Starting phenix.real_space_refine (version: 1.21rc1) on Tue Aug 22 11:28:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6chs_7476/08_2023/6chs_7476_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6chs_7476/08_2023/6chs_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6chs_7476/08_2023/6chs_7476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6chs_7476/08_2023/6chs_7476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6chs_7476/08_2023/6chs_7476_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6chs_7476/08_2023/6chs_7476_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "H ARG 481": "NH1" <-> "NH2" Residue "H ARG 492": "NH1" <-> "NH2" Residue "H ARG 529": "NH1" <-> "NH2" Residue "H ARG 752": "NH1" <-> "NH2" Residue "H ARG 772": "NH1" <-> "NH2" Residue "I ARG 233": "NH1" <-> "NH2" Residue "I ARG 481": "NH1" <-> "NH2" Residue "I ARG 492": "NH1" <-> "NH2" Residue "I ARG 529": "NH1" <-> "NH2" Residue "I ARG 752": "NH1" <-> "NH2" Residue "I ARG 772": "NH1" <-> "NH2" Residue "J ARG 233": "NH1" <-> "NH2" Residue "J ARG 481": "NH1" <-> "NH2" Residue "J ARG 492": "NH1" <-> "NH2" Residue "J ARG 529": "NH1" <-> "NH2" Residue "J ARG 752": "NH1" <-> "NH2" Residue "J ARG 772": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D ARG 481": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 529": "NH1" <-> "NH2" Residue "D ARG 752": "NH1" <-> "NH2" Residue "D ARG 772": "NH1" <-> "NH2" Residue "E ARG 233": "NH1" <-> "NH2" Residue "E ARG 481": "NH1" <-> "NH2" Residue "E ARG 492": "NH1" <-> "NH2" Residue "E ARG 529": "NH1" <-> "NH2" Residue "E ARG 752": "NH1" <-> "NH2" Residue "E ARG 772": "NH1" <-> "NH2" Residue "F ARG 233": "NH1" <-> "NH2" Residue "F ARG 481": "NH1" <-> "NH2" Residue "F ARG 492": "NH1" <-> "NH2" Residue "F ARG 529": "NH1" <-> "NH2" Residue "F ARG 752": "NH1" <-> "NH2" Residue "F ARG 772": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/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: 15.00, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 12.63 Conformation dependent library (CDL) restraints added in 4.4 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... running ksdssp... Secondary structure from input PDB file: 185 helices and 16 sheets defined 46.6% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain 'A' and resid 140 through 146 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 265 through 277 removed outlier: 4.045A pdb=" N ASP A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TRP A 275 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 removed outlier: 3.799A pdb=" N ASN A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 423 through 430 removed outlier: 3.559A pdb=" N VAL A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 489 removed outlier: 3.615A pdb=" N LEU A 489 " --> pdb=" O VAL A 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 486 through 489' Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.936A pdb=" N ALA A 528 " --> pdb=" O SER A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 Processing helix chain 'A' and resid 562 through 568 Processing helix chain 'A' and resid 574 through 580 Processing helix chain 'A' and resid 584 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 226 through 235 Processing helix chain 'H' and resid 237 through 241 Processing helix chain 'H' and resid 243 through 249 Processing helix chain 'H' and resid 267 through 277 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) removed outlier: 4.232A pdb=" N GLU H 277 " --> pdb=" O ALA H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 292 Processing helix chain 'H' and resid 297 through 311 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 322 through 325 No H-bonds generated for 'chain 'H' and resid 322 through 325' Processing helix chain 'H' and resid 335 through 349 removed outlier: 3.659A pdb=" N ASP H 349 " --> pdb=" O LEU H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 374 No H-bonds generated for 'chain 'H' and resid 371 through 374' Processing helix chain 'H' and resid 390 through 401 Processing helix chain 'H' and resid 412 through 418 Processing helix chain 'H' and resid 424 through 445 removed outlier: 4.735A pdb=" N ASP H 444 " --> pdb=" O ARG H 440 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU H 445 " --> pdb=" O GLU H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 455 through 459 Processing helix chain 'H' and resid 465 through 472 Processing helix chain 'H' and resid 500 through 509 Processing helix chain 'H' and resid 511 through 515 Processing helix chain 'H' and resid 518 through 523 Processing helix chain 'H' and resid 541 through 551 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 561 through 569 removed outlier: 3.609A pdb=" N LEU H 565 " --> pdb=" O GLY H 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 574 through 585 removed outlier: 3.691A pdb=" N PHE H 580 " --> pdb=" O ILE H 576 " (cutoff:3.500A) Processing helix chain 'H' and resid 596 through 603 removed outlier: 4.195A pdb=" N ARG H 603 " --> pdb=" O ILE H 599 " (cutoff:3.500A) Processing helix chain 'H' and resid 616 through 626 removed outlier: 3.663A pdb=" N THR H 623 " --> pdb=" O ASN H 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 643 through 645 No H-bonds generated for 'chain 'H' and resid 643 through 645' Processing helix chain 'H' and resid 667 through 680 removed outlier: 3.570A pdb=" N ARG H 679 " --> pdb=" O LYS H 675 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LYS H 680 " --> pdb=" O ALA H 676 " (cutoff:3.500A) Processing helix chain 'H' and resid 689 through 695 Processing helix chain 'H' and resid 701 through 724 removed outlier: 4.760A pdb=" N ALA H 721 " --> pdb=" O LYS H 717 " (cutoff:3.500A) Processing helix chain 'H' and resid 751 through 759 