530A pdb=" N LEU J 646 " --> pdb=" O PRO J 643 " (cutoff:3.500A) Processing helix chain 'J' and resid 666 through 678 Processing helix chain 'J' and resid 679 through 681 No H-bonds generated for 'chain 'J' and resid 679 through 681' Processing helix chain 'J' and resid 688 through 696 Processing helix chain 'J' and resid 700 through 725 removed outlier: 4.759A pdb=" N ALA J 721 " --> pdb=" O LYS J 717 " (cutoff:3.500A) Processing helix chain 'J' and resid 750 through 760 removed outlier: 3.541A pdb=" N GLU J 756 " --> pdb=" O ARG J 752 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA J 757 " --> pdb=" O HIS J 753 " (cutoff:3.500A) Processing helix chain 'J' and resid 766 through 779 Processing helix chain 'D' and resid 225 through 236 Processing helix chain 'D' and resid 236 through 242 removed outlier: 3.545A pdb=" N LEU D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 4.590A pdb=" N PHE D 246 " --> pdb=" O HIS D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 276 removed outlier: 3.594A pdb=" N ALA D 271 " --> pdb=" O LYS D 267 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 293 removed outlier: 3.627A pdb=" N LYS D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 312 removed outlier: 3.745A pdb=" N LEU D 302 " --> pdb=" O SER D 298 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 removed outlier: 4.158A pdb=" N ILE D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 350 removed outlier: 3.660A pdb=" N ASP D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 402 Processing helix chain 'D' and resid 411 through 419 Processing helix chain 'D' and resid 423 through 443 Processing helix chain 'D' and resid 444 through 446 No H-bonds generated for 'chain 'D' and resid 444 through 446' Processing helix chain 'D' and resid 454 through 460 removed outlier: 3.922A pdb=" N LEU D 458 " --> pdb=" O ASP D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 472 removed outlier: 3.699A pdb=" N PHE D 468 " --> pdb=" O THR D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 510 Processing helix chain 'D' and resid 510 through 516 removed outlier: 3.638A pdb=" N VAL D 514 " --> pdb=" O VAL D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 524 removed outlier: 3.549A pdb=" N LEU D 521 " --> pdb=" O PRO D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 552 removed outlier: 3.508A pdb=" N LEU D 544 " --> pdb=" O GLY D 540 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA D 545 " --> pdb=" O LYS D 541 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS D 546 " --> pdb=" O THR D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 570 removed outlier: 3.682A pdb=" N LEU D 564 " --> pdb=" O LYS D 560 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 565 " --> pdb=" O GLY D 561 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY D 570 " --> pdb=" O SER D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 586 removed outlier: 3.692A pdb=" N PHE D 580 " --> pdb=" O ILE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 602 removed outlier: 3.920A pdb=" N ILE D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 627 removed outlier: 3.663A pdb=" N THR D 623 " --> pdb=" O ASN D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 646 removed outlier: 3.530A pdb=" N LEU D 646 " --> pdb=" O PRO D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 678 Processing helix chain 'D' and resid 679 through 681 No H-bonds generated for 'chain 'D' and resid 679 through 681' Processing helix chain 'D' and resid 688 through 696 Processing helix chain 'D' and resid 700 through 725 removed outlier: 4.760A pdb=" N ALA D 721 " --> pdb=" O LYS D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 760 removed outlier: 3.541A pdb=" N GLU D 756 " --> pdb=" O ARG D 752 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 757 " --> pdb=" O HIS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 779 Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.545A pdb=" N LEU E 240 " --> pdb=" O VAL E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 250 removed outlier: 4.590A pdb=" N PHE E 246 " --> pdb=" O HIS E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 276 removed outlier: 3.594A pdb=" N ALA E 271 " --> pdb=" O LYS E 267 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG E 272 " --> pdb=" O THR E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 293 removed outlier: 3.626A pdb=" N LYS E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 312 removed outlier: 3.745A pdb=" N LEU E 302 " --> pdb=" O SER E 298 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 326 removed outlier: 4.158A pdb=" N ILE E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 350 removed outlier: 3.659A pdb=" N ASP E 349 " --> pdb=" O LEU E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 402 Processing helix chain 'E' and resid 411 through 419 Processing helix chain 'E' and resid 423 through 443 Processing helix chain 'E' and resid 444 through 446 No H-bonds generated for 'chain 'E' and resid 444 through 446' Processing helix chain 'E' and resid 454 through 460 removed outlier: 3.922A pdb=" N LEU E 458 " --> pdb=" O ASP E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 473 removed outlier: 3.698A pdb=" N PHE E 468 " --> pdb=" O THR E 464 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY E 473 " --> pdb=" O ARG E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 510 Processing helix chain 'E' and resid 510 through 516 removed outlier: 3.638A pdb=" N VAL E 514 " --> pdb=" O VAL E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 517 through 524 removed outlier: 3.549A pdb=" N LEU E 521 " --> pdb=" O PRO E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 552 removed outlier: 3.507A pdb=" N LEU E 544 " --> pdb=" O GLY E 540 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA E 545 " --> pdb=" O LYS E 541 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS E 546 " --> pdb=" O THR E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 570 removed outlier: 3.682A pdb=" N LEU E 564 " --> pdb=" O LYS E 560 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU E 565 " --> pdb=" O GLY E 561 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY E 570 " --> pdb=" O SER E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 586 removed outlier: 3.691A pdb=" N PHE E 580 " --> pdb=" O ILE E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 595 through 602 removed outlier: 3.920A pdb=" N ILE E 599 " --> pdb=" O GLU E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 627 removed outlier: 3.662A pdb=" N THR E 623 " --> pdb=" O ASN E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 642 through 646 removed outlier: 3.530A pdb=" N LEU E 646 " --> pdb=" O PRO E 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 666 through 678 Processing helix chain 'E' and resid 679 through 681 No H-bonds generated for 'chain 'E' and resid 679 through 681' Processing helix chain 'E' and resid 688 through 696 Processing helix chain 'E' and resid 700 through 725 removed outlier: 4.760A pdb=" N ALA E 721 " --> pdb=" O LYS E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 750 through 760 removed outlier: 3.540A pdb=" N GLU E 756 " --> pdb=" O ARG E 752 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA E 757 " --> pdb=" O HIS E 753 " (cutoff:3.500A) Processing helix chain 'E' and resid 766 through 779 Processing helix chain 'F' and resid 225 through 236 Processing helix chain 'F' and resid 236 through 242 removed outlier: 3.544A pdb=" N LEU F 240 " --> pdb=" O VAL F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 250 removed outlier: 4.590A pdb=" N PHE F 246 " --> pdb=" O HIS F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 276 removed outlier: 3.593A pdb=" N ALA F 271 " --> pdb=" O LYS F 267 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG F 272 " --> pdb=" O THR F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 293 removed outlier: 3.626A pdb=" N LYS F 293 " --> pdb=" O GLU F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 312 removed outlier: 3.745A pdb=" N LEU F 302 " --> pdb=" O SER F 298 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU F 308 " --> pdb=" O LYS F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 326 removed outlier: 4.157A pdb=" N ILE F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 350 removed outlier: 3.659A pdb=" N ASP F 349 " --> pdb=" O LEU F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 402 Processing helix chain 'F' and resid 411 through 419 Processing helix chain 'F' and resid 423 through 443 Processing helix chain 'F' and resid 444 through 446 No H-bonds generated for 'chain 'F' and resid 444 through 446' Processing helix chain 'F' and resid 454 through 460 removed outlier: 3.922A pdb=" N LEU F 458 " --> pdb=" O ASP F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 