Starting phenix.real_space_refine on Thu Feb 22 05:57:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6chs_7476/02_2024/6chs_7476_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6chs_7476/02_2024/6chs_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_7476/02_2024/6chs_7476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6chs_7476/02_2024/6chs_7476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6chs_7476/02_2024/6chs_7476_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6chs_7476/02_2024/6chs_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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 15.91, per 1000 atoms: 0.54 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: 13.39 Conformation dependent library (CDL) restraints added in 6.4 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: 6.42 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: 10.42 Time building geometry restraints manager: 13.03 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: 18197 26.46 - 52.92: 334 52.92 - 79.38: 32 79.38 - 105.84: 2 105.84 - 132.30: 11 Dihedral angle restraints: 18576 sinusoidal: 7770 harmonic: 10806 Sorted by residual: dihedral pdb=" CA LEU A 321 " pdb=" C LEU A 321 " pdb=" N ASN A 322 " pdb=" CA ASN A 322 " ideal model delta harmonic sigma weight residual 180.00 151.37 28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA PRO J 477 " pdb=" C PRO J 477 " pdb=" N SER J 478 " pdb=" CA SER J 478 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA PRO D 477 " pdb=" C PRO D 477 " pdb=" N SER D 478 " pdb=" CA SER D 478 " ideal model delta harmonic sigma weight residual 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 18573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4407 0.123 - 0.246: 128 0.246 - 0.368: 3 0.368 - 0.491: 4 0.491 - 0.614: 5 Chirality restraints: 4547 Sorted by residual: chirality pdb=" PB AGS J 901 " pdb=" O2B AGS J 901 " pdb=" O3A AGS J 901 " pdb=" O3B AGS J 901 " both_signs ideal model delta sigma weight residual True 3.18 -2.57 0.61 2.00e-01 2.50e+01 9.42e+00 chirality pdb=" PA AGS E 901 " pdb=" O2A AGS E 901 " pdb=" O3A AGS E 901 " pdb=" O5' AGS E 901 " both_signs ideal model delta sigma weight residual True 3.18 2.59 0.59 2.00e-01 2.50e+01 8.81e+00 chirality pdb=" PA AGS J 901 " pdb=" O2A AGS J 901 " pdb=" O3A AGS J 901 " pdb=" O5' AGS J 901 " both_signs ideal model delta sigma weight residual True 3.18 2.60 0.59 2.00e-01 2.50e+01 8.61e+00 ... (remaining 4544 not shown) Planarity restraints: 5321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 324 " -0.011 2.00e-02 2.50e+03 1.86e-02 8.62e+00 pdb=" CG TRP A 324 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 324 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 324 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP A 324 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 324 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 324 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 324 " -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 324 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP A 324 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 568 " 0.008 2.00e-02 2.50e+03 1.46e-02 5.32e+00 pdb=" CG TRP J 568 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP J 568 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP J 568 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 568 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP J 568 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 568 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 568 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 568 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP J 568 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 303 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.26e+00 pdb=" C ARG H 303 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG H 303 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS H 304 " -0.013 2.00e-02 2.50e+03 ... (remaining 5318 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.040 Extract box with map and model: 5.180 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 84.670 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.180 ------------------------------------------------------------------------------- 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 : 11.076 132.300 11588 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.36 % Favored : 94.43 % Rotamer: Outliers : 0.29 % Allowed : 1.12 % Favored : 98.