Starting phenix.real_space_refine on Thu Nov 20 08:32:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6chs_7476/11_2025/6chs_7476.cif Found real_map, /net/cci-nas-00/data/ceres_data/6chs_7476/11_2025/6chs_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6chs_7476/11_2025/6chs_7476.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6chs_7476/11_2025/6chs_7476.map" model { file = "/net/cci-nas-00/data/ceres_data/6chs_7476/11_2025/6chs_7476.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6chs_7476/11_2025/6chs_7476.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 6.26, per 1000 atoms: 0.21 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: 2.58 Conformation dependent library (CDL) restraints added in 1.3 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: 1.08 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: 3.32 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: 18197 26.46 - 52.92: 334 52.92 - 79.38: 32 79.38 - 105.84: 2 105.84 - 132.30: 11 Dihedral angle restraints: 18576 sinusoidal: 7770 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 18573 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 29.440 Find NCS groups from input model: 0.470 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: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 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 : 11.076 132.300 11588 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 covalent geometry : bond 0.00737 (30014) covalent geometry : angle 0.94070 (40638) hydrogen bonds : bond 0.27932 ( 1273) hydrogen bonds : angle 9.16845 ( 3747) metal coordination : bond 0.02733 ( 8) metal coordination : angle 4.18904 ( 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 : 0.861 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: 0.8364 (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: 0.6564 (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: 0.2218 time to fit residues: 280.7526 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 : 1.091 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3510 r_free = 0.3510 target = 0.077181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.064703 restraints weight = 123558.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066590 restraints weight = 76181.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.067917 restraints weight = 53091.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.068863 restraints weight = 40195.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.069550 restraints weight = 32483.688| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 30022 Z= 0.170 Angle : 0.697 12.879 40644 Z= 0.367 Chirality : 0.045 0.218 4547 Planarity : 0.006 0.166 5321 Dihedral : 10.485 125.816 4305 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.06 % 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 0.016 0.001 ARG D 481 TYR 0.059 0.003 TYR E 219 PHE 0.041 0.002 PHE F 776 TRP 0.019 0.002 TRP A 324 HIS 0.006 0.001 HIS A 231 Details of bonding type rmsd covalent geometry : bond 0.00378 (30014) covalent geometry : angle 0.69664 (40638) hydrogen bonds : bond 0.05391 ( 1273) hydrogen bonds : angle 5.71407 ( 3747) metal coordination : bond 0.02060 ( 8) metal coordination : angle 2.36863 ( 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 521 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 519 time to evaluate : 1.104 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: A 207 GLU cc_start: 0.7731 (mp0) cc_final: 0.7370 (tm-30) REVERT: A 377 PHE cc_start: 0.8740 (t80) cc_final: 0.7659 (m-80) REVERT: A 423 ASN cc_start: 0.8214 (m-40) cc_final: 0.7383 (t0) REVERT: A 424 ASP cc_start: 0.9265 (m-30) cc_final: 0.8190 (t0) REVERT: A 428 MET cc_start: 0.8925 (mtm) cc_final: 0.7136 (mtm) REVERT: I 308 GLU cc_start: 0.8049 (tp30) cc_final: 0.7688 (tp30) REVERT: I 342 SER cc_start: 0.8947 (m) cc_final: 0.8190 (p) REVERT: I 381 ARG cc_start: 0.8261 (mmt90) cc_final: 0.7796 (mmt90) REVERT: I 619 ASN cc_start: 0.9074 (t0) cc_final: 0.8797 (t0) REVERT: I 657 ASP cc_start: 0.7487 (p0) cc_final: 0.6507 (t0) REVERT: I 703 ASP cc_start: 0.8288 (t0) cc_final: 0.7837 (t0) REVERT: J 222 ILE cc_start: 0.9007 (tp) cc_final: 0.8525 (mt) REVERT: J 238 LEU cc_start: 0.9395 (tp) cc_final: 0.9136 (mp) REVERT: J 291 MET cc_start: 0.9127 (tpp) cc_final: 0.8849 (mmm) REVERT: J 342 SER cc_start: 0.9045 (m) cc_final: 0.8267 (p) REVERT: J 465 MET cc_start: 0.8450 (tpp) cc_final: 0.7785 (tpp) REVERT: J 474 VAL cc_start: 0.7431 (m) cc_final: 0.7076 (p) REVERT: J 520 PHE cc_start: 0.7212 (m-10) cc_final: 0.6751 (m-80) REVERT: J 758 MET cc_start: 0.8675 (ttm) cc_final: 0.8288 (ttm) REVERT: D 299 GLU cc_start: 0.8589 (pm20) cc_final: 0.8363 (pm20) REVERT: D 348 MET cc_start: 0.9121 (ttm) cc_final: 0.8920 (ttm) REVERT: D 354 ARG cc_start: 0.8147 (mpt-90) cc_final: 0.7919 (mpt-90) REVERT: D 543 MET cc_start: 0.7133 (ptt) cc_final: 0.6827 (ptt) REVERT: D 551 GLU cc_start: 0.8312 (tt0) cc_final: 0.8069 (tm-30) REVERT: D 574 SER cc_start: 0.7588 (p) cc_final: 0.6727 (t) REVERT: D 578 ASP cc_start: 0.8540 (m-30) cc_final: 0.8137 (m-30) REVERT: D 619 ASN cc_start: 0.8100 (t0) cc_final: 0.7882 (t0) REVERT: D 624 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8283 (mt-10) REVERT: D 758 MET cc_start: 0.8567 (ttm) cc_final: 0.8123 (mtp) REVERT: E 235 MET cc_start: 0.8931 (mpp) cc_final: 0.8476 (mmt) REVERT: E 286 ASN cc_start: 0.8796 (t0) cc_final: 0.8473 (t0) REVERT: E 364 ASN cc_start: 0.9301 (p0) cc_final: 0.9007 (p0) REVERT: E 419 THR cc_start: 0.8447 (p) cc_final: 0.8222 (p) REVERT: E 443 MET cc_start: 0.8775 (tpp) cc_final: 0.8563 (tpp) REVERT: E 512 TYR cc_start: 0.8242 (m-10) cc_final: 0.7970 (m-80) REVERT: E 657 ASP cc_start: 0.7992 (p0) cc_final: 0.7292 (t0) REVERT: E 758 MET cc_start: 0.8329 (ttm) cc_final: 0.7935 (ttm) REVERT: F 340 VAL cc_start: 0.9572 (p) cc_final: 0.9280 (m) REVERT: F 369 ILE cc_start: 0.9261 (mt) cc_final: 0.8965 (tp) REVERT: F 505 GLU cc_start: 0.8209 (tt0) cc_final: 0.7906 (tt0) REVERT: F 581 ASP cc_start: 0.8823 (m-30) cc_final: 0.8587 (m-30) outliers start: 2 outliers final: 0 residues processed: 521 average time/residue: 0.1940 time to fit residues: 157.5715 Evaluate side-chains 312 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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: 6.9990 chunk 155 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 295 optimal weight: 0.5980 chunk 129 optimal weight: 10.0000 chunk 353 optimal weight: 9.9990 chunk 133 optimal weight: 0.0060 chunk 169 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 323 optimal weight: 0.4980 chunk 334 optimal weight: 1.