472 removed outlier: 3.698A pdb=" N PHE F 468 " --> pdb=" O THR F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 510 Processing helix chain 'F' and resid 510 through 516 removed outlier: 3.639A pdb=" N VAL F 514 " --> pdb=" O VAL F 510 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 524 removed outlier: 3.549A pdb=" N LEU F 521 " --> pdb=" O PRO F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 552 removed outlier: 3.507A pdb=" N LEU F 544 " --> pdb=" O GLY F 540 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA F 545 " --> pdb=" O LYS F 541 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS F 546 " --> pdb=" O THR F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 570 removed outlier: 3.682A pdb=" N LEU F 564 " --> pdb=" O LYS F 560 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU F 565 " --> pdb=" O GLY F 561 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY F 570 " --> pdb=" O SER F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 586 removed outlier: 3.692A pdb=" N PHE F 580 " --> pdb=" O ILE F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 595 through 602 removed outlier: 3.920A pdb=" N ILE F 599 " --> pdb=" O GLU F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 627 removed outlier: 3.663A pdb=" N THR F 623 " --> pdb=" O ASN F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 642 through 646 removed outlier: 3.530A pdb=" N LEU F 646 " --> pdb=" O PRO F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 678 Processing helix chain 'F' and resid 679 through 681 No H-bonds generated for 'chain 'F' and resid 679 through 681' Processing helix chain 'F' and resid 688 through 696 Processing helix chain 'F' and resid 700 through 725 removed outlier: 4.760A pdb=" N ALA F 721 " --> pdb=" O LYS F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 760 removed outlier: 3.540A pdb=" N GLU F 756 " --> pdb=" O ARG F 752 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA F 757 " --> pdb=" O HIS F 753 " (cutoff:3.500A) Processing helix chain 'F' and resid 766 through 779 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 191 removed outlier: 6.612A pdb=" N MET A 190 " --> pdb=" O ARG A 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 248 removed outlier: 6.866A pdb=" N ILE A 247 " --> pdb=" O PHE A 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.588A pdb=" N VAL A 260 " --> pdb=" O GLY A 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 306 removed outlier: 6.639A pdb=" N TYR A 287 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 345 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLY A 288 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLN A 341 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 436 Processing sheet with id=AA7, first strand: chain 'H' and resid 281 through 286 removed outlier: 3.544A pdb=" N PHE H 318 " --> pdb=" O PHE H 283 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA H 315 " --> pdb=" O VAL H 358 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N MET H 360 " --> pdb=" O ALA H 315 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE H 317 " --> pdb=" O MET H 360 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA H 362 " --> pdb=" O ILE H 317 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE H 319 " --> pdb=" O ALA H 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 555 through 559 removed outlier: 6.318A pdb=" N ASN H 555 " --> pdb=" O VAL H 590 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE H 592 " --> pdb=" O ASN H 555 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE H 557 " --> pdb=" O PHE H 592 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS H 589 " --> pdb=" O PHE H 635 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE H 637 " --> pdb=" O CYS H 589 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL H 591 " --> pdb=" O ILE H 637 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA H 639 " --> pdb=" O VAL H 591 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU H 593 " --> pdb=" O ALA H 639 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 531 " --> pdb=" O VAL H 636 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 281 through 286 removed outlier: 6.576A pdb=" N ALA I 315 " --> pdb=" O VAL I 358 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N MET I 360 " --> pdb=" O ALA I 315 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE I 317 " --> pdb=" O MET I 360 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA I 362 " --> pdb=" O ILE I 317 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE I 319 " --> pdb=" O ALA I 362 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 555 through 559 removed outlier: 6.319A pdb=" N ASN I 555 " --> pdb=" O VAL I 590 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE I 592 " --> pdb=" O ASN I 555 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE I 557 " --> pdb=" O PHE I 592 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS I 589 " --> pdb=" O PHE I 635 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE I 637 " --> pdb=" O CYS I 589 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL I 591 " --> pdb=" O ILE I 637 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA I 639 " --> pdb=" O VAL I 591 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU I 593 " --> pdb=" O ALA I 639 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL I 531 " --> pdb=" O VAL I 636 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 281 through 286 removed outlier: 6.576A pdb=" N ALA J 315 " --> pdb=" O VAL J 358 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N MET J 360 " --> pdb=" O ALA J 315 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE J 317 " --> pdb=" O MET J 360 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA J 362 " --> pdb=" O ILE J 317 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE J 319 " --> pdb=" O ALA J 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 555 through 559 removed outlier: 6.318A pdb=" N ASN J 555 " --> pdb=" O VAL J 590 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE J 592 " --> pdb=" O ASN J 555 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE J 557 " --> pdb=" O PHE J 592 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS J 589 " --> pdb=" O PHE J 635 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE J 637 " --> pdb=" O CYS J 589 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL J 591 " --> pdb=" O ILE J 637 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA J 639 " --> pdb=" O VAL J 591 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU J 593 " --> pdb=" O ALA J 639 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL J 531 " --> pdb=" O VAL J 636 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 281 through 286 removed outlier: 6.577A pdb=" N ALA D 315 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N MET D 360 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE D 317 " --> pdb=" O MET D 360 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ALA D 362 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE D 319 " --> pdb=" O ALA D 362 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 555 through 559 removed outlier: 6.318A pdb=" N ASN D 555 " --> pdb=" O VAL D 590 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE D 592 " --> pdb=" O ASN D 555 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE D 557 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N CYS D 589 " --> pdb=" O PHE D 635 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE D 637 " --> pdb=" O CYS D 589 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL D 591 " --> pdb=" O ILE D 637 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA D 639 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU D 593 " --> pdb=" O ALA D 639 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 531 " --> pdb=" O VAL D 636 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 281 through 286 removed outlier: 3.957A pdb=" N PHE E 318 " --> pdb=" O PHE E 283 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA E 315 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N MET E 360 " --> pdb=" O ALA E 315 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE E 317 " --> pdb=" O MET E 360 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA E 362 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE E 319 " --> pdb=" O ALA E 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 555 through 559 removed outlier: 6.318A pdb=" N ASN E 555 " --> pdb=" O VAL E 590 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE E 592 " --> pdb=" O ASN E 555 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE E 557 " --> pdb=" O PHE E 592 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS E 589 " --> pdb=" O PHE E 635 