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 767 through 778 Processing helix chain 'I' and resid 226 through 235 Processing helix chain 'I' and resid 237 through 241 Processing helix chain 'I' and resid 243 through 249 Processing helix chain 'I' and resid 267 through 277 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) removed outlier: 4.232A pdb=" N GLU I 277 " --> pdb=" O ALA I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 292 Processing helix chain 'I' and resid 297 through 311 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 322 through 325 No H-bonds generated for 'chain 'I' and resid 322 through 325' Processing helix chain 'I' and resid 335 through 349 removed outlier: 3.659A pdb=" N ASP I 349 " --> pdb=" O LEU I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 371 through 374 No H-bonds generated for 'chain 'I' and resid 371 through 374' Processing helix chain 'I' and resid 390 through 401 Processing helix chain 'I' and resid 412 through 418 Processing helix chain 'I' and resid 424 through 445 removed outlier: 4.734A pdb=" N ASP I 444 " --> pdb=" O ARG I 440 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU I 445 " --> pdb=" O GLU I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 459 Processing helix chain 'I' and resid 465 through 472 Processing helix chain 'I' and resid 475 through 477 No H-bonds generated for 'chain 'I' and resid 475 through 477' Processing helix chain 'I' and resid 500 through 509 Processing helix chain 'I' and resid 511 through 515 Processing helix chain 'I' and resid 518 through 523 Processing helix chain 'I' and resid 541 through 551 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 561 through 569 removed outlier: 3.608A pdb=" N LEU I 565 " --> pdb=" O GLY I 561 " (cutoff:3.500A) Processing helix chain 'I' and resid 574 through 585 removed outlier: 3.691A pdb=" N PHE I 580 " --> pdb=" O ILE I 576 " (cutoff:3.500A) Processing helix chain 'I' and resid 596 through 603 removed outlier: 4.196A pdb=" N ARG I 603 " --> pdb=" O ILE I 599 " (cutoff:3.500A) Processing helix chain 'I' and resid 616 through 626 removed outlier: 3.663A pdb=" N THR I 623 " --> pdb=" O ASN I 619 " (cutoff:3.500A) Processing helix chain 'I' and resid 643 through 645 No H-bonds generated for 'chain 'I' and resid 643 through 645' Processing helix chain 'I' and resid 667 through 680 removed outlier: 3.571A pdb=" N ARG I 679 " --> pdb=" O LYS I 675 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS I 680 " --> pdb=" O ALA I 676 " (cutoff:3.500A) Processing helix chain 'I' and resid 689 through 695 Processing helix chain 'I' and resid 701 through 723 removed outlier: 4.758A pdb=" N ALA I 721 " --> pdb=" O LYS I 717 " (cutoff:3.500A) Processing helix chain 'I' and resid 751 through 759 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 767 through 778 Processing helix chain 'J' and resid 226 through 235 Processing helix chain 'J' and resid 237 through 241 Processing helix chain 'J' and resid 243 through 249 Processing helix chain 'J' and resid 267 through 277 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) removed outlier: 4.231A pdb=" N GLU J 277 " --> pdb=" O ALA J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 292 Processing helix chain 'J' and resid 297 through 311 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 322 through 325 No H-bonds generated for 'chain 'J' and resid 322 through 325' Processing helix chain 'J' and resid 335 through 349 removed outlier: 3.659A pdb=" N ASP J 349 " --> pdb=" O LEU J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 371 through 374 No H-bonds generated for 'chain 'J' and resid 371 through 374' Processing helix chain 'J' and resid 390 through 401 Processing helix chain 'J' and resid 412 through 418 Processing helix chain 'J' and resid 424 through 445 removed outlier: 4.735A pdb=" N ASP J 444 " --> pdb=" O ARG J 440 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU J 445 " --> pdb=" O GLU J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 455 through 459 Processing helix chain 'J' and resid 465 through 471 Processing helix chain 'J' and resid 500 through 509 Processing helix chain 'J' and resid 511 through 515 Processing helix chain 'J' and resid 518 through 523 Processing helix chain 'J' and resid 541 through 551 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 561 through 569 removed outlier: 3.609A pdb=" N LEU J 565 " --> pdb=" O GLY J 561 " (cutoff:3.500A) Processing helix chain 'J' and resid 574 through 585 removed outlier: 3.692A pdb=" N PHE J 580 " --> pdb=" O ILE J 576 " (cutoff:3.500A) Processing helix chain 'J' and resid 596 through 603 removed outlier: 4.195A pdb=" N ARG J 603 " --> pdb=" O ILE J 599 " (cutoff:3.500A) Processing helix chain 'J' and resid 616 through 626 removed outlier: 3.663A pdb=" N THR J 623 " --> pdb=" O ASN J 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 643 through 645 No H-bonds generated for 'chain 'J' and resid 643 through 645' Processing helix chain 'J' and resid 667 through 680 removed outlier: 3.569A pdb=" N ARG J 679 " --> pdb=" O LYS J 675 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LYS J 680 " --> pdb=" O ALA J 676 " (cutoff:3.500A) Processing helix chain 'J' and resid 689 through 695 Processing helix chain 'J' and resid 701 through 724 removed outlier: 4.759A pdb=" N ALA J 721 " --> pdb=" O LYS J 717 " (cutoff:3.500A) Processing helix chain 'J' and resid 751 through 759 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 767 through 778 Processing helix chain 'D' and resid 226 through 235 Processing helix chain 'D' and resid 237 through 241 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 267 through 277 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) removed outlier: 4.232A pdb=" N GLU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 