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 276 ASN I 367 ASN ** I 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 619 ASN J 333 ASN J 438 GLN J 476 ASN ** 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 F 620 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.076602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.063729 restraints weight = 125698.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.065709 restraints weight = 75894.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.067070 restraints weight = 51951.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.068036 restraints weight = 39067.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.068752 restraints weight = 31364.637| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30022 Z= 0.130 Angle : 0.604 9.418 40644 Z= 0.313 Chirality : 0.044 0.201 4547 Planarity : 0.005 0.074 5321 Dihedral : 10.037 122.765 4305 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -1.32 (0.13), residues: 3732 helix: -0.69 (0.11), residues: 1970 sheet: -0.90 (0.21), residues: 470 loop : -0.86 (0.18), residues: 1292 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 0.024 0.002 PHE J 318 TRP 0.018 0.002 TRP J 568 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00285 (30014) covalent geometry : angle 0.60329 (40638) hydrogen bonds : bond 0.04171 ( 1273) hydrogen bonds : angle 5.14104 ( 3747) metal coordination : bond 0.01829 ( 8) metal coordination : angle 2.18673 ( 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 439 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 1.172 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: A 196 MET cc_start: 0.8908 (tpp) cc_final: 0.8217 (tpp) REVERT: A 207 GLU cc_start: 0.7648 (mp0) cc_final: 0.7298 (tm-30) REVERT: A 258 ASP cc_start: 0.8009 (m-30) cc_final: 0.7690 (m-30) REVERT: A 377 PHE cc_start: 0.8748 (t80) cc_final: 0.7626 (m-80) REVERT: A 423 ASN cc_start: 0.8266 (m-40) cc_final: 0.7401 (t0) REVERT: A 424 ASP cc_start: 0.9252 (m-30) cc_final: 0.8183 (t0) REVERT: A 428 MET cc_start: 0.9056 (mtm) cc_final: 0.7654 (mtm) REVERT: A 549 CYS cc_start: 0.7480 (m) cc_final: 0.6989 (t) REVERT: H 238 LEU cc_start: 0.8865 (tt) cc_final: 0.8658 (mt) REVERT: H 401 THR cc_start: 0.9148 (p) cc_final: 0.7846 (p) REVERT: H 422 TYR cc_start: 0.8468 (m-10) cc_final: 0.8175 (m-80) REVERT: H 567 MET cc_start: 0.6745 (tpt) cc_final: 0.6244 (tpt) REVERT: I 342 SER cc_start: 0.8966 (m) cc_final: 0.8179 (p) REVERT: I 381 ARG cc_start: 0.8369 (mmt90) cc_final: 0.7896 (mmm-85) REVERT: I 619 ASN cc_start: 0.9072 (t0) cc_final: 0.8756 (t0) REVERT: I 657 ASP cc_start: 0.7462 (p0) cc_final: 0.6511 (t0) REVERT: I 703 ASP cc_start: 0.8142 (t0) cc_final: 0.7871 (t0) REVERT: J 222 ILE cc_start: 0.9044 (tp) cc_final: 0.8600 (mt) REVERT: J 291 MET cc_start: 0.8932 (tpp) cc_final: 0.8678 (mmm) REVERT: J 342 SER cc_start: 0.9039 (m) cc_final: 0.8343 (p) REVERT: J 465 MET cc_start: 0.8814 (tpp) cc_final: 0.8384 (tpp) REVERT: J 474 VAL cc_start: 0.7141 (m) cc_final: 0.6893 (p) REVERT: J 578 ASP cc_start: 0.7810 (m-30) cc_final: 0.7599 (m-30) REVERT: J 758 MET cc_start: 0.8724 (ttm) cc_final: 0.8306 (ttm) REVERT: D 443 MET cc_start: 0.9098 (tpp) cc_final: 0.8821 (tpp) REVERT: D 543 MET cc_start: 0.7634 (ptt) cc_final: 0.7412 (ptp) REVERT: D 574 SER cc_start: 0.7779 (p) cc_final: 0.6969 (t) REVERT: D 578 ASP cc_start: 0.8355 (m-30) cc_final: 0.7903 (m-30) REVERT: D 619 ASN cc_start: 0.8018 (t0) cc_final: 0.7567 (t0) REVERT: D 758 MET cc_start: 0.8501 (ttm) cc_final: 0.8110 (mtp) REVERT: E 222 ILE cc_start: 0.9432 (tp) cc_final: 0.9161 (pt) REVERT: E 225 CYS cc_start: 0.8227 (m) cc_final: 0.7982 (m) REVERT: E 286 ASN cc_start: 0.8758 (t0) cc_final: 0.8412 (t0) REVERT: E 297 GLU cc_start: 0.8589 (mp0) cc_final: 0.8275 (mp0) REVERT: E 443 MET cc_start: 0.8924 (tpp) cc_final: 0.8679 (tpp) REVERT: E 512 TYR cc_start: 0.8176 (m-10) cc_final: 0.7866 (m-80) REVERT: E 657 ASP cc_start: 0.7989 (p0) cc_final: 0.7314 (t0) REVERT: E 758 MET cc_start: 0.8462 (ttm) cc_final: 0.8151 (ttm) REVERT: F 369 ILE cc_start: 0.9326 (mt) cc_final: 0.8977 (tp) REVERT: F 505 GLU cc_start: 0.8309 (tt0) cc_final: 0.7967 (tt0) REVERT: F 512 TYR cc_start: 0.8767 (m-80) cc_final: 0.8377 (m-10) REVERT: F 563 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8154 (mt-10) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.1754 time to fit residues: 124.9570 Evaluate side-chains 294 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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: 3.9990 chunk 311 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 180 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 372 optimal weight: 0.0070 chunk 15 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 GLN A 553 GLN H 367 ASN ** H 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 555 ASN H 619 ASN I 438 GLN ** I 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 619 ASN J 276 ASN J 333 ASN ** J 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 ASN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 555 ASN D 619 ASN ** E 467 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 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.074866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.061967 restraints weight = 125392.