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE E 637 " --> pdb=" O CYS E 589 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL E 591 " --> pdb=" O ILE E 637 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA E 639 " --> pdb=" O VAL E 591 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU E 593 " --> pdb=" O ALA E 639 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL E 531 " --> pdb=" O VAL E 636 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 281 through 286 removed outlier: 6.577A pdb=" N ALA F 315 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N MET F 360 " --> pdb=" O ALA F 315 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE F 317 " --> pdb=" O MET F 360 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA F 362 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE F 319 " --> pdb=" O ALA F 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 555 through 559 removed outlier: 6.319A pdb=" N ASN F 555 " --> pdb=" O VAL F 590 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE F 592 " --> pdb=" O ASN F 555 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE F 557 " --> pdb=" O PHE F 592 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS F 589 " --> pdb=" O PHE F 635 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE F 637 " --> pdb=" O CYS F 589 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL F 591 " --> pdb=" O ILE F 637 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA F 639 " --> pdb=" O VAL F 591 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU F 593 " --> pdb=" O ALA F 639 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 531 " --> pdb=" O VAL F 636 " (cutoff:3.500A) 1273 hydrogen bonds defined for protein. 3747 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: 5.80 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 10169 1.36 - 1.51: 9548 1.51 - 1.66: 10018 1.66 - 1.80: 254 1.80 - 1.95: 25 Bond restraints: 30014 Sorted by residual: bond pdb=" O2A AGS J 901 " pdb=" PA AGS J 901 " ideal model delta sigma weight residual 1.531 1.451 0.080 1.60e-02 3.91e+03 2.52e+01 bond pdb=" O2A AGS E 901 " pdb=" PA AGS E 901 " ideal model delta sigma weight residual 1.531 1.454 0.077 1.60e-02 3.91e+03 2.31e+01 bond pdb=" O2A AGS I 902 " pdb=" PA AGS I 902 " ideal model delta sigma weight residual 1.531 1.466 0.065 1.60e-02 3.91e+03 1.63e+01 bond pdb=" O2A AGS F 902 " pdb=" PA AGS F 902 " ideal model delta sigma weight residual 1.531 1.469 0.062 1.60e-02 3.91e+03 1.51e+01 bond pdb=" O2B AGS H 901 " pdb=" PB AGS H 901 " ideal model delta sigma weight residual 1.531 1.471 0.060 1.60e-02 3.91e+03 1.39e+01 ... (remaining 30009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 39428 2.32 - 4.65: 1038 4.65 - 6.97: 125 6.97 - 9.30: 37 9.30 - 11.62: 10 Bond angle restraints: 40638 Sorted by residual: angle pdb=" N TRP A 234 " pdb=" CA TRP A 234 " pdb=" C TRP A 234 " ideal model delta sigma weight residual 112.35 100.73 11.62 1.34e+00 5.57e-01 7.52e+01 angle pdb=" C ASN D 476 " pdb=" N PRO D 477 " pdb=" CA PRO D 477 " ideal model delta sigma weight residual 119.84 130.41 -10.57 1.25e+00 6.40e-01 7.15e+01 angle pdb=" C ASN F 476 " pdb=" N PRO F 477 " pdb=" CA PRO F 477 " ideal model delta sigma weight residual 119.84 130.37 -10.53 1.25e+00 6.40e-01 7.10e+01 angle pdb=" CA TRP A 234 " pdb=" C TRP A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 120.81 115.49 5.32 8.60e-01 1.35e+00 3.83e+01 angle pdb=" N ASN F 476 " pdb=" CA ASN F 476 " pdb=" C ASN F 476 " ideal model delta sigma weight residual 112.75 104.96 7.79 1.36e+00 5.41e-01 3.28e+01 ... (remaining 40633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.46: 18118 26.46 - 52.92: 290 52.92 - 79.38: 23 79.38 - 105.84: 2 105.84 - 132.30: 11 Dihedral angle restraints: 18444 sinusoidal: 7638 harmonic: 10806 Sorted by residual: dihedral pdb=" CA LEU A 321 " pdb=" C LEU A 321 " pdb=" N ASN A 322 " pdb=" CA ASN A 322 " ideal model delta harmonic sigma weight residual 180.00 151.37 28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA PRO J 477 " pdb=" C PRO J 477 " pdb=" N SER J 478 " pdb=" CA SER J 478 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA PRO D 477 " pdb=" C PRO D 477 " pdb=" N SER D 478 " pdb=" CA SER D 478 " ideal model delta harmonic sigma weight residual 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 18441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4407 0.123 - 0.246: 128 0.246 - 0.368: 3 0.368 - 0.491: 4 0.491 - 0.614: 5 Chirality restraints: 4547 Sorted by residual: chirality pdb=" PB AGS J 901 " pdb=" O2B AGS J 901 " pdb=" O3A AGS J 901 " pdb=" O3B AGS J 901 " both_signs ideal model delta sigma weight residual True 3.18 -2.57 0.61 2.00e-01 2.50e+01 9.42e+00 chirality pdb=" PA AGS E 901 " pdb=" O2A AGS E 901 " pdb=" O3A AGS E 901 " pdb=" O5' AGS E 901 " both_signs ideal model delta sigma weight residual True 3.18 2.59 0.59 2.00e-01 2.50e+01 8.81e+00 chirality pdb=" PA AGS J 901 " pdb=" O2A AGS J 901 " pdb=" O3A AGS J 901 " pdb=" O5' AGS J 901 " both_signs ideal model delta sigma weight residual True 3.18 2.60 0.59 2.00e-01 2.50e+01 8.61e+00 ... (remaining 4544 not shown) Planarity restraints: 5321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 324 " -0.011 2.00e-02 2.50e+03 1.86e-02 8.62e+00 pdb=" CG TRP A 324 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 324 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 324 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP A 324 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 324 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 324 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 324 " -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 324 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP A 324 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 568 " 0.008 2.00e-02 2.50e+03 1.46e-02 5.32e+00 pdb=" CG TRP J 568 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP J 568 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP J 568 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 568 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP J 568 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 568 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 568 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 568 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP J 568 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 303 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C ARG H 303 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG H 303 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS H 304 " -0.013 2.00e-02 2.50e+03 ... (remaining 5318 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 448 2.61 - 3.18: 26913 3.18 - 3.76: 48426 3.76 - 4.33: 69175 4.33 - 4.90: 104185 Nonbonded interactions: 249147 Sorted by model distance: nonbonded pdb=" O1A AGS D 902 " pdb="MG MG D 904 " model vdw 2.040 2.170 nonbonded pdb=" O1B AGS F 901 " pdb="MG MG F 903 " model vdw 2.042 2.170 nonbonded pdb=" O2A AGS I 902 " pdb="MG MG I 904 " model vdw 2.043 2.170 nonbonded pdb=" O2A AGS H 902 " pdb="MG MG H 904 " model vdw 2.043 2.170 nonbonded pdb=" O1B AGS D 901 " pdb="MG MG D 903 " model vdw 2.044 2.170 ... (remaining 249142 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 'D' selection = chain 'E' selection = chain 'F' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 29.750 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.007 0.080 30022 Z= 0.357 Angle : 0.942 11.620 40644 Z= 0.532 Chirality : 0.057 0.614 4547 Planarity : 0.007 0.055 5321 Dihedral : 10.672 132.300 11456 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.36 % Favored : 94.43 % Rotamer: Outliers : 0.29 % Allowed : 1.12 % Favored : 98.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.11), residues: 3732 helix: -3.20 (0.08), residues: 1631 sheet: -0.74 (0.23), residues: 450 loop : -1.51 (0.14), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 270 TYR 0.033 0.004 TYR D 219 PHE 0.025 0.004 PHE J 520 TRP 0.037 0.006 TRP A 324 HIS 0.016 0.004 HIS A 364 Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.36 (30014) covalent geometry : angle 0.94070 / 0.53 (40638) hydrogen bonds : bond 0.27932 / 18.39 ( 1273) hydrogen bonds : angle 9.16845 / 6.35 ( 3747) metal coordination : bond 0.02733 / 1.22 ( 8) metal coordination : angle 4.18904 / 2.