292 Processing helix chain 'D' and resid 297 through 311 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 322 through 325 No H-bonds generated for 'chain 'D' and resid 322 through 325' Processing helix chain 'D' and resid 335 through 349 removed outlier: 3.660A pdb=" N ASP D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 374 No H-bonds generated for 'chain 'D' and resid 371 through 374' Processing helix chain 'D' and resid 390 through 401 Processing helix chain 'D' and resid 412 through 418 Processing helix chain 'D' and resid 424 through 445 removed outlier: 4.734A pdb=" N ASP D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 459 Processing helix chain 'D' and resid 465 through 471 Processing helix chain 'D' and resid 500 through 509 Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 518 through 523 Processing helix chain 'D' and resid 541 through 551 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 561 through 569 removed outlier: 3.608A pdb=" N LEU D 565 " --> pdb=" O GLY D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 585 removed outlier: 3.692A pdb=" N PHE D 580 " --> pdb=" O ILE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 603 removed outlier: 4.195A pdb=" N ARG D 603 " --> pdb=" O ILE D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 626 removed outlier: 3.663A pdb=" N THR D 623 " --> pdb=" O ASN D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 645 No H-bonds generated for 'chain 'D' and resid 643 through 645' Processing helix chain 'D' and resid 667 through 680 removed outlier: 3.570A pdb=" N ARG D 679 " --> pdb=" O LYS D 675 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LYS D 680 " --> pdb=" O ALA D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 695 Processing helix chain 'D' and resid 701 through 724 removed outlier: 4.760A pdb=" N ALA D 721 " --> pdb=" O LYS D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 759 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 767 through 778 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 237 through 241 Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 267 through 277 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) removed outlier: 4.231A pdb=" N GLU E 277 " --> pdb=" O ALA E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 292 Processing helix chain 'E' and resid 297 through 311 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 322 through 325 No H-bonds generated for 'chain 'E' and resid 322 through 325' Processing helix chain 'E' and resid 335 through 349 removed outlier: 3.659A pdb=" N ASP E 349 " --> pdb=" O LEU E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 374 No H-bonds generated for 'chain 'E' and resid 371 through 374' Processing helix chain 'E' and resid 390 through 401 Processing helix chain 'E' and resid 412 through 418 Processing helix chain 'E' and resid 424 through 445 removed outlier: 4.734A pdb=" N ASP E 444 " --> pdb=" O ARG E 440 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU E 445 " --> pdb=" O GLU E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 459 Processing helix chain 'E' and resid 465 through 473 removed outlier: 3.980A pdb=" N GLY E 473 " --> pdb=" O ARG E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 509 Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'E' and resid 518 through 523 Processing helix chain 'E' and resid 541 through 551 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 561 through 569 removed outlier: 3.609A pdb=" N LEU E 565 " --> pdb=" O GLY E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 585 removed outlier: 3.691A pdb=" N PHE E 580 " --> pdb=" O ILE E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 596 through 603 removed outlier: 4.195A pdb=" N ARG E 603 " --> pdb=" O ILE E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 616 through 626 removed outlier: 3.662A pdb=" N THR E 623 " --> pdb=" O ASN E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 645 No H-bonds generated for 'chain 'E' and resid 643 through 645' Processing helix chain 'E' and resid 667 through 680 removed outlier: 3.570A pdb=" N ARG E 679 " --> pdb=" O LYS E 675 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS E 680 " --> pdb=" O ALA E 676 " (cutoff:3.500A) Processing helix chain 'E' and resid 689 through 695 Processing helix chain 'E' and resid 701 through 724 removed outlier: 4.760A pdb=" N ALA E 721 " --> pdb=" O LYS E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 751 through 759 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 767 through 778 Processing helix chain 'F' and resid 226 through 235 Processing helix chain 'F' and resid 237 through 241 Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 267 through 277 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) removed outlier: 4.231A pdb=" N GLU F 277 " --> pdb=" O ALA F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 292 Processing helix chain 'F' and resid 297 through 311 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 322 through 325 No H-bonds generated for 'chain 'F' and resid 322 through 325' Processing helix chain 'F' and resid 335 through 349 removed outlier: 3.659A pdb=" N ASP F 349 " --> pdb=" O LEU F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 374 No H-bonds generated for 'chain 'F' and resid 371 through 374' Processing helix chain 'F' and resid 390 through 401 Processing helix chain 'F' and resid 412 through 418 Processing helix chain 'F' and resid 424 through 445 removed outlier: 4.733A pdb=" N ASP F 444 " --> pdb=" O ARG F 440 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU F 445 " --> pdb=" O GLU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 459 Processing helix chain 'F' and resid 465 through 471 Processing helix chain 'F' and resid 500 through 509 Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 518 through 523 Processing helix chain 'F' and resid 541 through 551 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 561 through 569 removed outlier: 3.608A pdb=" N LEU F 565 " --> pdb=" O GLY F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 585 removed outlier: 3.692A pdb=" N PHE F 580 " --> pdb=" O ILE F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 596 through 603 removed outlier: 4.195A pdb=" N ARG F 603 " --> pdb=" O ILE F 599 " (cutoff:3.500A) Processing helix chain 'F' and resid 616 through 626 removed outlier: 3.663A pdb=" N THR F 623 " --> pdb=" O ASN F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 643 through 645 No H-bonds generated for 'chain 'F' and resid 643 through 645' Processing helix chain 'F' and resid 667 through 680 removed outlier: 3.570A pdb=" N ARG F 679 " --> pdb=" O LYS F 675 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS F 680 " --> pdb=" O ALA F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 689 through 695 Processing helix chain 'F' and resid 701 through 724 removed outlier: 4.760A pdb=" N ALA F 721 " --> pdb=" O LYS F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 759 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 767 through 778 Processing sheet with id= A, first strand: chain 'A' and resid 259 through 262 removed outlier: 7.024A pdb=" N THR A 494 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE A 262 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLY A 496 " --> pdb=" O PHE A 262 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 312 through 314 Processing sheet with id= C, first strand: chain 'A' and resid 414 through 419 removed outlier: 6.544A pdb=" N LEU A 286 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL A 344 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY A 284 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ARG A 289 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL A 304 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A 291 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ALA A 302 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 293 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE A 300 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 434 through 436 Processing sheet with id= E, first strand: chain 'H' and resid 381 through 385 removed outlier: 8.249A pdb=" N VAL H 257 " --> pdb=" O VAL H 357 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL H 359 " --> pdb=" O VAL H 257 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU H 259 " --> pdb=" O VAL H 359 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA H 361 " --> pdb=" O LEU H 259 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N GLY H 261 " --> pdb=" O ALA H 361 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR H 363 " --> pdb=" O GLY H 261 " (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) removed outlier: 6.681A pdb=" N PHE H 281 " --> pdb=" O ILE H 316 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N PHE H 318 " --> pdb=" O PHE H 281 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE H 283 " --> pdb=" O PHE H 318 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ASP H 320 " --> pdb=" O PHE H 283 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE H 285 " --> pdb=" O ASP H 320 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 658 through 662 removed outlier: 6.695A pdb=" N VAL H 636 " --> pdb=" O VAL H 531 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N PHE H 533 " --> pdb=" O VAL H 636 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY H 638 " --> pdb=" O PHE H 533 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLY H 535 " --> pdb=" O GLY H 638 " (cutoff:3.500A) 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) Processing sheet with id= G, first strand: chain 'I' and resid 381 through 385 removed outlier: 8.249A pdb=" N VAL I 257 " --> pdb=" O VAL I 357 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL I 359 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU I 259 " --> pdb=" O VAL I 359 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA I 361 " --> pdb=" O LEU I 259 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY I 261 " --> pdb=" O ALA I 361 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR I 363 " --> pdb=" O GLY I 261 " (cutoff:3.500A) 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) removed outlier: 6.682A pdb=" N PHE I 281 " --> pdb=" O ILE I 316 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N PHE I 318 " --> pdb=" O PHE I 281 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE I 283 " --> pdb=" O PHE I 318 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ASP I 320 " --> pdb=" O PHE I 283 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE I 285 " --> pdb=" O ASP I 320 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'I' and resid 658 through 662 removed outlier: 6.695A pdb=" N VAL I 636 " --> pdb=" O VAL I 531 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N PHE I 533 " --> pdb=" O VAL I 636 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY I 638 " --> pdb=" O PHE I 533 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N GLY I 535 " --> pdb=" O GLY I 638 " (cutoff:3.500A) 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) Processing sheet with id= I, first strand: chain 'J' and resid 381 through 385 removed outlier: 8.249A pdb=" N VAL J 257 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL J 359 " --> pdb=" O VAL J 257 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU J 259 " --> pdb=" O VAL J 359 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA J 361 " --> pdb=" O LEU J 259 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N GLY J 261 " --> pdb=" O ALA J 361 