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.063877 restraints weight = 76515.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.065223 restraints weight = 52878.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.066188 restraints weight = 40029.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.066871 restraints weight = 32301.636| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4819 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= 0.166 Angle : 0.609 7.693 40644 Z= 0.316 Chirality : 0.043 0.200 4547 Planarity : 0.005 0.055 5321 Dihedral : 9.905 123.111 4305 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % 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: -0.33 (0.12), residues: 1953 sheet: -0.74 (0.22), residues: 458 loop : -0.51 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 655 TYR 0.019 0.002 TYR E 219 PHE 0.024 0.002 PHE J 318 TRP 0.031 0.003 TRP A 324 HIS 0.005 0.001 HIS J 753 Details of bonding type rmsd covalent geometry : bond 0.00367 (30014) covalent geometry : angle 0.60885 (40638) hydrogen bonds : bond 0.03842 ( 1273) hydrogen bonds : angle 4.93916 ( 3747) metal coordination : bond 0.01502 ( 8) metal coordination : angle 2.05559 ( 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 372 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.059 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: 0.8863 (tpp) cc_final: 0.8268 (tpp) REVERT: A 207 GLU cc_start: 0.7738 (mp0) cc_final: 0.7389 (tm-30) REVERT: A 258 ASP cc_start: 0.7995 (m-30) cc_final: 0.7674 (m-30) REVERT: A 377 PHE cc_start: 0.8764 (t80) cc_final: 0.7786 (m-80) REVERT: A 423 ASN cc_start: 0.8288 (m-40) cc_final: 0.7523 (t0) REVERT: A 424 ASP cc_start: 0.9287 (m-30) cc_final: 0.8271 (t0) REVERT: A 428 MET cc_start: 0.9204 (mtm) cc_final: 0.7805 (mtm) REVERT: H 260 TYR cc_start: 0.8759 (p90) cc_final: 0.8164 (p90) REVERT: H 443 MET cc_start: 0.8531 (mmm) cc_final: 0.8219 (mmm) REVERT: H 567 MET cc_start: 0.6934 (tpt) cc_final: 0.6061 (ttm) REVERT: I 294 MET cc_start: 0.7827 (mmp) cc_final: 0.7103 (ttt) REVERT: I 337 GLU cc_start: 0.8761 (mp0) cc_final: 0.8309 (mp0) REVERT: I 342 SER cc_start: 0.9022 (m) cc_final: 0.8267 (p) REVERT: I 619 ASN cc_start: 0.9007 (t0) cc_final: 0.8748 (t0) REVERT: I 657 ASP cc_start: 0.7712 (p0) cc_final: 0.6881 (t0) REVERT: I 703 ASP cc_start: 0.8042 (t0) cc_final: 0.7813 (t0) REVERT: J 222 ILE cc_start: 0.8929 (tp) cc_final: 0.8527 (mt) REVERT: J 342 SER cc_start: 0.9187 (m) cc_final: 0.8546 (p) REVERT: J 465 MET cc_start: 0.8745 (tpp) cc_final: 0.8462 (tpp) REVERT: J 474 VAL cc_start: 0.7131 (m) cc_final: 0.6910 (p) REVERT: J 563 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8642 (mp0) REVERT: J 578 ASP cc_start: 0.7668 (m-30) cc_final: 0.7373 (m-30) REVERT: J 590 VAL cc_start: 0.9343 (m) cc_final: 0.9114 (t) REVERT: D 299 GLU cc_start: 0.8599 (pm20) cc_final: 0.8303 (pm20) REVERT: D 443 MET cc_start: 0.9170 (tpp) cc_final: 0.8865 (tpp) REVERT: D 543 MET cc_start: 0.7852 (ptt) cc_final: 0.7509 (ptt) REVERT: D 574 SER cc_start: 0.7692 (p) cc_final: 0.7438 (t) REVERT: D 619 ASN cc_start: 0.7851 (t0) cc_final: 0.7502 (t0) REVERT: D 758 MET cc_start: 0.8594 (ttm) cc_final: 0.8340 (mtp) REVERT: E 222 ILE cc_start: 0.9488 (tp) cc_final: 0.9247 (pt) REVERT: E 225 CYS cc_start: 0.8159 (m) cc_final: 0.7929 (m) REVERT: E 286 ASN cc_start: 0.8843 (t0) cc_final: 0.8492 (t0) REVERT: E 297 GLU cc_start: 0.8692 (mp0) cc_final: 0.8353 (mp0) REVERT: E 402 LYS cc_start: 0.9093 (pttt) cc_final: 0.8879 (pmtt) REVERT: E 443 MET cc_start: 0.8895 (tpp) cc_final: 0.8657 (tpp) REVERT: E 595 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8141 (tp30) REVERT: E 657 ASP cc_start: 0.8253 (p0) cc_final: 0.7515 (t0) REVERT: E 758 MET cc_start: 0.8479 (ttm) cc_final: 0.8138 (ttm) REVERT: F 439 ILE cc_start: 0.9371 (mt) cc_final: 0.8860 (tp) REVERT: F 505 GLU cc_start: 0.8283 (tt0) cc_final: 0.7942 (tt0) REVERT: F 620 GLN cc_start: 0.8986 (tp-100) cc_final: 0.8472 (tm-30) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.1774 time to fit residues: 107.5573 Evaluate side-chains 257 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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: 7.9990 chunk 167 optimal weight: 4.9990 chunk 353 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 363 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 290 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 I 778 GLN ** J 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 555 ASN J 619 ASN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 509 GLN ** E 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 619 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.073743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.060752 restraints weight = 128173.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.062616 restraints weight = 78234.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.063932 restraints weight = 54697.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.064854 restraints weight = 41696.