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 844 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8667 (ttm) cc_final: 0.8365 (tpp) REVERT: A 207 GLU cc_start: 0.7476 (mp0) cc_final: 0.7210 (tm-30) REVERT: A 377 PHE cc_start: 0.7763 (t80) cc_final: 0.7539 (m-80) REVERT: A 423 ASN cc_start: 0.8232 (m-40) cc_final: 0.7735 (t0) REVERT: A 424 ASP cc_start: 0.8966 (m-30) cc_final: 0.8462 (m-30) REVERT: A 428 MET cc_start: 0.8686 (mtm) cc_final: 0.8266 (mtt) REVERT: A 574 LEU cc_start: 0.7253 (tp) cc_final: 0.6868 (pp) REVERT: H 260 TYR cc_start: 0.7994 (p90) cc_final: 0.7748 (p90) REVERT: I 217 VAL cc_start: 0.8860 (t) cc_final: 0.8622 (t) REVERT: I 291 MET cc_start: 0.9021 (mmm) cc_final: 0.8410 (mmp) REVERT: I 598 SER cc_start: 0.8156 (m) cc_final: 0.6810 (t) REVERT: I 657 ASP cc_start: 0.6565 (p0) cc_final: 0.5656 (t0) REVERT: J 222 ILE cc_start: 0.8444 (tp) cc_final: 0.8116 (mt) REVERT: J 323 ASP cc_start: 0.8261 (p0) cc_final: 0.8031 (p0) REVERT: J 342 SER cc_start: 0.8087 (m) cc_final: 0.7800 (p) REVERT: J 357 VAL cc_start: 0.9132 (t) cc_final: 0.8931 (p) REVERT: J 485 VAL cc_start: 0.7642 (p) cc_final: 0.7300 (m) REVERT: D 597 ASP cc_start: 0.7101 (p0) cc_final: 0.6815 (t70) REVERT: D 617 VAL cc_start: 0.8425 (t) cc_final: 0.8212 (t) REVERT: E 219 TYR cc_start: 0.6897 (m-80) cc_final: 0.5284 (m-10) REVERT: E 657 ASP cc_start: 0.7113 (p0) cc_final: 0.6669 (t0) REVERT: F 397 LEU cc_start: 0.8638 (mt) cc_final: 0.8377 (mm) REVERT: F 576 ILE cc_start: 0.7348 (mm) cc_final: 0.7096 (mm) outliers start: 9 outliers final: 2 residues processed: 851 average time/residue: 0.2328 time to fit residues: 297.3825 Evaluate side-chains 393 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 391 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 HIS ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 HIS H 333 ASN ** H 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 509 GLN ** H 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 619 ASN J 467 ASN ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 509 GLN ** J 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN D 467 ASN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN D 620 GLN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 619 ASN ** E 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 GLN F 467 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 555 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.077189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.064706 restraints weight = 123132.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066561 restraints weight = 76264.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067878 restraints weight = 53390.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068821 restraints weight = 40595.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.069500 restraints weight = 32883.461| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 30022 Z= 0.169 Angle : 0.691 12.754 40644 Z= 0.363 Chirality : 0.045 0.233 4547 Planarity : 0.006 0.144 5321 Dihedral : 9.563 123.838 4173 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.06 % Allowed : 2.94 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.13), residues: 3732 helix: -1.38 (0.11), residues: 1939 sheet: -0.38 (0.23), residues: 408 loop : -1.35 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 481 TYR 0.054 0.002 TYR E 219 PHE 0.027 0.002 PHE J 468 TRP 0.017 0.002 TRP A 324 HIS 0.006 0.001 HIS A 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (30014) covalent geometry : angle 0.69086 / 0.36 (40638) hydrogen bonds : bond 0.05411 / 3.54 ( 1273) hydrogen bonds : angle 5.70123 / 3.91 ( 3747) metal coordination : bond 0.02174 / 1.09 ( 8) metal coordination : angle 2.45410 / 1.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 520 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7733 (mp0) cc_final: 0.7373 (tm-30) REVERT: A 377 PHE cc_start: 0.8809 (t80) cc_final: 0.7660 (m-80) REVERT: A 423 ASN cc_start: 0.8215 (m-40) cc_final: 0.7377 (t0) REVERT: A 424 ASP cc_start: 0.9277 (m-30) cc_final: 0.8305 (t0) REVERT: A 428 MET cc_start: 0.8931 (mtm) cc_final: 0.7138 (mtm) REVERT: A 574 LEU cc_start: 0.7320 (tp) cc_final: 0.7056 (pp) REVERT: I 308 GLU cc_start: 0.8052 (tp30) cc_final: 0.7680 (tp30) REVERT: I 342 SER cc_start: 0.8950 (m) cc_final: 0.8191 (p) REVERT: I 619 ASN cc_start: 0.9081 (t0) cc_final: 0.8811 (t0) REVERT: I 657 ASP cc_start: 0.7475 (p0) cc_final: 0.6498 (t0) REVERT: I 703 ASP cc_start: 0.8288 (t0) cc_final: 0.7839 (t0) REVERT: J 222 ILE cc_start: 0.9007 (tp) cc_final: 0.8509 (mt) REVERT: J 291 MET cc_start: 0.9114 (tpp) cc_final: 0.8842 (mmm) REVERT: J 342 SER cc_start: 0.9047 (m) cc_final: 0.8260 (p) REVERT: J 465 MET cc_start: 0.8452 (tpp) cc_final: 0.7783 (tpp) REVERT: J 474 VAL cc_start: 0.7413 (m) cc_final: 0.7067 (p) REVERT: J 520 PHE cc_start: 0.7211 (m-10) cc_final: 0.6750 (m-80) REVERT: J 758 MET cc_start: 0.8635 (ttm) cc_final: 0.8193 (ttm) REVERT: D 299 GLU cc_start: 0.8597 (pm20) cc_final: 0.8357 (pm20) REVERT: D 354 ARG cc_start: 0.8144 (mpt-90) cc_final: 0.7917 (mpt-90) REVERT: D 551 GLU cc_start: 0.8294 (tt0) cc_final: 0.8052 (tm-30) REVERT: D 574 SER cc_start: 0.7776 (p) cc_final: 0.6981 (t) REVERT: D 578 ASP cc_start: 0.8538 (m-30) cc_final: 0.8128 (m-30) REVERT: D 624 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8286 (mt-10) REVERT: E 286 ASN cc_start: 0.8796 (t0) cc_final: 0.8475 (t0) REVERT: E 364 ASN cc_start: 0.9295 (p0) cc_final: 0.9006 (p0) REVERT: E 419 THR cc_start: 0.8443 (p) cc_final: 0.8222 (p) REVERT: E 443 MET cc_start: 0.8769 (tpp) cc_final: 0.8559 (tpp) REVERT: E 512 TYR cc_start: 0.8247 (m-10) cc_final: 0.7951 (m-80) REVERT: E 657 ASP cc_start: 0.7989 (p0) cc_final: 0.7291 (t0) REVERT: E 758 MET cc_start: 0.8331 (ttm) cc_final: 0.7931 (ttm) REVERT: F 337 GLU cc_start: 0.7939 (tt0) cc_final: 0.7734 (tp30) REVERT: F 340 VAL cc_start: 0.9548 (p) cc_final: 0.9220 (m) REVERT: F 369 ILE cc_start: 0.9262 (mt) cc_final: 0.8966 (tp) REVERT: F 505 GLU cc_start: 0.8205 (tt0) cc_final: 0.7904 (tt0) REVERT: F 581 ASP cc_start: 0.8825 (m-30) cc_final: 0.8591 (m-30) outliers start: 2 outliers final: 0 residues processed: 522 average time/residue: 0.2097 time to fit residues: 171.5593 Evaluate side-chains 311 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 288 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 295 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 353 optimal weight: 10.0000 chunk 133 optimal weight: 0.0070 chunk 169 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 323 optimal weight: 0.0570 chunk 334 optimal weight: 2.9990 overall best weight: 0.9718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 619 ASN I 367 ASN ** I 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 619 ASN J 333 ASN ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 619 ASN F 367 ASN F 438 GLN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 555 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.076291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.063463 restraints weight = 125721.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065396 restraints weight = 75611.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.066767 restraints weight = 52110.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.067739 restraints weight = 39127.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.068445 restraints weight = 31377.308| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30022 Z= 0.140 Angle : 0.613 9.382 40644 Z= 0.319 Chirality : 0.044 0.197 4547 Planarity : 0.005 0.087 5321 Dihedral : 9.218 121.289 4173 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.13), residues: 3732 helix: -0.74 (0.11), residues: 1969 sheet: -0.98 (0.21), residues: 476 loop : -0.86 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 679 TYR 0.024 0.002 TYR E 219 PHE 0.025 0.002 PHE D 520 TRP 0.017 0.002 TRP J 568 HIS 0.005 0.001 HIS F 400 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (30014) covalent geometry : angle 0.61270 / 0.32 (40638) hydrogen bonds : bond 0.04336 / 2.84 ( 1273) hydrogen bonds : angle 5.20421 / 3.56 ( 3747) metal coordination : bond 0.01951 / 0.99 ( 8) metal coordination : angle 2.27028 / 1.