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR J 363 " --> pdb=" O GLY J 261 " (cutoff:3.500A) 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) removed outlier: 6.681A pdb=" N PHE J 281 " --> pdb=" O ILE J 316 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE J 318 " --> pdb=" O PHE J 281 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE J 283 " --> pdb=" O PHE J 318 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASP J 320 " --> pdb=" O PHE J 283 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE J 285 " --> pdb=" O ASP J 320 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 658 through 662 removed outlier: 6.695A pdb=" N VAL J 636 " --> pdb=" O VAL J 531 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N PHE J 533 " --> pdb=" O VAL J 636 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY J 638 " --> pdb=" O PHE J 533 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLY J 535 " --> pdb=" O GLY J 638 " (cutoff:3.500A) 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) Processing sheet with id= K, first strand: chain 'D' and resid 381 through 385 removed outlier: 8.249A pdb=" N VAL D 257 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL D 359 " --> pdb=" O VAL D 257 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU D 259 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA D 361 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY D 261 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR D 363 " --> pdb=" O GLY D 261 " (cutoff:3.500A) 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) removed outlier: 6.682A pdb=" N PHE D 281 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N PHE D 318 " --> pdb=" O PHE D 281 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE D 283 " --> pdb=" O PHE D 318 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASP D 320 " --> pdb=" O PHE D 283 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE D 285 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 658 through 662 removed outlier: 6.694A pdb=" N VAL D 636 " --> pdb=" O VAL D 531 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N PHE D 533 " --> pdb=" O VAL D 636 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY D 638 " --> pdb=" O PHE D 533 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLY D 535 " --> pdb=" O GLY D 638 " (cutoff:3.500A) 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) Processing sheet with id= M, first strand: chain 'E' and resid 381 through 385 removed outlier: 8.249A pdb=" N VAL E 257 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL E 359 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU E 259 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA E 361 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY E 261 " --> pdb=" O ALA E 361 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR E 363 " --> pdb=" O GLY E 261 " (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) removed outlier: 6.753A pdb=" N PHE E 281 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE E 318 " --> pdb=" O PHE E 281 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE E 283 " --> pdb=" O PHE E 318 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ASP E 320 " --> pdb=" O PHE E 283 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE E 285 " --> pdb=" O ASP E 320 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 658 through 662 removed outlier: 6.695A pdb=" N VAL E 636 " --> pdb=" O VAL E 531 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N PHE E 533 " --> pdb=" O VAL E 636 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY E 638 " --> pdb=" O PHE E 533 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLY E 535 " --> pdb=" O GLY E 638 " (cutoff:3.500A) 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) Processing sheet with id= O, first strand: chain 'F' and resid 381 through 385 removed outlier: 8.249A pdb=" N VAL F 257 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL F 359 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU F 259 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA F 361 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY F 261 " --> pdb=" O ALA F 361 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR F 363 " --> pdb=" O GLY F 261 " (cutoff:3.500A) 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) removed outlier: 6.681A pdb=" N PHE F 281 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N PHE F 318 " --> pdb=" O PHE F 281 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE F 283 " --> pdb=" O PHE F 318 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASP F 320 " --> pdb=" O PHE F 283 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE F 285 " --> pdb=" O ASP F 320 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 658 through 662 removed outlier: 6.695A pdb=" N VAL F 636 " --> pdb=" O VAL F 531 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N PHE F 533 " --> pdb=" O VAL F 636 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY F 638 " --> pdb=" O PHE F 533 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLY F 535 " --> pdb=" O GLY F 638 " (cutoff:3.500A) 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) 1012 hydrogen bonds defined for protein. 