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.065538 restraints weight = 33932.718| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30022 Z= 0.163 Angle : 0.592 8.425 40644 Z= 0.308 Chirality : 0.044 0.208 4547 Planarity : 0.005 0.058 5321 Dihedral : 9.775 123.554 4305 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.03 % Allowed : 2.11 % Favored : 97.86 % 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: -0.50 (0.14), residues: 3732 helix: -0.05 (0.12), residues: 1947 sheet: -0.70 (0.22), residues: 459 loop : -0.35 (0.19), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 642 TYR 0.042 0.002 TYR A 189 PHE 0.025 0.002 PHE J 318 TRP 0.030 0.002 TRP A 324 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00364 (30014) covalent geometry : angle 0.59152 (40638) hydrogen bonds : bond 0.03605 ( 1273) hydrogen bonds : angle 4.81203 ( 3747) metal coordination : bond 0.01524 ( 8) metal coordination : angle 2.31664 ( 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 346 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 345 time to evaluate : 1.207 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: A 167 MET cc_start: 0.8636 (ttm) cc_final: 0.8401 (ttm) REVERT: A 196 MET cc_start: 0.8868 (tpp) cc_final: 0.8372 (tpp) REVERT: A 207 GLU cc_start: 0.7782 (mp0) cc_final: 0.7429 (tm-30) REVERT: A 258 ASP cc_start: 0.7916 (m-30) cc_final: 0.7614 (m-30) REVERT: A 377 PHE cc_start: 0.8804 (t80) cc_final: 0.7869 (m-80) REVERT: A 424 ASP cc_start: 0.9298 (m-30) cc_final: 0.8393 (t0) REVERT: A 428 MET cc_start: 0.9329 (mtm) cc_final: 0.8182 (mtm) REVERT: A 540 MET cc_start: 0.4693 (mtp) cc_final: 0.4430 (mtp) REVERT: H 237 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7645 (tp30) REVERT: H 260 TYR cc_start: 0.8787 (p90) cc_final: 0.8016 (p90) REVERT: H 443 MET cc_start: 0.8556 (mmm) cc_final: 0.8308 (mmm) REVERT: H 567 MET cc_start: 0.6881 (tpt) cc_final: 0.6153 (ttm) REVERT: I 342 SER cc_start: 0.8923 (m) cc_final: 0.8229 (p) REVERT: I 381 ARG cc_start: 0.8347 (mmt90) cc_final: 0.7964 (mmm-85) REVERT: I 481 ARG cc_start: 0.8683 (mpp80) cc_final: 0.8433 (mpp80) REVERT: I 619 ASN cc_start: 0.8974 (t0) cc_final: 0.8668 (t0) REVERT: I 657 ASP cc_start: 0.7669 (p0) cc_final: 0.6565 (t0) REVERT: I 703 ASP cc_start: 0.8101 (t0) cc_final: 0.7843 (t0) REVERT: J 318 PHE cc_start: 0.8883 (t80) cc_final: 0.8567 (t80) REVERT: J 342 SER cc_start: 0.9081 (m) cc_final: 0.8447 (p) REVERT: J 465 MET cc_start: 0.8832 (tpp) cc_final: 0.8481 (tpp) REVERT: J 474 VAL cc_start: 0.7385 (m) cc_final: 0.7181 (p) REVERT: J 563 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8618 (mp0) REVERT: J 578 ASP cc_start: 0.7773 (m-30) cc_final: 0.7435 (m-30) REVERT: J 590 VAL cc_start: 0.9418 (m) cc_final: 0.9150 (t) REVERT: J 628 MET cc_start: 0.7367 (ptp) cc_final: 0.6445 (ptp) REVERT: D 348 MET cc_start: 0.9160 (ttm) cc_final: 0.8866 (ttm) REVERT: D 443 MET cc_start: 0.9127 (tpp) cc_final: 0.8844 (tpp) REVERT: D 543 MET cc_start: 0.8114 (ptt) cc_final: 0.7761 (ptt) REVERT: D 574 SER cc_start: 0.7892 (p) cc_final: 0.7464 (t) REVERT: D 578 ASP cc_start: 0.8434 (m-30) cc_final: 0.8112 (m-30) REVERT: D 625 MET cc_start: 0.8727 (ppp) cc_final: 0.8507 (ppp) REVERT: D 651 CYS cc_start: 0.9082 (m) cc_final: 0.8845 (p) REVERT: D 758 MET cc_start: 0.8626 (ttm) cc_final: 0.8360 (mtp) REVERT: E 222 ILE cc_start: 0.9528 (tp) cc_final: 0.9241 (pt) REVERT: E 225 CYS cc_start: 0.8174 (m) cc_final: 0.7955 (m) REVERT: E 235 MET cc_start: 0.8991 (mpp) cc_final: 0.8432 (mmt) REVERT: E 286 ASN cc_start: 0.8880 (t0) cc_final: 0.8594 (t0) REVERT: E 297 GLU cc_start: 0.8657 (mp0) cc_final: 0.8375 (mp0) REVERT: E 402 LYS cc_start: 0.9140 (pttt) cc_final: 0.8857 (pttt) REVERT: E 443 MET cc_start: 0.8946 (tpp) cc_final: 0.8744 (tpp) REVERT: E 512 TYR cc_start: 0.8263 (m-80) cc_final: 0.7903 (m-80) REVERT: E 595 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8169 (tp30) REVERT: E 657 ASP cc_start: 0.8294 (p0) cc_final: 0.7526 (t0) REVERT: F 304 LYS cc_start: 0.9594 (mmmt) cc_final: 0.9093 (mmtt) REVERT: F 512 TYR cc_start: 0.8937 (m-80) cc_final: 0.8681 (m-10) REVERT: F 620 GLN cc_start: 0.8953 (tp-100) cc_final: 0.8459 (tm-30) REVERT: F 724 ILE cc_start: 0.8917 (pt) cc_final: 0.8689 (tp) outliers start: 1 outliers final: 0 residues processed: 346 average time/residue: 0.1737 time to fit residues: 98.5822 Evaluate side-chains 253 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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: 0.6980 chunk 266 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 373 optimal weight: 9.9990 chunk 314 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 361 optimal weight: 0.8980 chunk 150 optimal weight: 0.0040 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** 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 511 GLN J 619 ASN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 ASN ** E 467 ASN ** 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 276 ASN F 367 ASN ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.074875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.062052 restraints weight = 125458.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.063962 restraints weight = 75965.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.065258 restraints weight = 52673.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066189 restraints weight = 40006.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066864 restraints weight = 32526.900| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30022 Z= 0.113 Angle : 0.567 10.798 40644 Z= 0.290 Chirality : 0.043 0.207 4547 Planarity : 0.004 0.059 5321 Dihedral : 9.596 123.236 4305 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.03 % Allowed : 1.28 % Favored : 98.69 % 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: -0.28 (0.14), residues: 3732 helix: 0.14 (0.12), residues: 1935 sheet: -0.49 (0.22), residues: 453 loop : -0.30 (0.19), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 492 TYR 0.025 0.002 TYR E 422 PHE 0.026 0.002 PHE D 580 TRP 0.023 0.002 TRP A 324 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00255 (30014) covalent geometry : angle 0.56627 (40638) hydrogen bonds : bond 0.03389 ( 1273) hydrogen bonds : angle 4.68756 ( 3747) metal coordination : bond 