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 432 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8941 (tpp) cc_final: 0.8332 (tpp) REVERT: A 207 GLU cc_start: 0.7662 (mp0) cc_final: 0.7385 (tm-30) REVERT: A 258 ASP cc_start: 0.8036 (m-30) cc_final: 0.7719 (m-30) REVERT: A 324 TRP cc_start: 0.6961 (t60) cc_final: 0.6660 (t60) REVERT: A 377 PHE cc_start: 0.8745 (t80) cc_final: 0.7628 (m-80) REVERT: A 423 ASN cc_start: 0.8162 (m-40) cc_final: 0.7343 (t0) REVERT: A 424 ASP cc_start: 0.9272 (m-30) cc_final: 0.8210 (t0) REVERT: A 428 MET cc_start: 0.9055 (mtm) cc_final: 0.7631 (mtm) REVERT: A 549 CYS cc_start: 0.7450 (m) cc_final: 0.7003 (t) REVERT: H 238 LEU cc_start: 0.8833 (tt) cc_final: 0.8618 (mt) REVERT: H 260 TYR cc_start: 0.8707 (p90) cc_final: 0.8098 (p90) REVERT: H 395 GLU cc_start: 0.8720 (tt0) cc_final: 0.8502 (tt0) REVERT: H 401 THR cc_start: 0.9159 (p) cc_final: 0.7839 (p) REVERT: H 422 TYR cc_start: 0.8557 (m-10) cc_final: 0.8227 (m-80) REVERT: I 217 VAL cc_start: 0.9246 (t) cc_final: 0.9035 (t) REVERT: I 342 SER cc_start: 0.8993 (m) cc_final: 0.8171 (p) REVERT: I 381 ARG cc_start: 0.8366 (mmt90) cc_final: 0.7812 (mmt90) REVERT: I 619 ASN cc_start: 0.9087 (t0) cc_final: 0.8808 (t0) REVERT: I 657 ASP cc_start: 0.7608 (p0) cc_final: 0.6519 (t0) REVERT: I 703 ASP cc_start: 0.8139 (t0) cc_final: 0.7874 (t0) REVERT: J 222 ILE cc_start: 0.9046 (tp) cc_final: 0.8620 (mt) REVERT: J 291 MET cc_start: 0.8957 (tpp) cc_final: 0.8680 (mmm) REVERT: J 342 SER cc_start: 0.9043 (m) cc_final: 0.8343 (p) REVERT: J 465 MET cc_start: 0.8740 (tpp) cc_final: 0.8436 (tpp) REVERT: J 474 VAL cc_start: 0.7168 (m) cc_final: 0.6894 (p) REVERT: J 563 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8589 (mp0) REVERT: J 758 MET cc_start: 0.8727 (ttm) cc_final: 0.8293 (ttm) REVERT: D 299 GLU cc_start: 0.8688 (pm20) cc_final: 0.8025 (pm20) REVERT: D 348 MET cc_start: 0.9077 (ttm) cc_final: 0.8726 (ttm) REVERT: D 443 MET cc_start: 0.9109 (tpp) cc_final: 0.8790 (tpp) REVERT: D 574 SER cc_start: 0.7735 (p) cc_final: 0.6892 (t) REVERT: D 578 ASP cc_start: 0.8373 (m-30) cc_final: 0.7935 (m-30) REVERT: D 619 ASN cc_start: 0.8041 (t0) cc_final: 0.7540 (t0) REVERT: D 758 MET cc_start: 0.8632 (ttm) cc_final: 0.8152 (mtp) REVERT: E 222 ILE cc_start: 0.9427 (tp) cc_final: 0.9165 (pt) REVERT: E 225 CYS cc_start: 0.8135 (m) cc_final: 0.7895 (m) REVERT: E 235 MET cc_start: 0.8999 (mpp) cc_final: 0.8565 (mmt) REVERT: E 286 ASN cc_start: 0.8799 (t0) cc_final: 0.8438 (t0) REVERT: E 297 GLU cc_start: 0.8568 (mp0) cc_final: 0.8263 (mp0) REVERT: E 443 MET cc_start: 0.8919 (tpp) cc_final: 0.8672 (tpp) REVERT: E 512 TYR cc_start: 0.8180 (m-10) cc_final: 0.7939 (m-80) REVERT: E 657 ASP cc_start: 0.7969 (p0) cc_final: 0.7279 (t0) REVERT: E 758 MET cc_start: 0.8436 (ttm) cc_final: 0.8073 (ttm) REVERT: F 369 ILE cc_start: 0.9327 (mt) cc_final: 0.8984 (tp) REVERT: F 439 ILE cc_start: 0.9293 (mt) cc_final: 0.9019 (tp) REVERT: F 505 GLU cc_start: 0.8210 (tt0) cc_final: 0.7833 (tt0) REVERT: F 512 TYR cc_start: 0.8750 (m-80) cc_final: 0.8351 (m-10) REVERT: F 563 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8276 (mt-10) outliers start: 1 outliers final: 0 residues processed: 433 average time/residue: 0.1911 time to fit residues: 134.9270 Evaluate side-chains 298 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 342 optimal weight: 1.9990 chunk 325 optimal weight: 6.9990 chunk 360 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 chunk 311 optimal weight: 0.0050 chunk 77 optimal weight: 7.9990 chunk 180 optimal weight: 0.2980 chunk 2 optimal weight: 10.0000 chunk 372 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 overall best weight: 2.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 GLN A 553 GLN H 367 ASN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 555 ASN ** H 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 438 GLN ** I 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 555 ASN I 619 ASN J 276 ASN J 438 GLN J 555 ASN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 ASN D 619 ASN E 467 ASN ** E 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.061378 restraints weight = 125318.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.063235 restraints weight = 76601.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.064549 restraints weight = 53344.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.065475 restraints weight = 40518.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.066156 restraints weight = 32917.321| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30022 Z= 0.184 Angle : 0.633 8.856 40644 Z= 0.328 Chirality : 0.044 0.210 4547 Planarity : 0.005 0.064 5321 Dihedral : 9.062 124.020 4173 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3732 helix: -0.34 (0.12), residues: 1947 sheet: -0.53 (0.23), residues: 422 loop : -0.59 (0.18), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 655 TYR 0.021 0.002 TYR E 219 PHE 0.025 0.002 PHE J 318 TRP 0.029 0.003 TRP J 568 HIS 0.006 0.001 HIS J 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (30014) covalent geometry : angle 0.63287 / 0.33 (40638) hydrogen bonds : bond 0.03964 / 2.60 ( 1273) hydrogen bonds : angle 4.98351 / 3.42 ( 3747) metal coordination : bond 0.01745 / 0.88 ( 8) metal coordination : angle 2.13393 / 1.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8852 (tpp) cc_final: 0.8285 (tpp) REVERT: A 207 GLU cc_start: 0.7735 (mp0) cc_final: 0.7371 (tm-30) REVERT: A 216 LEU cc_start: 0.9009 (mt) cc_final: 0.8799 (mt) REVERT: A 258 ASP cc_start: 0.7847 (m-30) cc_final: 0.7525 (m-30) REVERT: A 377 PHE cc_start: 0.8785 (t80) cc_final: 0.7794 (m-80) REVERT: A 424 ASP cc_start: 0.9284 (m-30) cc_final: 0.8306 (t0) REVERT: A 428 MET cc_start: 0.9191 (mtm) cc_final: 0.7533 (mtm) REVERT: H 238 LEU cc_start: 0.8789 (tt) cc_final: 0.8537 (mt) REVERT: H 567 MET cc_start: 0.6844 (tpt) cc_final: 0.6001 (ttm) REVERT: I 294 MET cc_start: 0.7902 (mmp) cc_final: 0.7259 (ttt) REVERT: I 342 SER cc_start: 0.9037 (m) cc_final: 0.8314 (p) REVERT: I 619 ASN cc_start: 0.8992 (t0) cc_final: 0.8742 (t0) REVERT: I 657 ASP cc_start: 0.7660 (p0) cc_final: 0.6780 (t0) REVERT: J 222 ILE cc_start: 0.9040 (tp) cc_final: 0.8720 (mt) REVERT: J 342 SER cc_start: 0.9211 (m) cc_final: 0.8604 (p) REVERT: J 465 MET cc_start: 0.8649 (tpp) cc_final: 0.8265 (tpp) REVERT: J 474 VAL cc_start: 0.7245 (m) cc_final: 0.6967 (p) REVERT: J 563 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8648 (mp0) REVERT: J 578 ASP cc_start: 0.7612 (m-30) cc_final: 0.7399 (m-30) REVERT: J 590 VAL cc_start: 0.9360 (m) cc_final: 0.9120 (t) REVERT: J 628 MET cc_start: 0.7544 (ptp) cc_final: 0.6517 (ptp) REVERT: D 299 GLU cc_start: 0.8642 (pm20) cc_final: 0.8212 (pm20) REVERT: D 348 MET cc_start: 0.9113 (ttm) cc_final: 0.8864 (ttt) REVERT: D 443 MET cc_start: 0.9167 (tpp) cc_final: 0.8824 (tpp) REVERT: D 574 SER cc_start: 0.7343 (p) cc_final: 0.6586 (t) REVERT: D 578 ASP cc_start: 0.8338 (m-30) cc_final: 0.7835 (m-30) REVERT: D 758 MET cc_start: 0.8635 (ttm) cc_final: 0.8415 (mtp) REVERT: E 222 ILE cc_start: 0.9495 (tp) cc_final: 0.9263 (pt) REVERT: E 225 CYS cc_start: 0.8116 (m) cc_final: 0.7891 (m) REVERT: E 286 ASN cc_start: 0.8880 (t0) cc_final: 0.8541 (t0) REVERT: E 297 GLU cc_start: 0.8719 (mp0) cc_final: 0.8358 (mp0) REVERT: E 402 LYS cc_start: 0.9082 (pttt) cc_final: 0.8872 (pmtt) REVERT: E 443 MET cc_start: 0.8968 (tpp) cc_final: 0.8705 (tpp) REVERT: E 657 ASP cc_start: 0.8278 (p0) cc_final: 0.7523 (t0) REVERT: E 758 MET cc_start: 0.8483 (ttm) cc_final: 0.8137 (ttm) REVERT: F 436 MET cc_start: 0.8630 (mmm) cc_final: 0.8266 (tpp) REVERT: F 439 ILE cc_start: 0.9388 (mt) cc_final: 0.9041 (tp) REVERT: F 505 GLU cc_start: 0.8188 (tt0) cc_final: 0.7770 (tt0) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.1877 time to fit residues: 113.0813 Evaluate side-chains 247 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 274 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 chunk 353 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 208 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 363 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 290 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 619 ASN I 276 ASN ** I 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 619 ASN ** I 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 778 GLN ** J 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 619 ASN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 GLN ** E 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 555 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.074798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.061793 restraints weight = 126295.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.063698 restraints weight = 75948.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.065013 restraints weight = 52646.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.065981 restraints weight = 39913.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066562 restraints weight = 32296.382| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30022 Z= 0.122 Angle : 0.567 6.660 40644 Z= 0.293 Chirality : 0.043 0.199 4547 Planarity : 0.004 0.060 5321 Dihedral : 8.854 124.676 4173 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.06 % Allowed : 1.95 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3732 helix: -0.08 (0.12), residues: 1952 sheet: -0.48 (0.23), residues: 423 loop : -0.47 (0.18), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 492 TYR 0.027 0.002 TYR A 189 PHE 0.024 0.001 PHE J 318 TRP 0.018 0.002 TRP A 133 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (30014) covalent geometry : angle 0.56631 / 0.29 (40638) hydrogen bonds : bond 0.03517 / 2.31 ( 1273) hydrogen bonds : angle 4.78614 / 3.27 ( 3747) metal coordination : bond 0.01040 / 0.53 ( 8) metal coordination : angle 2.26094 / 1.