2967 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: 9.71 Time building geometry restraints manager: 13.42 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: 97.99 - 105.23: 860 105.23 - 112.47: 15476 112.47 - 119.72: 10269 119.72 - 126.96: 13729 126.96 - 134.20: 304 Bond angle restraints: 40638 Sorted by residual: angle pdb=" N TRP A 234 " pdb=" CA TRP A 234 " pdb=" C TRP A 234 " ideal model delta sigma weight residual 112.35 100.73 11.62 1.34e+00 5.57e-01 7.52e+01 angle pdb=" C ASN D 476 " pdb=" N PRO D 477 " pdb=" CA PRO D 477 " ideal model delta sigma weight residual 119.84 130.41 -10.57 1.25e+00 6.40e-01 7.15e+01 angle pdb=" C ASN F 476 " pdb=" N PRO F 477 " pdb=" CA PRO F 477 " ideal model delta sigma weight residual 119.84 130.37 -10.53 1.25e+00 6.40e-01 7.10e+01 angle pdb=" CA TRP A 234 " pdb=" C TRP A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 120.81 115.49 5.32 8.60e-01 1.35e+00 3.83e+01 angle pdb=" N ASN F 476 " pdb=" CA ASN F 476 " pdb=" C ASN F 476 " ideal model delta sigma weight residual 112.75 104.96 7.79 1.36e+00 5.41e-01 3.28e+01 ... (remaining 40633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.46: 18118 26.46 - 52.92: 290 52.92 - 79.38: 23 79.38 - 105.84: 2 105.84 - 132.30: 11 Dihedral angle restraints: 18444 sinusoidal: 7638 harmonic: 10806 Sorted by residual: dihedral pdb=" CA LEU A 321 " pdb=" C LEU A 321 " pdb=" N ASN A 322 " pdb=" CA ASN A 322 " ideal model delta harmonic sigma weight residual 180.00 151.37 28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA PRO J 477 " pdb=" C PRO J 477 " pdb=" N SER J 478 " pdb=" CA SER J 478 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA PRO D 477 " pdb=" C PRO D 477 " pdb=" N SER D 478 " pdb=" CA SER D 478 " ideal model delta harmonic sigma weight residual 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 18441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4407 0.123 - 0.246: 128 0.246 - 0.368: 3 0.368 - 0.491: 4 0.491 - 0.614: 5 Chirality restraints: 4547 Sorted by residual: chirality pdb=" PB AGS J 901 " pdb=" O2B AGS J 901 " pdb=" O3A AGS J 901 " pdb=" O3B AGS J 901 " both_signs ideal model delta sigma weight residual True 3.18 -2.57 0.61 2.00e-01 2.50e+01 9.42e+00 chirality pdb=" PA AGS E 901 " pdb=" O2A AGS E 901 " pdb=" O3A AGS E 901 " pdb=" O5' AGS E 901 " both_signs ideal model delta sigma weight residual True 3.18 2.59 0.59 2.00e-01 2.50e+01 8.81e+00 chirality pdb=" PA AGS J 901 " pdb=" O2A AGS J 901 " pdb=" O3A AGS J 901 " pdb=" O5' AGS J 901 " both_signs ideal model delta sigma weight residual True 3.18 2.60 0.59 2.00e-01 2.50e+01 8.61e+00 ... (remaining 4544 not shown) Planarity restraints: 5321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 324 " -0.011 2.00e-02 2.50e+03 1.86e-02 8.62e+00 pdb=" CG TRP A 324 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 324 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 324 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP A 324 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 324 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 324 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 324 " -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 324 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP A 324 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 568 " 0.008 2.00e-02 2.50e+03 1.46e-02 5.32e+00 pdb=" CG TRP J 568 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP J 568 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP J 568 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 568 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP J 568 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 568 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 568 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 568 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP J 568 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 303 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C ARG H 303 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG H 303 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS H 304 " -0.013 2.00e-02 2.50e+03 ... (remaining 5318 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 491 2.61 - 3.18: 27084 3.18 - 3.76: 48775 3.76 - 4.33: 69625 4.33 - 4.90: 104216 Nonbonded interactions: 250191 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 250186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 6.310 Check model and map are aligned: 0.430 Set scattering table: 0.280 Process input model: 78.130 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.190 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.060 ------------------------------------------------------------------------------- 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 30014 Z= 0.479 Angle : 0.941 11.620 40638 Z= 0.532 Chirality : 0.057 0.614 4547 Planarity : 0.007 0.055 5321 Dihedral : 10.672 132.300 11456 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.36 % Favored : 94.43 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 fitting. rotamer outliers: 9 poor density : 844 time to evaluate : 3.343 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 outliers start: 9 outliers final: 2 residues processed: 851 average time/residue: 0.4997 time to fit residues: 627.6870 Evaluate side-chains 378 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 376 time to evaluate : 3.399 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2998 time to fit residues: 5.6335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 0.0770 chunk 284 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 294 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 341 optimal weight: 3.