0.00994 ( 8) metal coordination : angle 2.25604 ( 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 365 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 1.052 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: A 190 MET cc_start: 0.8680 (pmm) cc_final: 0.8261 (pmm) REVERT: A 196 MET cc_start: 0.8901 (tpp) cc_final: 0.8224 (tpp) REVERT: A 258 ASP cc_start: 0.7822 (m-30) cc_final: 0.7494 (m-30) REVERT: A 377 PHE cc_start: 0.8721 (t80) cc_final: 0.7848 (m-10) REVERT: A 424 ASP cc_start: 0.9227 (m-30) cc_final: 0.8465 (t70) REVERT: A 428 MET cc_start: 0.9425 (mtm) cc_final: 0.8850 (mtm) REVERT: H 217 VAL cc_start: 0.8898 (t) cc_final: 0.8629 (t) REVERT: H 260 TYR cc_start: 0.8454 (p90) cc_final: 0.8151 (p90) REVERT: H 436 MET cc_start: 0.8919 (mmm) cc_final: 0.8642 (tpp) REVERT: H 443 MET cc_start: 0.8592 (mmm) cc_final: 0.8344 (mmm) REVERT: I 291 MET cc_start: 0.9537 (mmp) cc_final: 0.9261 (mmt) REVERT: I 337 GLU cc_start: 0.8593 (mp0) cc_final: 0.8250 (mp0) REVERT: I 342 SER cc_start: 0.8864 (m) cc_final: 0.8119 (p) REVERT: I 381 ARG cc_start: 0.8329 (mmt90) cc_final: 0.7979 (mmm-85) REVERT: I 619 ASN cc_start: 0.8893 (t0) cc_final: 0.8654 (t0) REVERT: I 622 LEU cc_start: 0.9215 (mt) cc_final: 0.8969 (mt) REVERT: I 625 MET cc_start: 0.8527 (tmm) cc_final: 0.8302 (tmm) REVERT: I 657 ASP cc_start: 0.7498 (p0) cc_final: 0.6717 (t0) REVERT: I 703 ASP cc_start: 0.8081 (t0) cc_final: 0.7811 (t0) REVERT: J 272 ARG cc_start: 0.8472 (mtt90) cc_final: 0.8002 (mtp180) REVERT: J 342 SER cc_start: 0.9017 (m) cc_final: 0.8320 (p) REVERT: J 465 MET cc_start: 0.8819 (tpp) cc_final: 0.8445 (tpp) REVERT: J 563 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8581 (mp0) REVERT: J 578 ASP cc_start: 0.7662 (m-30) cc_final: 0.7300 (m-30) REVERT: J 625 MET cc_start: 0.8497 (tpp) cc_final: 0.8194 (tpp) REVERT: J 628 MET cc_start: 0.7112 (ptp) cc_final: 0.6473 (ptp) REVERT: D 299 GLU cc_start: 0.8561 (pm20) cc_final: 0.8290 (pm20) REVERT: D 351 MET cc_start: 0.7781 (ptm) cc_final: 0.6737 (ppp) REVERT: D 443 MET cc_start: 0.9065 (tpp) cc_final: 0.8832 (tpp) REVERT: D 543 MET cc_start: 0.8179 (ptt) cc_final: 0.7867 (ptt) REVERT: D 574 SER cc_start: 0.7706 (p) cc_final: 0.6875 (t) REVERT: D 578 ASP cc_start: 0.8209 (m-30) cc_final: 0.7671 (m-30) REVERT: E 225 CYS cc_start: 0.8213 (m) cc_final: 0.8003 (m) REVERT: E 286 ASN cc_start: 0.8915 (t0) cc_final: 0.8533 (t0) REVERT: E 297 GLU cc_start: 0.8690 (mp0) cc_final: 0.8347 (mp0) REVERT: E 512 TYR cc_start: 0.8150 (m-10) cc_final: 0.7777 (m-80) REVERT: E 657 ASP cc_start: 0.8125 (p0) cc_final: 0.7609 (t0) REVERT: F 291 MET cc_start: 0.9368 (mmm) cc_final: 0.8948 (mmm) REVERT: F 304 LYS cc_start: 0.9529 (mmmt) cc_final: 0.9195 (mtpt) REVERT: F 337 GLU cc_start: 0.8379 (tt0) cc_final: 0.7999 (mt-10) REVERT: F 369 ILE cc_start: 0.9417 (mt) cc_final: 0.9106 (tp) REVERT: F 439 ILE cc_start: 0.9345 (mt) cc_final: 0.8828 (tp) REVERT: F 534 TYR cc_start: 0.8782 (p90) cc_final: 0.8536 (p90) REVERT: F 620 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8433 (tm-30) REVERT: F 724 ILE cc_start: 0.8865 (pt) cc_final: 0.8600 (tp) REVERT: F 780 MET cc_start: 0.7366 (pmm) cc_final: 0.6769 (pmm) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.1746 time to fit residues: 103.7364 Evaluate side-chains 261 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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: 3.9990 chunk 267 optimal weight: 1.9990 chunk 275 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 338 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 219 optimal weight: 0.5980 chunk 298 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 83 optimal weight: 0.0470 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN 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 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 437 GLN J 619 ASN D 276 ASN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** 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 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.061966 restraints weight = 127921.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.063756 restraints weight = 78829.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.065028 restraints weight = 55322.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065933 restraints weight = 42298.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.066508 restraints weight = 34399.033| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30022 Z= 0.111 Angle : 0.552 7.334 40644 Z= 0.282 Chirality : 0.043 0.210 4547 Planarity : 0.004 0.063 5321 Dihedral : 9.475 121.205 4305 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 0.31 (0.12), residues: 1929 sheet: -0.47 (0.23), residues: 454 loop : -0.25 (0.19), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 481 TYR 0.020 0.002 TYR F 512 PHE 0.026 0.001 PHE J 318 TRP 0.019 0.002 TRP A 324 HIS 0.003 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00251 (30014) covalent geometry : angle 0.55164 (40638) hydrogen bonds : bond 0.03262 ( 1273) hydrogen bonds : angle 4.58473 ( 3747) metal coordination : bond 0.01232 ( 8) metal coordination : angle 2.27736 ( 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 345 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.162 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: 0.8772 (pmm) cc_final: 0.8456 (pmm) REVERT: A 196 MET cc_start: 0.8778 (tpp) cc_final: 0.8156 (tpp) REVERT: A 258 ASP cc_start: 0.7810 (m-30) cc_final: 0.7499 (m-30) REVERT: A 424 ASP cc_start: 0.9316 (m-30) cc_final: 0.8719 (t70) REVERT: H 217 VAL cc_start: 0.8956 (t) cc_final: 0.8721 (m) REVERT: H 294 MET cc_start: 0.7619 (mpp) cc_final: 0.7404 (mpp) REVERT: H 436 MET cc_start: 0.8922 (mmm) cc_final: 0.8565 (tpp) REVERT: H 443 MET cc_start: 0.8593 (mmm) cc_final: 0.8386 (mmm) REVERT: I 