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 368 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.8551 (ttm) cc_final: 0.8335 (ttm) REVERT: A 196 MET cc_start: 0.8912 (tpp) cc_final: 0.8381 (tpp) REVERT: A 207 GLU cc_start: 0.7797 (mp0) cc_final: 0.7433 (tm-30) REVERT: A 258 ASP cc_start: 0.8106 (m-30) cc_final: 0.7847 (m-30) REVERT: A 377 PHE cc_start: 0.8758 (t80) cc_final: 0.7839 (m-80) REVERT: A 424 ASP cc_start: 0.9277 (m-30) cc_final: 0.8389 (t0) REVERT: A 428 MET cc_start: 0.9303 (mtm) cc_final: 0.8208 (mtm) REVERT: A 459 ARG cc_start: 0.6835 (ptt180) cc_final: 0.6436 (ptt180) REVERT: H 260 TYR cc_start: 0.8519 (p90) cc_final: 0.8269 (p90) REVERT: H 322 ILE cc_start: 0.9530 (tp) cc_final: 0.9325 (tp) REVERT: H 567 MET cc_start: 0.6719 (tpt) cc_final: 0.6089 (ttm) REVERT: I 342 SER cc_start: 0.8880 (m) cc_final: 0.8179 (p) REVERT: I 381 ARG cc_start: 0.8287 (mmt90) cc_final: 0.7789 (mmm-85) REVERT: I 619 ASN cc_start: 0.8948 (t0) cc_final: 0.8658 (t0) REVERT: I 657 ASP cc_start: 0.7705 (p0) cc_final: 0.6659 (t0) REVERT: I 703 ASP cc_start: 0.8157 (t0) cc_final: 0.7914 (t0) REVERT: J 318 PHE cc_start: 0.8934 (t80) cc_final: 0.8382 (t80) REVERT: J 342 SER cc_start: 0.9162 (m) cc_final: 0.8425 (p) REVERT: J 474 VAL cc_start: 0.7319 (m) cc_final: 0.7094 (p) REVERT: J 563 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8622 (mp0) REVERT: J 578 ASP cc_start: 0.7635 (m-30) cc_final: 0.7324 (m-30) REVERT: D 299 GLU cc_start: 0.8481 (pm20) cc_final: 0.8086 (pm20) REVERT: D 348 MET cc_start: 0.8979 (ttm) cc_final: 0.8772 (ttm) REVERT: D 351 MET cc_start: 0.7803 (ptm) cc_final: 0.6720 (ppp) REVERT: D 443 MET cc_start: 0.9119 (tpp) cc_final: 0.8862 (tpp) REVERT: D 574 SER cc_start: 0.7478 (p) cc_final: 0.6673 (t) REVERT: D 578 ASP cc_start: 0.8382 (m-30) cc_final: 0.8097 (m-30) REVERT: E 222 ILE cc_start: 0.9508 (tp) cc_final: 0.9220 (pt) REVERT: E 225 CYS cc_start: 0.8150 (m) cc_final: 0.7942 (m) REVERT: E 235 MET cc_start: 0.8966 (mpp) cc_final: 0.8425 (mmt) REVERT: E 286 ASN cc_start: 0.8888 (t0) cc_final: 0.8672 (t0) REVERT: E 297 GLU cc_start: 0.8645 (mp0) cc_final: 0.8324 (mp0) REVERT: E 402 LYS cc_start: 0.9112 (pttt) cc_final: 0.8828 (pttt) REVERT: E 443 MET cc_start: 0.8913 (tpp) cc_final: 0.8709 (tpp) REVERT: E 512 TYR cc_start: 0.8267 (m-10) cc_final: 0.7916 (m-80) REVERT: E 657 ASP cc_start: 0.8215 (p0) cc_final: 0.7488 (t0) REVERT: E 758 MET cc_start: 0.8487 (ttm) cc_final: 0.8279 (ttm) REVERT: F 304 LYS cc_start: 0.9564 (mmmt) cc_final: 0.9089 (mtpt) REVERT: F 436 MET cc_start: 0.8638 (mmm) cc_final: 0.8238 (tpp) REVERT: F 439 ILE cc_start: 0.9314 (mt) cc_final: 0.8877 (tp) REVERT: F 505 GLU cc_start: 0.8275 (tt0) cc_final: 0.7949 (tt0) REVERT: F 512 TYR cc_start: 0.8878 (m-80) cc_final: 0.8623 (m-10) REVERT: F 724 ILE cc_start: 0.8748 (pt) cc_final: 0.8540 (tp) outliers start: 2 outliers final: 1 residues processed: 370 average time/residue: 0.1773 time to fit residues: 107.1503 Evaluate side-chains 256 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 95 optimal weight: 0.7980 chunk 266 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 373 optimal weight: 5.9990 chunk 314 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 361 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 GLN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 333 ASN J 619 ASN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.061238 restraints weight = 125980.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.063114 restraints weight = 75760.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064415 restraints weight = 52354.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.065350 restraints weight = 39688.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.066009 restraints weight = 32124.294| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30022 Z= 0.149 Angle : 0.581 6.482 40644 Z= 0.300 Chirality : 0.043 0.212 4547 Planarity : 0.004 0.059 5321 Dihedral : 8.811 124.650 4173 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.03 % Allowed : 1.37 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3732 helix: 0.11 (0.12), residues: 1934 sheet: -0.60 (0.22), residues: 459 loop : -0.29 (0.19), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 616 TYR 0.031 0.002 TYR A 189 PHE 0.028 0.002 PHE D 580 TRP 0.023 0.002 TRP J 568 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (30014) covalent geometry : angle 0.57989 / 0.30 (40638) hydrogen bonds : bond 0.03490 / 2.29 ( 1273) hydrogen bonds : angle 4.75345 / 3.25 ( 3747) metal coordination : bond 0.01248 / 0.64 ( 8) metal coordination : angle 2.35328 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 352 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8970 (tpp) cc_final: 0.8400 (tpp) REVERT: A 207 GLU cc_start: 0.7735 (mp0) cc_final: 0.7451 (tm-30) REVERT: A 258 ASP cc_start: 0.7964 (m-30) cc_final: 0.7607 (m-30) REVERT: A 377 PHE cc_start: 0.8777 (t80) cc_final: 0.7865 (m-10) REVERT: A 424 ASP cc_start: 0.9280 (m-30) cc_final: 0.8476 (t70) REVERT: A 428 MET cc_start: 0.9391 (mtm) cc_final: 0.8677 (mtm) REVERT: A 459 ARG cc_start: 0.6696 (ptt180) cc_final: 0.6467 (ptt180) REVERT: H 237 GLU cc_start: 0.7751 (tp30) cc_final: 0.7517 (tp30) REVERT: H 567 MET cc_start: 0.6925 (tpt) cc_final: 0.6366 (ttm) REVERT: I 294 MET cc_start: 0.7203 (ttt) cc_final: 0.6994 (ttp) REVERT: I 342 SER cc_start: 0.8936 (m) cc_final: 0.8214 (p) REVERT: I 619 ASN cc_start: 0.8929 (t0) cc_final: 0.8659 (t0) REVERT: I 657 ASP cc_start: 0.7750 (p0) cc_final: 0.6736 (t0) REVERT: I 703 ASP cc_start: 0.8122 (t0) cc_final: 0.7878 (t0) REVERT: J 272 ARG cc_start: 0.8511 (mtt90) cc_final: 0.7994 (mtp180) REVERT: J 291 MET cc_start: 0.9113 (tpp) cc_final: 0.8788 (tpp) REVERT: J 342 SER cc_start: 0.9171 (m) cc_final: 0.8474 (p) REVERT: J 474 VAL cc_start: 0.7320 (m) cc_final: 0.7091 (p) REVERT: J 578 ASP cc_start: 0.7566 (m-30) cc_final: 0.7219 (m-30) REVERT: J 635 PHE cc_start: 0.7800 (t80) cc_final: 0.7073 (t80) REVERT: D 299 GLU cc_start: 0.8538 (pm20) cc_final: 0.8045 (pm20) REVERT: D 342 SER cc_start: 0.9510 (m) cc_final: 0.8817 (p) REVERT: D 348 MET cc_start: 0.9014 (ttm) cc_final: 0.8773 (ttm) REVERT: D 443 MET cc_start: 0.9119 (tpp) cc_final: 0.8844 (tpp) REVERT: D 574 SER cc_start: 0.7338 (p) cc_final: 0.6636 (t) REVERT: D 578 ASP cc_start: 0.8413 (m-30) cc_final: 0.8138 (m-30) REVERT: D 780 MET cc_start: 0.4277 (mmt) cc_final: 0.3925 (tpp) REVERT: E 222 ILE cc_start: 0.9521 (tp) cc_final: 0.9267 (pt) REVERT: E 225 CYS cc_start: 0.8127 (m) cc_final: 0.7895 (m) REVERT: E 286 ASN cc_start: 0.9048 (t0) cc_final: 0.8758 (t0) REVERT: E 297 GLU cc_start: 0.8711 (mp0) cc_final: 0.8322 (mp0) REVERT: E 512 TYR cc_start: 0.8184 (m-10) cc_final: 0.7925 (m-80) REVERT: E 657 ASP cc_start: 0.8273 (p0) cc_final: 0.7583 (t0) REVERT: F 291 MET cc_start: 0.9413 (mmm) cc_final: 0.9028 (mmm) REVERT: F 304 LYS cc_start: 0.9594 (mmmt) cc_final: 0.9184 (mmmt) REVERT: F 369 ILE cc_start: 0.9433 (mt) cc_final: 0.9025 (tp) REVERT: F 436 MET cc_start: 0.8656 (mmm) cc_final: 0.8290 (tpp) REVERT: F 439 ILE cc_start: 0.9341 (mt) cc_final: 0.9007 (tp) REVERT: F 724 ILE cc_start: 0.8831 (pt) cc_final: 0.8626 (tp) outliers start: 1 outliers final: 0 residues processed: 352 average time/residue: 0.1864 time to fit residues: 107.0915 Evaluate side-chains 248 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 102 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 338 optimal weight: 0.0970 chunk 46 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 298 optimal weight: 0.0370 chunk 19 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 GLN A 475 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 619 ASN ** I 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 619 ASN J 619 ASN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 ASN ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 ASN ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.074735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.061864 restraints weight = 127652.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.063748 restraints weight = 77078.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.065050 restraints weight = 53313.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.065895 restraints weight = 40619.