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 HIS ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 HIS H 333 ASN H 509 GLN I 301 ASN ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 619 ASN J 333 ASN J 476 ASN ** J 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN D 620 GLN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 619 ASN ** E 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 GLN ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 30014 Z= 0.235 Angle : 0.653 12.961 40638 Z= 0.341 Chirality : 0.044 0.204 4547 Planarity : 0.006 0.115 5321 Dihedral : 9.519 130.122 4173 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3732 helix: -1.43 (0.11), residues: 1869 sheet: -0.43 (0.23), residues: 434 loop : -1.19 (0.17), residues: 1429 *********************** 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 487 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 485 time to evaluate : 3.508 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 outliers start: 2 outliers final: 0 residues processed: 487 average time/residue: 0.4576 time to fit residues: 343.6059 Evaluate side-chains 285 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 3.261 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 284 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 342 optimal weight: 8.9990 chunk 369 optimal weight: 10.0000 chunk 304 optimal weight: 9.9990 chunk 339 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 619 ASN H 709 GLN I 301 ASN I 619 ASN ** I 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 276 ASN ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 509 GLN ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 619 ASN ** E 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 30014 Z= 0.246 Angle : 0.608 10.996 40638 Z= 0.313 Chirality : 0.043 0.197 4547 Planarity : 0.005 0.052 5321 Dihedral : 9.233 127.619 4173 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3732 helix: -0.75 (0.11), residues: 1930 sheet: -0.26 (0.23), residues: 428 loop : -0.85 (0.18), residues: 1374 *********************** 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 379 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 3.608 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 outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.4203 time to fit residues: 253.8861 Evaluate side-chains 249 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 3.383 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 8.9990 chunk 257 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 163 optimal weight: 7.9990 chunk 229 optimal weight: 0.0970 chunk 343 optimal weight: 0.7980 chunk 363 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 chunk 325 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 GLN H 619 ASN I 276 ASN I 367 ASN I 438 GLN I 619 ASN I 778 GLN ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN J 619 ASN D 276 ASN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 619 ASN E 709 GLN F 333 ASN ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 30014 Z= 0.162 Angle : 0.548 8.670 40638 Z= 0.282 Chirality : 0.042 0.214 4547 Planarity : 0.004 0.057 5321 Dihedral : 8.996 127.797 4173 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3732 helix: -0.46 (0.12), residues: 1913 sheet: -0.11 (0.23), residues: 437 loop : -0.63 (0.18), residues: 1382 *********************** 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 378 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 376 time to evaluate : 3.362 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 outliers start: 2 outliers final: 0 residues processed: 378 average time/residue: 0.4039 time to fit residues: 247.9697 Evaluate side-chains 244 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 3.445 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 251 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 326 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN A 312 GLN ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 709 GLN ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 GLN ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 30014 Z= 0.340 Angle : 0.683 15.171 40638 Z= 0.348 Chirality : 0.044 0.195 4547 Planarity : 0.005 0.066 5321 Dihedral : 9.056 126.306 4173 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3732 helix: -0.23 (0.12), residues: 1920 sheet: -0.21 (0.24), residues: 434 loop : -0.38 (0.19), residues: 1378 *********************** 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 307 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 306 time to evaluate : 3.345 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 outliers start: 1 outliers final: 0 residues processed: 307 average time/residue: 0.3991 time to fit residues: 198.7946 Evaluate side-chains 212 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.338 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 363 optimal weight: 3.9990 chunk 301 optimal weight: 1.9990 chunk 168 optimal weight: 0.3980 chunk 30 optimal weight: 8.9990 chunk 120 optimal weight: 0.0010 chunk 190 optimal weight: 0.7980 overall best weight: 0.8390 ------------------------------------------------------------------------------- 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 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 619 ASN I 619 ASN ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 619 ASN ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 30014 Z= 0.167 Angle : 0.552 8.540 40638 Z= 0.282 Chirality : 0.043 0.219 4547 Planarity : 0.004 0.059 5321 Dihedral : 8.878 130.119 4173 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3732 helix: -0.01 (0.12), residues: 1920 sheet: -0.03 (0.24), residues: 428 loop : -0.36 (0.18), residues: 1384 *********************** 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 333 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 3.632 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 outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.3998 time to fit residues: 217.2084 Evaluate side-chains 222 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 3.381 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 207 optimal weight: 0.0010 chunk 265 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 chunk 306 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 362 optimal weight: 0.0970 chunk 226 optimal weight: 0.4980 chunk 220 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- 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 