337 GLU cc_start: 0.8628 (mp0) cc_final: 0.8279 (mp0) REVERT: I 342 SER cc_start: 0.8873 (m) cc_final: 0.8154 (p) REVERT: I 657 ASP cc_start: 0.7318 (p0) cc_final: 0.6577 (t0) REVERT: I 703 ASP cc_start: 0.8111 (t0) cc_final: 0.7813 (t0) REVERT: J 235 MET cc_start: 0.8289 (tpt) cc_final: 0.8026 (tpt) REVERT: J 272 ARG cc_start: 0.8595 (mtt90) cc_final: 0.8053 (mtp180) REVERT: J 291 MET cc_start: 0.9210 (mmm) cc_final: 0.8869 (tpp) REVERT: J 342 SER cc_start: 0.9062 (m) cc_final: 0.8390 (p) REVERT: J 465 MET cc_start: 0.8807 (tpp) cc_final: 0.8482 (tpp) REVERT: J 563 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8517 (mp0) REVERT: J 578 ASP cc_start: 0.7650 (m-30) cc_final: 0.7256 (m-30) REVERT: D 543 MET cc_start: 0.8174 (ptt) cc_final: 0.7871 (ptt) REVERT: D 574 SER cc_start: 0.7716 (p) cc_final: 0.6858 (t) REVERT: D 578 ASP cc_start: 0.8198 (m-30) cc_final: 0.7584 (m-30) REVERT: E 286 ASN cc_start: 0.8935 (t0) cc_final: 0.8587 (t0) REVERT: E 297 GLU cc_start: 0.8685 (mp0) cc_final: 0.8316 (mp0) REVERT: E 422 TYR cc_start: 0.8534 (m-80) cc_final: 0.8127 (m-10) REVERT: E 512 TYR cc_start: 0.8051 (m-10) cc_final: 0.7830 (m-80) REVERT: E 657 ASP cc_start: 0.8098 (p0) cc_final: 0.7580 (t0) REVERT: F 291 MET cc_start: 0.9379 (mmm) cc_final: 0.9108 (mmm) REVERT: F 304 LYS cc_start: 0.9489 (mmmt) cc_final: 0.9241 (mtpt) REVERT: F 369 ILE cc_start: 0.9307 (mt) cc_final: 0.9066 (tp) REVERT: F 439 ILE cc_start: 0.9337 (mt) cc_final: 0.8912 (tp) REVERT: F 505 GLU cc_start: 0.8333 (tt0) cc_final: 0.8130 (tt0) REVERT: F 555 ASN cc_start: 0.8339 (m-40) cc_final: 0.8135 (m-40) REVERT: F 620 GLN cc_start: 0.8835 (tp-100) cc_final: 0.8416 (tm-30) REVERT: F 724 ILE cc_start: 0.8876 (pt) cc_final: 0.8596 (tp) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.1700 time to fit residues: 96.8256 Evaluate side-chains 245 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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: 0.9980 chunk 111 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 363 optimal weight: 0.6980 chunk 241 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 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 658 GLN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** 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 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 HIS ** F 511 GLN ** 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 = 0.3439 r_free = 0.3439 target = 0.074445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.061508 restraints weight = 127521.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.063339 restraints weight = 76977.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.064651 restraints weight = 53721.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.065570 restraints weight = 41060.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.066239 restraints weight = 33443.545| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5841 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= 0.113 Angle : 0.562 8.831 40644 Z= 0.286 Chirality : 0.043 0.234 4547 Planarity : 0.004 0.060 5321 Dihedral : 9.363 120.937 4305 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 0.40 (0.12), residues: 1923 sheet: -0.39 (0.23), residues: 458 loop : -0.24 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 338 TYR 0.022 0.002 TYR A 472 PHE 0.018 0.001 PHE D 776 TRP 0.019 0.002 TRP A 346 HIS 0.003 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00259 (30014) covalent geometry : angle 0.56102 (40638) hydrogen bonds : bond 0.03203 ( 1273) hydrogen bonds : angle 4.58051 ( 3747) metal coordination : bond 0.01155 ( 8) metal coordination : angle 2.55827 ( 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 344 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.804 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: 0.8758 (pmm) cc_final: 0.8454 (pmm) REVERT: A 196 MET cc_start: 0.8767 (tpp) cc_final: 0.8099 (tpp) REVERT: A 258 ASP cc_start: 0.7654 (m-30) cc_final: 0.7337 (m-30) REVERT: A 424 ASP cc_start: 0.9340 (m-30) cc_final: 0.8722 (t70) REVERT: H 260 TYR cc_start: 0.8511 (p90) cc_final: 0.8283 (p90) REVERT: H 436 MET cc_start: 0.8931 (mmm) cc_final: 0.8651 (tpp) REVERT: H 443 MET cc_start: 0.8595 (mmm) cc_final: 0.8393 (mmm) REVERT: I 291 MET cc_start: 0.9495 (mmp) cc_final: 0.9283 (mmp) REVERT: I 337 GLU cc_start: 0.8708 (mp0) cc_final: 0.8269 (mp0) REVERT: I 342 SER cc_start: 0.8843 (m) cc_final: 0.8043 (p) REVERT: I 418 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8399 (mm-30) REVERT: I 619 ASN cc_start: 0.9117 (t0) cc_final: 0.8858 (t0) REVERT: I 657 ASP cc_start: 0.7246 (p0) cc_final: 0.6579 (t0) REVERT: I 703 ASP cc_start: 0.8007 (t0) cc_final: 0.7667 (t0) REVERT: J 272 ARG cc_start: 0.8584 (mtt90) cc_final: 0.8047 (mtp180) REVERT: J 342 SER cc_start: 0.9085 (m) cc_final: 0.8366 (p) REVERT: J 465 MET cc_start: 0.8840 (tpp) cc_final: 0.8519 (tpp) REVERT: J 568 TRP cc_start: 0.7571 (t60) cc_final: 0.7371 (t-100) REVERT: J 578 ASP cc_start: 0.7697 (m-30) cc_final: 0.7299 (m-30) REVERT: D 543 MET cc_start: 0.8271 (ptt) cc_final: 0.7957 (ptt) REVERT: D 574 SER cc_start: 0.7587 (p) cc_final: 0.6713 (t) REVERT: D 578 ASP cc_start: 0.8192 (m-30) cc_final: 0.7600 (m-30) REVERT: E 222 ILE cc_start: 0.9493 (tp) cc_final: 0.9289 (tt) REVERT: E 286 ASN cc_start: 0.8931 (t0) cc_final: 0.8577 (t0) REVERT: E 297 GLU cc_start: 0.8717 (mp0) cc_final: 0.8366 (mp0) REVERT: E 317 ILE cc_start: 0.9636 (tp) cc_final: 0.9427 (pt) REVERT: E 422 TYR cc_start: 0.8516 (m-80) cc_final: 0.8123 (m-80) REVERT: E 512 TYR cc_start: 0.8057 (m-10) cc_final: 0.7831 (m-80) REVERT: E 657 ASP cc_start: 0.8038 (p0) cc_final: 0.7499 (t0) REVERT: F 291 MET cc_start: 0.9432 (mmm) cc_final: 0.9113 (mmm) REVERT: F 304 LYS cc_start: 0.9499 (mmmt) cc_final: 0.9238 (mtpt) REVERT: F 369 ILE cc_start: 0.9284 (mt) cc_final: 0.9061 (tp) REVERT: F 439 ILE cc_start: 0.9316 (mt) cc_final: 0.9002 (tp) REVERT: F 505 GLU cc_start: 0.8417 (tt0) cc_final: 0.8214 (tt0) REVERT: F 512 TYR cc_start: 0.8894 (m-80) cc_final: 0.8556 (m-80) REVERT: F 620 GLN cc_start: 0.8774 (tp-100) cc_final: 0.8392 (tm-30) REVERT: F 724 ILE cc_start: 0.8912 (pt) cc_final: 0.8620 (tp) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1739 time to fit residues: 98.4877 Evaluate side-chains 245 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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: 10.0000 chunk 140 optimal weight: 30.0000 chunk 211 optimal weight: 8.9990 chunk 180 optimal weight: 5.9990 chunk 294 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 315 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 354 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 193 HIS ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN 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 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 658 GLN J 677 GLN D 276 ASN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 400 HIS E 467 ASN E 509 GLN E 555 ASN ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN F 400 HIS ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 620 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.071022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.058301 restraints weight = 131597.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.060012 restraints weight = 81161.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.061183 restraints weight = 57429.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.062033 restraints weight = 44646.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.062496 restraints weight = 36913.992| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 30022 Z= 0.265 Angle : 0.713 10.720 40644 Z= 0.366 Chirality : 0.046 0.182 4547 Planarity : 0.005 0.056 5321 Dihedral : 9.681 123.293 4305 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 0.32 (0.12), residues: 1913 sheet: -0.56 (0.23), residues: 443 loop : -0.25 (0.18), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 393 TYR 0.027 0.003 TYR A 472 PHE 0.030 0.003 PHE J 318 TRP 0.026 0.003 TRP J 568 HIS 0.010 0.002 HIS F 420 Details of bonding type rmsd covalent geometry : bond 0.00578 (30014) covalent geometry : angle 0.71181 (40638) hydrogen bonds : bond 0.03902 ( 1273) hydrogen bonds : angle 4.87081 ( 3747) metal coordination : bond 0.01612 ( 8) metal coordination : angle 3.42575 ( 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 304 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.179 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: 0.8883 (pmm) cc_final: 0.8532 (pmm) REVERT: A 196 MET cc_start: 0.8760 (tpp) cc_final: 0.8111 (tpp) REVERT: A 256 MET cc_start: 0.8415 (mmt) cc_final: 0.8092 (mmt) REVERT: A 258 ASP cc_start: 0.7909 (m-30) cc_final: 0.7488 (m-30) REVERT: A 424 ASP cc_start: 0.9323 (m-30) cc_final: 0.8586 (t70) REVERT: A 428 MET cc_start: 0.9316 (mtm) cc_final: 0.8659 (mtm) REVERT: A 460 TYR cc_start: 0.6086 (t80) cc_final: 0.5596 (t80) REVERT: H 294 MET cc_start: 0.7737 (mpp) cc_final: 0.7245 (mpp) REVERT: H 436 MET cc_start: 0.9047 (mmm) cc_final: 0.8516 (tpp) REVERT: H 443 MET cc_start: 0.8640 (mmm) cc_final: 0.8433 (mmm) REVERT: H 581 ASP cc_start: 0.7769 (m-30) cc_final: 0.7521 (m-30) REVERT: I 337 GLU cc_start: 0.8684 (mp0) cc_final: 0.8307 (mp0) REVERT: I 342 SER cc_start: 0.9068 (m) cc_final: 0.8362 (p) REVERT: I 625 MET cc_start: 0.8675 (tmm) cc_final: 0.8407 (tmm) REVERT: I 657 ASP cc_start: 0.7884 (p0) cc_final: 0.6783 (t0) REVERT: I 758 MET cc_start: 0.7623 (mtt) cc_final: 0.6241 (tmm) REVERT: J 272 ARG cc_start: 0.8580 (mtt90) cc_final: 0.8133 (mtp180) REVERT: J 291 MET cc_start: 0.9075 (tpp) cc_final: 0.8728 (tpp) REVERT: J 342 SER cc_start: 0.9222 (m) cc_final: 0.8638 (p) REVERT: J 568 TRP cc_start: 0.7711 (t60) cc_final: 0.7464 (t-100) REVERT: J 578 ASP cc_start: 0.7612 (m-30) cc_final: 0.7190 (m-30) REVERT: J 628 MET cc_start: 0.8033 (ptp) cc_final: 0.7722 (ptp) REVERT: D 574 SER cc_start: 0.7708 (p) cc_final: 0.7286 (t) REVERT: D 635 PHE cc_start: 0.7673 (m-10) cc_final: 0.7385 (m-10) REVERT: E 235 MET cc_start: 0.8930 (mpp) cc_final: 0.8526 (mmt) REVERT: E 286 ASN cc_start: 0.9119 (t0) cc_final: 0.8808 (t0) REVERT: E 297 GLU cc_start: 0.8800 (mp0) cc_final: 0.8443 (mp0) REVERT: E 317 ILE cc_start: 0.9683 (tp) cc_final: 0.9386 (pt) REVERT: E 422 TYR cc_start: 0.8768 (m-80) cc_final: 0.8362 (m-80) REVERT: E 584 ARG cc_start: 0.8378 (ttm110) cc_final: 0.7695 (mtp-110) REVERT: E 657 ASP cc_start: 0.8412 (p0) cc_final: 0.7578 (t0) REVERT: F 291 MET cc_start: 0.9358 (mmm) cc_final: 0.8987 (mmm) REVERT: F 304 LYS cc_start: 0.9605 (mmmt) cc_final: 0.9214 (mtpt) REVERT: F 439 ILE cc_start: 0.9441 (mt) cc_final: 0.9054 (tp) REVERT: F 620 GLN cc_start: 0.9036 (tp40) cc_final: 0.8632 (tm-30) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.1756 time to fit residues: 88.2300 Evaluate side-chains 222 residues out of total 3131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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: 1.9990 chunk 147 optimal weight: 1.9990 chunk 260 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 251 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 183 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 328 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 553 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 555 ASN ** I 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 677 GLN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.072864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.060158 restraints weight = 127755.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.061919 restraints weight = 78832.