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066644 restraints weight = 33283.726| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30022 Z= 0.106 Angle : 0.562 6.845 40644 Z= 0.286 Chirality : 0.043 0.238 4547 Planarity : 0.004 0.060 5321 Dihedral : 8.668 125.315 4173 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3732 helix: 0.26 (0.12), residues: 1928 sheet: -0.46 (0.23), residues: 453 loop : -0.32 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 492 TYR 0.021 0.002 TYR A 189 PHE 0.028 0.002 PHE J 318 TRP 0.041 0.002 TRP J 568 HIS 0.003 0.001 HIS J 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (30014) covalent geometry : angle 0.56078 / 0.29 (40638) hydrogen bonds : bond 0.03214 / 2.13 ( 1273) hydrogen bonds : angle 4.59524 / 3.14 ( 3747) metal coordination : bond 0.00991 / 0.48 ( 8) metal coordination : angle 2.49190 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.8730 (pmm) cc_final: 0.8370 (pmm) REVERT: A 196 MET cc_start: 0.8888 (tpp) cc_final: 0.8177 (tpp) REVERT: A 207 GLU cc_start: 0.8026 (mp0) cc_final: 0.7426 (tm-30) REVERT: A 258 ASP cc_start: 0.7828 (m-30) cc_final: 0.7507 (m-30) REVERT: A 424 ASP cc_start: 0.9301 (m-30) cc_final: 0.8627 (t70) REVERT: H 237 GLU cc_start: 0.7691 (tp30) cc_final: 0.7386 (tp30) REVERT: H 260 TYR cc_start: 0.8472 (p90) cc_final: 0.8173 (p90) REVERT: H 567 MET cc_start: 0.6956 (tpt) cc_final: 0.6576 (mmm) REVERT: I 342 SER cc_start: 0.8854 (m) cc_final: 0.8145 (p) REVERT: I 657 ASP cc_start: 0.7306 (p0) cc_final: 0.6584 (t0) REVERT: I 703 ASP cc_start: 0.8182 (t0) cc_final: 0.7879 (t0) REVERT: J 272 ARG cc_start: 0.8505 (mtt90) cc_final: 0.7942 (mtp180) REVERT: J 342 SER cc_start: 0.9152 (m) cc_final: 0.8452 (p) REVERT: J 474 VAL cc_start: 0.6984 (m) cc_final: 0.6732 (p) REVERT: J 578 ASP cc_start: 0.7664 (m-30) cc_final: 0.7300 (m-30) REVERT: J 658 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8489 (mp10) REVERT: D 299 GLU cc_start: 0.8432 (pm20) cc_final: 0.8076 (pm20) REVERT: D 342 SER cc_start: 0.9393 (m) cc_final: 0.8703 (p) REVERT: D 465 MET cc_start: 0.8920 (tpt) cc_final: 0.8716 (tpp) REVERT: D 780 MET cc_start: 0.4144 (mmt) cc_final: 0.3732 (tpp) REVERT: E 225 CYS cc_start: 0.8195 (m) cc_final: 0.7993 (m) REVERT: E 235 MET cc_start: 0.8897 (mpp) cc_final: 0.8491 (mmt) REVERT: E 286 ASN cc_start: 0.8983 (t0) cc_final: 0.8648 (t0) REVERT: E 297 GLU cc_start: 0.8689 (mp0) cc_final: 0.8351 (mp0) REVERT: E 443 MET cc_start: 0.8783 (tpt) cc_final: 0.8564 (tpp) REVERT: E 512 TYR cc_start: 0.8070 (m-10) cc_final: 0.7742 (m-80) REVERT: E 657 ASP cc_start: 0.8173 (p0) cc_final: 0.7613 (t0) REVERT: F 304 LYS cc_start: 0.9564 (mmmt) cc_final: 0.9297 (mmmt) REVERT: F 369 ILE cc_start: 0.9279 (mt) cc_final: 0.9068 (tp) REVERT: F 436 MET cc_start: 0.8574 (mmm) cc_final: 0.8170 (tpp) REVERT: F 439 ILE cc_start: 0.9303 (mt) cc_final: 0.8914 (tp) REVERT: F 563 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7880 (mt-10) REVERT: F 620 GLN cc_start: 0.8937 (tp40) cc_final: 0.8388 (tm-30) REVERT: F 724 ILE cc_start: 0.8928 (pt) cc_final: 0.8647 (tp) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.1767 time to fit residues: 106.8118 Evaluate side-chains 260 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 24 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 363 optimal weight: 7.9990 chunk 241 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 GLN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 437 GLN J 753 HIS ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 GLN ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.059984 restraints weight = 129887.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.061741 restraints weight = 79158.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.062972 restraints weight = 55436.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.063855 restraints weight = 42468.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.064402 restraints weight = 34655.700| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30022 Z= 0.169 Angle : 0.601 11.019 40644 Z= 0.308 Chirality : 0.044 0.214 4547 Planarity : 0.005 0.059 5321 Dihedral : 8.704 126.671 4173 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3732 helix: 0.38 (0.12), residues: 1936 sheet: -0.47 (0.23), residues: 459 loop : -0.17 (0.19), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 492 TYR 0.030 0.002 TYR A 472 PHE 0.023 0.002 PHE A 550 TRP 0.021 0.002 TRP A 133 HIS 0.004 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (30014) covalent geometry : angle 0.60042 / 0.31 (40638) hydrogen bonds : bond 0.03421 / 2.26 ( 1273) hydrogen bonds : angle 4.67562 / 3.20 ( 3747) metal coordination : bond 0.01248 / 0.64 ( 8) metal coordination : angle 2.53733 / 1.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 ASP cc_start: 0.7052 (m-30) cc_final: 0.6730 (t70) REVERT: A 196 MET cc_start: 0.8773 (tpp) cc_final: 0.8080 (tpp) REVERT: A 207 GLU cc_start: 0.8041 (mp0) cc_final: 0.7443 (tm-30) REVERT: A 324 TRP cc_start: 0.7280 (t60) cc_final: 0.7077 (t60) REVERT: A 424 ASP cc_start: 0.9295 (m-30) cc_final: 0.8796 (p0) REVERT: H 237 GLU cc_start: 0.7593 (tp30) cc_final: 0.7216 (tp30) REVERT: H 581 ASP cc_start: 0.7655 (m-30) cc_final: 0.7419 (m-30) REVERT: I 342 SER cc_start: 0.9007 (m) cc_final: 0.8259 (p) REVERT: I 404 MET cc_start: 0.8219 (ppp) cc_final: 0.7971 (ppp) REVERT: I 619 ASN cc_start: 0.9115 (t0) cc_final: 0.8760 (t0) REVERT: I 625 MET cc_start: 0.8545 (tmm) cc_final: 0.8199 (tmm) REVERT: I 657 ASP cc_start: 0.7562 (p0) cc_final: 0.6660 (t0) REVERT: I 703 ASP cc_start: 0.8028 (t0) cc_final: 0.7803 (t0) REVERT: J 272 ARG cc_start: 0.8483 (mtt90) cc_final: 0.8153 (mtp180) REVERT: J 291 MET cc_start: 0.9133 (tpp) cc_final: 0.8786 (tpp) REVERT: J 342 SER cc_start: 0.9034 (m) cc_final: 0.8393 (p) REVERT: J 465 MET cc_start: 0.8508 (tmm) cc_final: 0.8167 (tmm) REVERT: J 474 VAL cc_start: 0.7121 (m) cc_final: 0.6855 (p) REVERT: J 578 ASP cc_start: 0.7556 (m-30) cc_final: 0.7186 (m-30) REVERT: D 299 GLU cc_start: 0.8565 (pm20) cc_final: 0.8071 (pm20) REVERT: D 342 SER cc_start: 0.9453 (m) cc_final: 0.8797 (p) REVERT: D 348 MET cc_start: 0.8770 (ttm) cc_final: 0.8465 (ttm) REVERT: D 465 MET cc_start: 0.8897 (tpt) cc_final: 0.8590 (tpt) REVERT: D 574 SER cc_start: 0.7586 (p) cc_final: 0.6881 (t) REVERT: D 578 ASP cc_start: 0.8332 (m-30) cc_final: 0.7908 (m-30) REVERT: E 235 MET cc_start: 0.8918 (mpp) cc_final: 0.8534 (mmt) REVERT: E 286 ASN cc_start: 0.9126 (t0) cc_final: 0.8818 (t0) REVERT: E 297 GLU cc_start: 0.8757 (mp0) cc_final: 0.8451 (mp0) REVERT: E 512 TYR cc_start: 0.8070 (m-10) cc_final: 0.7827 (m-80) REVERT: E 657 ASP cc_start: 0.8247 (p0) cc_final: 0.7543 (t0) REVERT: E 780 MET cc_start: 0.4607 (tpt) cc_final: 0.3386 (tpt) REVERT: F 304 LYS cc_start: 0.9593 (mmmt) cc_final: 0.9361 (mmmt) REVERT: F 369 ILE cc_start: 0.9317 (mt) cc_final: 0.9101 (tp) REVERT: F 436 MET cc_start: 0.8626 (mmm) cc_final: 0.8250 (tpp) REVERT: F 439 ILE cc_start: 0.9380 (mt) cc_final: 0.8957 (tp) REVERT: F 620 GLN cc_start: 0.9022 (tp40) cc_final: 0.8577 (tm-30) REVERT: F 724 ILE cc_start: 0.8934 (pt) cc_final: 0.8625 (tp) REVERT: F 780 MET cc_start: 0.7187 (pmm) cc_final: 0.5886 (pmm) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1730 time to fit residues: 94.1537 Evaluate side-chains 239 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 318 optimal weight: 8.9990 chunk 140 optimal weight: 40.0000 chunk 211 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 294 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 315 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 354 optimal weight: 0.3980 chunk 263 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 GLN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 276 ASN H 367 ASN H 438 GLN H 467 ASN ** H 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 555 ASN ** I 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 753 HIS ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.073022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.060350 restraints weight = 128775.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.062121 restraints weight = 78623.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.063375 restraints weight = 55063.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.064195 restraints weight = 42181.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.064864 restraints weight = 34801.063| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30022 Z= 0.133 Angle : 0.591 7.634 40644 Z= 0.301 Chirality : 0.044 0.225 4547 Planarity : 0.004 0.059 5321 Dihedral : 8.614 127.164 4173 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3732 helix: 0.46 (0.12), residues: 1924 sheet: -0.44 (0.23), residues: 459 loop : -0.17 (0.19), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 492 TYR 0.020 0.002 TYR F 512 PHE 0.026 0.001 PHE A 550 TRP 0.017 0.002 TRP A 346 HIS 0.006 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (30014) covalent geometry : angle 0.58837 / 0.30 (40638) hydrogen bonds : bond 0.03331 / 2.21 ( 1273) hydrogen bonds : angle 4.66598 / 3.20 ( 3747) metal coordination : bond 0.01325 / 0.63 ( 8) metal coordination : angle 4.27532 / 2.