276 ASN ** H 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 619 ASN J 403 ASN J 437 GLN ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 619 ASN ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 ASN ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 30014 Z= 0.166 Angle : 0.538 7.949 40638 Z= 0.274 Chirality : 0.042 0.175 4547 Planarity : 0.004 0.059 5321 Dihedral : 8.707 129.006 4173 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3732 helix: 0.13 (0.12), residues: 1918 sheet: 0.13 (0.24), residues: 423 loop : -0.29 (0.18), residues: 1391 *********************** 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 334 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 3.164 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 outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.3918 time to fit residues: 215.2289 Evaluate side-chains 227 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 3.455 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 230 optimal weight: 7.9990 chunk 246 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 284 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 GLN ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 30014 Z= 0.209 Angle : 0.564 7.797 40638 Z= 0.287 Chirality : 0.043 0.249 4547 Planarity : 0.004 0.056 5321 Dihedral : 8.672 128.830 4173 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.14), residues: 3732 helix: 0.31 (0.12), residues: 1905 sheet: 0.19 (0.24), residues: 423 loop : -0.29 (0.18), residues: 1404 *********************** 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 316 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 315 time to evaluate : 3.634 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 outliers start: 1 outliers final: 1 residues processed: 316 average time/residue: 0.3980 time to fit residues: 206.9953 Evaluate side-chains 219 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 3.386 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3256 time to fit residues: 5.4328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 1.9990 chunk 347 optimal weight: 2.9990 chunk 316 optimal weight: 0.9980 chunk 337 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 265 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 305 optimal weight: 30.0000 chunk 319 optimal weight: 0.9990 chunk 336 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 400 HIS ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 30014 Z= 0.170 Angle : 0.544 7.637 40638 Z= 0.275 Chirality : 0.042 0.176 4547 Planarity : 0.004 0.058 5321 Dihedral : 8.571 130.071 4173 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3732 helix: 0.32 (0.12), residues: 1905 sheet: 0.12 (0.24), residues: 453 loop : -0.21 (0.18), residues: 1374 *********************** 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 317 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 3.528 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 outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.4126 time to fit residues: 214.6017 Evaluate side-chains 216 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 3.409 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 3.9990 chunk 357 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 374 optimal weight: 5.9990 chunk 344 optimal weight: 4.9990 chunk 298 optimal weight: 0.0000 chunk 30 optimal weight: 9.9990 chunk 230 optimal weight: 9.9990 chunk 182 optimal weight: 5.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- 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 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 619 ASN ** E 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.6226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 30014 Z= 0.204 Angle : 0.576 11.750 40638 Z= 0.289 Chirality : 0.043 0.174 4547 Planarity : 0.004 0.056 5321 Dihedral : 8.551 129.053 4173 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3732 helix: 0.35 (0.12), residues: 1905 sheet: 0.07 (0.24), residues: 462 loop : -0.15 (0.18), residues: 1365 ********************** 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 305 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 3.421 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 outliers start: 1 outliers final: 0 residues processed: 304 average time/residue: 0.3919 time to fit residues: 197.4498 Evaluate side-chains 215 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.360 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 0.4980 chunk 317 optimal weight: 0.0570 chunk 91 optimal weight: 6.9990 chunk 275 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 298 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 chunk 306 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- 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 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 619 ASN ** D 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 467 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 = 0.3401 r_free = 0.3401 target = 0.072838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.060370 restraints weight = 129420.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.062113 restraints weight = 79538.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.063339 restraints weight = 55922.887| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 30014 Z= 0.181 Angle : 0.564 9.214 40638 Z= 0.281 Chirality : 0.042 0.198 4547 Planarity : 0.004 0.055 5321 Dihedral : 8.475 129.982 4173 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3732 helix: 0.34 (0.12), residues: 1917 sheet: 0.10 (0.24), residues: 462 loop : -0.10 (0.18), residues: 1353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5536.34 seconds wall clock time: 102 minutes 4.39 seconds (6124.39 seconds total)