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.063149 restraints weight = 55624.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.064017 restraints weight = 42782.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.064655 restraints weight = 35040.632| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 30022 Z= 0.124 Angle : 0.609 13.273 40644 Z= 0.308 Chirality : 0.044 0.229 4547 Planarity : 0.005 0.060 5321 Dihedral : 9.403 122.027 4305 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: 0.05 (0.14), residues: 3732 helix: 0.43 (0.12), residues: 1924 sheet: -0.47 (0.23), residues: 473 loop : -0.12 (0.19), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 771 TYR 0.049 0.002 TYR E 512 PHE 0.028 0.002 PHE D 318 TRP 0.057 0.003 TRP A 133 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00284 (30014) covalent geometry : angle 0.60791 (40638) hydrogen bonds : bond 0.03420 ( 1273) hydrogen bonds : angle 4.67429 ( 3747) metal coordination : bond 0.01090 ( 8) metal coordination : angle 3.05616 ( 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 : 1.130 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 190 MET cc_start: 0.8764 (pmm) cc_final: 0.8472 (pmm) REVERT: A 196 MET cc_start: 0.8735 (tpp) cc_final: 0.8062 (tpp) REVERT: A 258 ASP cc_start: 0.7529 (m-30) cc_final: 0.7226 (m-30) REVERT: A 424 ASP cc_start: 0.9295 (m-30) cc_final: 0.8662 (t70) REVERT: A 460 TYR cc_start: 0.5863 (t80) cc_final: 0.5602 (t80) REVERT: H 294 MET cc_start: 0.7625 (mpp) cc_final: 0.7232 (mpp) REVERT: H 436 MET cc_start: 0.8910 (mmm) cc_final: 0.8428 (tpp) REVERT: H 443 MET cc_start: 0.8703 (mmm) cc_final: 0.8405 (mmm) REVERT: H 567 MET cc_start: 0.6975 (mmm) cc_final: 0.6664 (ttm) REVERT: H 577 ARG cc_start: 0.8337 (ttm110) cc_final: 0.7636 (mtp-110) REVERT: H 581 ASP cc_start: 0.7674 (m-30) cc_final: 0.7436 (m-30) REVERT: I 337 GLU cc_start: 0.8715 (mp0) cc_final: 0.8283 (mp0) REVERT: I 342 SER cc_start: 0.8923 (m) cc_final: 0.8120 (p) REVERT: I 619 ASN cc_start: 0.9127 (t0) cc_final: 0.8888 (t0) REVERT: I 625 MET cc_start: 0.8663 (tmm) cc_final: 0.8239 (tmm) REVERT: I 657 ASP cc_start: 0.7737 (p0) cc_final: 0.6827 (t0) REVERT: J 272 ARG cc_start: 0.8473 (mtt90) cc_final: 0.8160 (mtp180) REVERT: J 291 MET cc_start: 0.9074 (tpp) cc_final: 0.8652 (tpp) REVERT: J 294 MET cc_start: 0.7423 (tpp) cc_final: 0.7099 (tpp) REVERT: J 318 PHE cc_start: 0.8386 (t80) cc_final: 0.8174 (t80) REVERT: J 342 SER cc_start: 0.9071 (m) cc_final: 0.8402 (p) REVERT: J 465 MET cc_start: 0.8862 (tpp) cc_final: 0.8174 (tmm) REVERT: J 578 ASP cc_start: 0.7638 (m-30) cc_final: 0.7227 (m-30) REVERT: J 581 ASP cc_start: 0.8191 (m-30) cc_final: 0.7954 (m-30) REVERT: D 235 MET cc_start: 0.8335 (ttm) cc_final: 0.8131 (ttt) REVERT: D 342 SER cc_start: 0.9383 (m) cc_final: 0.8742 (p) REVERT: D 465 MET cc_start: 0.8497 (mmp) cc_final: 0.7796 (mmm) REVERT: D 543 MET cc_start: 0.8669 (pmm) cc_final: 0.8393 (pmm) REVERT: D 574 SER cc_start: 0.7671 (p) cc_final: 0.6934 (t) REVERT: D 578 ASP cc_start: 0.8182 (m-30) cc_final: 0.7639 (m-30) REVERT: E 286 ASN cc_start: 0.9070 (t0) cc_final: 0.8765 (t0) REVERT: E 297 GLU cc_start: 0.8688 (mp0) cc_final: 0.8354 (mp0) REVERT: E 317 ILE cc_start: 0.9646 (tp) cc_final: 0.9369 (pt) REVERT: E 384 ASP cc_start: 0.8423 (t70) cc_final: 0.8092 (p0) REVERT: E 422 TYR cc_start: 0.8660 (m-80) cc_final: 0.8302 (m-80) REVERT: E 512 TYR cc_start: 0.8616 (m-80) cc_final: 0.8365 (m-80) REVERT: E 543 MET cc_start: 0.8089 (ptp) cc_final: 0.7318 (pmm) REVERT: E 657 ASP cc_start: 0.8310 (p0) cc_final: 0.7559 (t0) REVERT: F 291 MET cc_start: 0.9394 (mmm) cc_final: 0.9048 (mmm) REVERT: F 304 LYS cc_start: 0.9577 (mmmt) cc_final: 0.9196 (mtpt) REVERT: F 439 ILE cc_start: 0.9389 (mt) cc_final: 0.9046 (tp) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.1726 time to fit residues: 89.8147 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 : 1.054 ------------------------------------------------------------------------------- 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: 4.9990 chunk 70 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 346 optimal weight: 0.7980 chunk 230 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN ** 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 ** 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 619 ASN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.072436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.059683 restraints weight = 129524.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.061453 restraints weight = 79863.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062700 restraints weight = 56279.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.063551 restraints weight = 43268.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.064182 restraints weight = 35631.421| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30022 Z= 0.143 Angle : 0.610 11.651 40644 Z= 0.310 Chirality : 0.044 0.218 4547 Planarity : 0.005 0.059 5321 Dihedral : 9.354 120.552 4305 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.03 % Allowed : 0.19 % 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: 0.08 (0.14), residues: 3732 helix: 0.43 (0.12), residues: 1924 sheet: -0.43 (0.23), residues: 467 loop : -0.08 (0.19), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 303 TYR 0.038 0.002 TYR E 512 PHE 0.032 0.002 PHE A 465 TRP 0.020 0.002 TRP A 346 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00327 (30014) covalent geometry : angle 0.60894 (40638) hydrogen bonds : bond 0.03387 ( 1273) hydrogen bonds : angle 4.68054 ( 3747) metal coordination : bond 0.01178 ( 8) metal coordination : angle 2.99108 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4372.95 seconds wall clock time: 76 minutes 44.14 seconds (4604.14 seconds total)