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8767 (tpp) cc_final: 0.8093 (tpp) REVERT: A 207 GLU cc_start: 0.8029 (mp0) cc_final: 0.7483 (tm-30) REVERT: A 258 ASP cc_start: 0.7526 (m-30) cc_final: 0.6997 (m-30) REVERT: H 577 ARG cc_start: 0.8255 (ttm110) cc_final: 0.7691 (mtp-110) REVERT: H 624 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8067 (tp30) REVERT: I 342 SER cc_start: 0.8973 (m) cc_final: 0.8190 (p) REVERT: I 404 MET cc_start: 0.8149 (ppp) cc_final: 0.7860 (ppp) REVERT: I 619 ASN cc_start: 0.9099 (t0) cc_final: 0.8751 (t0) REVERT: I 625 MET cc_start: 0.8645 (tmm) cc_final: 0.8229 (tmm) REVERT: I 657 ASP cc_start: 0.7492 (p0) cc_final: 0.6704 (t0) REVERT: I 703 ASP cc_start: 0.8094 (t0) cc_final: 0.7882 (t0) REVERT: J 272 ARG cc_start: 0.8483 (mtt90) cc_final: 0.8089 (mtp180) REVERT: J 291 MET cc_start: 0.9119 (tpp) cc_final: 0.8812 (tpp) REVERT: J 342 SER cc_start: 0.8944 (m) cc_final: 0.8325 (p) REVERT: J 465 MET cc_start: 0.8541 (tmm) cc_final: 0.8179 (tmm) REVERT: J 578 ASP cc_start: 0.7528 (m-30) cc_final: 0.7142 (m-30) REVERT: J 628 MET cc_start: 0.7922 (ptp) cc_final: 0.7696 (ptp) REVERT: D 299 GLU cc_start: 0.8494 (pm20) cc_final: 0.8090 (pm20) REVERT: D 321 GLU cc_start: 0.8570 (pm20) cc_final: 0.8305 (mp0) REVERT: D 342 SER cc_start: 0.9415 (m) cc_final: 0.8756 (p) REVERT: D 578 ASP cc_start: 0.8317 (m-30) cc_final: 0.8115 (m-30) REVERT: D 619 ASN cc_start: 0.8997 (t0) cc_final: 0.8754 (t0) REVERT: D 635 PHE cc_start: 0.7464 (m-10) cc_final: 0.7228 (m-10) REVERT: D 780 MET cc_start: 0.4084 (mmt) cc_final: 0.3722 (mpp) REVERT: E 235 MET cc_start: 0.8958 (mpp) cc_final: 0.8554 (mmt) REVERT: E 286 ASN cc_start: 0.9112 (t0) cc_final: 0.8861 (t0) REVERT: E 297 GLU cc_start: 0.8729 (mp0) cc_final: 0.8430 (mp0) REVERT: E 512 TYR cc_start: 0.8022 (m-10) cc_final: 0.7781 (m-80) REVERT: E 657 ASP cc_start: 0.8259 (p0) cc_final: 0.7546 (t0) REVERT: E 780 MET cc_start: 0.4688 (tpt) cc_final: 0.3404 (tpt) REVERT: F 304 LYS cc_start: 0.9565 (mmmt) cc_final: 0.9308 (mmmt) REVERT: F 436 MET cc_start: 0.8648 (mmm) cc_final: 0.8252 (tpp) REVERT: F 439 ILE cc_start: 0.9359 (mt) cc_final: 0.8982 (tp) REVERT: F 620 GLN cc_start: 0.8980 (tp40) cc_final: 0.8575 (tm-30) REVERT: F 724 ILE cc_start: 0.8936 (pt) cc_final: 0.8642 (tp) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1711 time to fit residues: 92.8333 Evaluate side-chains 242 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 242 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 260 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 251 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 328 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 GLN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 555 ASN ** I 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 509 GLN J 511 GLN J 677 GLN J 753 HIS ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 ASN ** E 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 HIS ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 555 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.060505 restraints weight = 129131.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.062273 restraints weight = 79005.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.063527 restraints weight = 55695.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.064420 restraints weight = 42755.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.065038 restraints weight = 34976.206| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.6228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30022 Z= 0.126 Angle : 0.588 8.953 40644 Z= 0.298 Chirality : 0.043 0.188 4547 Planarity : 0.004 0.059 5321 Dihedral : 8.568 126.567 4173 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3732 helix: 0.50 (0.12), residues: 1918 sheet: -0.31 (0.23), residues: 448 loop : -0.18 (0.18), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 378 TYR 0.014 0.002 TYR A 472 PHE 0.037 0.001 PHE J 318 TRP 0.021 0.002 TRP A 346 HIS 0.005 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (30014) covalent geometry : angle 0.58694 / 0.30 (40638) hydrogen bonds : bond 0.03263 / 2.16 ( 1273) hydrogen bonds : angle 4.61900 / 3.17 ( 3747) metal coordination : bond 0.00895 / 0.47 ( 8) metal coordination : angle 3.06503 / 1.52 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7464 Ramachandran restraints generated. 3732 Oldfield, 0 Emsley, 3732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.881 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 190 MET cc_start: 0.9065 (pmm) cc_final: 0.8299 (pmm) REVERT: A 196 MET cc_start: 0.8725 (tpp) cc_final: 0.8053 (tpp) REVERT: A 258 ASP cc_start: 0.7529 (m-30) cc_final: 0.7025 (m-30) REVERT: A 380 ARG cc_start: 0.7509 (mtt180) cc_final: 0.7125 (ttm-80) REVERT: A 540 MET cc_start: 0.6320 (mtp) cc_final: 0.5966 (mtp) REVERT: H 294 MET cc_start: 0.7696 (mpp) cc_final: 0.7260 (mpp) REVERT: H 577 ARG cc_start: 0.8288 (ttm110) cc_final: 0.7564 (mtp-110) REVERT: H 624 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8067 (tp30) REVERT: I 342 SER cc_start: 0.8956 (m) cc_final: 0.8141 (p) REVERT: I 404 MET cc_start: 0.8150 (ppp) cc_final: 0.7794 (ppp) REVERT: I 567 MET cc_start: 0.8157 (ppp) cc_final: 0.7926 (ppp) REVERT: I 619 ASN cc_start: 0.9085 (t0) cc_final: 0.8743 (t0) REVERT: I 625 MET cc_start: 0.8705 (tmm) cc_final: 0.8237 (tmm) REVERT: I 657 ASP cc_start: 0.7470 (p0) cc_final: 0.6741 (t0) REVERT: I 703 ASP cc_start: 0.8100 (t0) cc_final: 0.7887 (t0) REVERT: J 272 ARG cc_start: 0.8519 (mtt90) cc_final: 0.7997 (mtp180) REVERT: J 291 MET cc_start: 0.9092 (tpp) cc_final: 0.8886 (mmm) REVERT: J 342 SER cc_start: 0.8945 (m) cc_final: 0.8364 (p) REVERT: J 465 MET cc_start: 0.8573 (tmm) cc_final: 0.8222 (tmm) REVERT: J 578 ASP cc_start: 0.7532 (m-30) cc_final: 0.7166 (m-30) REVERT: J 758 MET cc_start: 0.8168 (ttt) cc_final: 0.7909 (ttp) REVERT: D 299 GLU cc_start: 0.8648 (pm20) cc_final: 0.8047 (pm20) REVERT: D 321 GLU cc_start: 0.8559 (pm20) cc_final: 0.8302 (mp0) REVERT: D 342 SER cc_start: 0.9411 (m) cc_final: 0.8746 (p) REVERT: D 578 ASP cc_start: 0.8304 (m-30) cc_final: 0.8092 (m-30) REVERT: D 619 ASN cc_start: 0.8983 (t0) cc_final: 0.8701 (t0) REVERT: D 635 PHE cc_start: 0.7615 (m-10) cc_final: 0.7403 (m-10) REVERT: D 780 MET cc_start: 0.4100 (mmt) cc_final: 0.3775 (mpp) REVERT: E 512 TYR cc_start: 0.8055 (m-10) cc_final: 0.7817 (m-80) REVERT: E 657 ASP cc_start: 0.8251 (p0) cc_final: 0.7518 (t0) REVERT: E 780 MET cc_start: 0.4684 (tpt) cc_final: 0.4427 (tpt) REVERT: F 304 LYS cc_start: 0.9528 (mmmt) cc_final: 0.9298 (mmmt) REVERT: F 337 GLU cc_start: 0.8670 (mt-10) cc_final: 0.7968 (mt-10) REVERT: F 436 MET cc_start: 0.8636 (mmm) cc_final: 0.8261 (tpp) REVERT: F 439 ILE cc_start: 0.9342 (mt) cc_final: 0.9058 (tp) REVERT: F 620 GLN cc_start: 0.8891 (tp40) cc_final: 0.8487 (tm-30) REVERT: F 724 ILE cc_start: 0.8871 (pt) cc_final: 0.8621 (tp) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.1648 time to fit residues: 86.2370 Evaluate side-chains 237 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 199 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 346 optimal weight: 0.8980 chunk 230 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 275 optimal weight: 6.9990 chunk 316 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 GLN A 193 HIS H 367 ASN ** H 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 555 ASN ** I 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 509 GLN J 677 GLN ** J 753 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 ASN E 438 GLN E 555 ASN E 575 ASN ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.072631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.059902 restraints weight = 130159.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.061645 restraints weight = 80042.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062880 restraints weight = 56429.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.063733 restraints weight = 43426.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.064361 restraints weight = 35775.928| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30022 Z= 0.149 Angle : 0.604 9.836 40644 Z= 0.308 Chirality : 0.044 0.177 4547 Planarity : 0.005 0.097 5321 Dihedral : 8.586 127.273 4173 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3732 helix: 0.50 (0.12), residues: 1918 sheet: -0.55 (0.23), residues: 478 loop : -0.07 (0.19), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 616 TYR 0.028 0.002 TYR A 472 PHE 0.041 0.002 PHE J 318 TRP 0.025 0.002 TRP A 133 HIS 0.007 0.001 HIS F 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (30014) covalent geometry : angle 0.60286 / 0.31 (40638) hydrogen bonds : bond 0.03405 / 2.24 ( 1273) hydrogen bonds : angle 4.64279 / 3.17 ( 3747) metal coordination : bond 0.01239 / 0.61 ( 8) metal coordination : angle 3.47567 / 1.69 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4599.30 seconds wall clock time: 80 minutes 42.20 seconds (4842.20 seconds total)