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.006 TRP A 324 HIS 0.016 0.004 HIS A 364 PHE 0.025 0.004 PHE J 520 TYR 0.033 0.004 TYR D 219 ARG 0.014 0.001 ARG A 270 *********************** 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 : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8667 (ttm) cc_final: 0.8366 (tpp) REVERT: A 207 GLU cc_start: 0.7476 (mp0) cc_final: 0.7212 (tm-30) REVERT: A 377 PHE cc_start: 0.7763 (t80) cc_final: 0.7539 (m-80) REVERT: A 423 ASN cc_start: 0.8232 (m-40) cc_final: 0.7740 (t0) REVERT: A 424 ASP cc_start: 0.8966 (m-30) cc_final: 0.8459 (m-30) REVERT: A 428 MET cc_start: 0.8686 (mtm) cc_final: 0.8266 (mtt) REVERT: A 574 LEU cc_start: 0.7253 (tp) cc_final: 0.6871 (pp) REVERT: H 260 TYR cc_start: 0.7994 (p90) cc_final: 0.7744 (p90) REVERT: I 217 VAL cc_start: 0.8860 (t) cc_final: 0.8622 (t) REVERT: I 291 MET cc_start: 0.9021 (mmm) cc_final: 0.8409 (mmp) REVERT: I 598 SER cc_start: 0.8156 (m) cc_final: 0.6814 (t) REVERT: I 657 ASP cc_start: 0.6564 (p0) cc_final: 0.5653 (t0) REVERT: J 222 ILE cc_start: 0.8444 (tp) cc_final: 0.8117 (mt) REVERT: J 323 ASP cc_start: 0.8261 (p0) cc_final: 0.8031 (p0) REVERT: J 342 SER cc_start: 0.8087 (m) cc_final: 0.7799 (p) REVERT: J 357 VAL cc_start: 0.9132 (t) cc_final: 0.8932 (p) REVERT: J 485 VAL cc_start: 0.7642 (p) cc_final: 0.7300 (m) REVERT: D 597 ASP cc_start: 0.7101 (p0) cc_final: 0.6813 (t70) REVERT: D 617 VAL cc_start: 0.8425 (t) cc_final: 0.8208 (t) REVERT: E 219 TYR cc_start: 0.6897 (m-80) cc_final: 0.5286 (m-10) REVERT: E 544 LEU cc_start: 0.7851 (mt) cc_final: 0.7579 (tp) REVERT: E 657 ASP cc_start: 0.7113 (p0) cc_final: 0.6650 (t0) REVERT: F 397 LEU cc_start: 0.8638 (mt) cc_final: 0.8377 (mm) REVERT: F 576 ILE cc_start: 0.7348 (mm) cc_final: 0.7094 (mm) outliers start: 9 outliers final: 2 residues processed: 851 average time/residue: 0.4956 time to fit residues: 624.6135 Evaluate side-chains 394 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 392 time to evaluate : 3.588 ------------------------------------------------------------------------------- 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: 2.9990 chunk 114 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 341 optimal weight: 0.5980 overall best weight: 1.1344 ------------------------------------------------------------------------------- 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: 0.7015 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 30014 Z= 0.233 Angle : 0.646 12.911 40638 Z= 0.339 Chirality : 0.044 0.212 4547 Planarity : 0.006 0.118 5321 Dihedral : 10.458 134.065 4305 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.06 % Allowed : 2.75 % Favored : 97.19 % 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: -1.97 (0.13), residues: 3732 helix: -1.41 (0.11), residues: 1851 sheet: -0.33 (0.23), residues: 426 loop : -1.22 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 324 HIS 0.006 0.001 HIS A 231 PHE 0.022 0.002 PHE J 468 TYR 0.041 0.002 TYR E 219 ARG 0.013 0.001 ARG F 655 *********************** 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 501 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 499 time to evaluate : 3.584 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: A 377 PHE cc_start: 0.8068 (t80) cc_final: 0.7473 (m-80) REVERT: A 423 ASN cc_start: 0.8561 (m-40) cc_final: 0.7821 (t0) REVERT: A 424 ASP cc_start: 0.8887 (m-30) cc_final: 0.8097 (t0) REVERT: A 428 MET cc_start: 0.8384 (mtm) cc_final: 0.6599 (mtm) REVERT: A 574 LEU cc_start: 0.7102 (tp) cc_final: 0.6879 (pp) REVERT: H 236 VAL cc_start: 0.7934 (t) cc_final: 0.7608 (t) REVERT: H 401 THR cc_start: 0.8036 (p) cc_final: 0.7693 (p) REVERT: H 674 LEU cc_start: 0.8042 (mt) cc_final: 0.7801 (mm) REVERT: I 342 SER cc_start: 0.8428 (m) cc_final: 0.8003 (p) REVERT: I 598 SER cc_start: 0.8168 (m) cc_final: 0.7898 (t) REVERT: I 657 ASP cc_start: 0.6150 (p0) cc_final: 0.5551 (t0) REVERT: J 222 ILE cc_start: 0.8511 (tp) cc_final: 0.7878 (mt) REVERT: J 229 LEU cc_start: 0.7110 (mm) cc_final: 0.6793 (mm) REVERT: J 291 MET cc_start: 0.8427 (tpp) cc_final: 0.8167 (mmm) REVERT: J 342 SER cc_start: 0.8430 (m) cc_final: 0.7851 (p) REVERT: J 357 VAL cc_start: 0.9145 (t) cc_final: 0.8860 (p) REVERT: D 291 MET cc_start: 0.8709 (mmp) cc_final: 0.8487 (mmp) REVERT: D 543 MET cc_start: 0.5732 (ptt) cc_final: 0.5465 (ptt) REVERT: D 574 SER cc_start: 0.7168 (p) cc_final: 0.6674 (t) REVERT: E 364 ASN cc_start: 0.8395 (p0) cc_final: 0.8067 (p0) REVERT: E 543 MET cc_start: 0.6868 (mpp) cc_final: 0.5928 (mtm) outliers start: 2 outliers final: 0 residues processed: 501 average time/residue: 0.4515 time to fit residues: 352.0851 Evaluate side-chains 292 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 3.655 ------------------------------------------------------------------------------- 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: 0.8980 chunk 105 optimal weight: 0.8980 chunk 284 optimal weight: 0.9990 chunk 232 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 342 optimal weight: 0.8980 chunk 369 optimal weight: 9.9990 chunk 304 optimal weight: 9.9990 chunk 339 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 274 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 619 ASN H 709 GLN I 301 ASN I 367 ASN I 619 ASN I 778 GLN ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 509 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30014 Z= 0.189 Angle : 0.576 10.267 40638 Z= 0.296 Chirality : 0.043 0.206 4547 Planarity : 0.005 0.049 5321 Dihedral : 10.073 133.478 4305 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: -1.37 (0.13), residues: 3732 helix: -0.83 (0.11), residues: 1900 sheet: -0.16 (0.23), residues: 420 loop : -1.02 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 346 HIS 0.006 0.001 HIS J 420 PHE 0.021 0.001 PHE J 318 TYR 0.024 0.002 TYR E 219 ARG 0.005 0.000 ARG D 679 *********************** 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 417 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8849 (tpp) cc_final: 0.8441 (tpp) REVERT: A 377 PHE cc_start: 0.8047 (t80) cc_final: 0.7450 (m-80) REVERT: A 423 ASN cc_start: 0.8456 (m-40) cc_final: 0.7651 (t0) REVERT: A 424 ASP cc_start: 0.8956 (m-30) cc_final: 0.8185 (t0) REVERT: A 428 MET cc_start: 0.8367 (mtm) cc_final: 0.7095 (mtm) REVERT: A 574 LEU cc_start: 0.7164 (tp) cc_final: 0.6574 (pt) REVERT: A 591 MET cc_start: 0.7187 (mmm) cc_final: 0.6937 (mpp) REVERT: H 260 TYR cc_start: 0.8299 (p90) cc_final: 0.7618 (p90) REVERT: H 674 LEU cc_start: 0.8035 (mt) cc_final: 0.7776 (mm) REVERT: H 758 MET cc_start: 0.6717 (tmm) cc_final: 0.6515 (tmm) REVERT: I 342 SER cc_start: 0.8478 (m) cc_final: 0.7855 (p) REVERT: I 651 CYS cc_start: 0.5932 (t) cc_final: 0.5715 (t) REVERT: I 657 ASP cc_start: 0.6166 (p0) cc_final: 0.5596 (t0) REVERT: J 222 ILE cc_start: 0.8378 (tp) cc_final: 0.8048 (mt) REVERT: J 342 SER cc_start: 0.8510 (m) cc_final: 0.8053 (p) REVERT: J 357 VAL cc_start: 0.9094 (t) cc_final: 0.8827 (p) REVERT: J 465 MET cc_start: 0.7312 (tpp) cc_final: 0.6735 (tpp) REVERT: J 590 VAL cc_start: 0.8790 (m) cc_final: 0.8522 (t) REVERT: D 436 MET cc_start: 0.6900 (tpp) cc_final: 0.6611 (tpp) REVERT: D 543 MET cc_start: 0.6033 (ptt) cc_final: 0.5766 (ptt) REVERT: E 297 GLU cc_start: 0.6550 (mp0) cc_final: 0.5981 (mp0) REVERT: E 364 ASN cc_start: 0.8634 (p0) cc_final: 0.8377 (p0) REVERT: F 439 ILE cc_start: 0.9383 (mt) cc_final: 0.8918 (tp) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.4017 time to fit residues: 269.6661 Evaluate side-chains 277 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 3.360 ------------------------------------------------------------------------------- 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: 1.9990 chunk 257 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 37 optimal weight: 0.0060 chunk 163 optimal weight: 4.9990 chunk 229 optimal weight: 0.8980 chunk 343 optimal weight: 3.9990 chunk 363 optimal weight: 8.9990 chunk 179 optimal weight: 0.0570 chunk 325 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 619 ASN I 276 ASN I 438 GLN I 619 ASN J 276 ASN ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 509 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 ASN ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30014 Z= 0.177 Angle : 0.548 7.033 40638 Z= 0.282 Chirality : 0.042 0.215 4547 Planarity : 0.004 0.055 5321 Dihedral : 9.876 133.574 4305 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: -0.94 (0.14), residues: 3732 helix: -0.51 (0.12), residues: 1930 sheet: -0.10 (0.23), residues: 435 loop : -0.72 (0.18), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 568 HIS 0.004 0.001 HIS A 162 PHE 0.023 0.001 PHE E 776 TYR 0.028 0.002 TYR I 260 ARG 0.008 0.000 ARG D 255 *********************** 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 382 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8763 (tpp) cc_final: 0.8385 (tpp) REVERT: A 377 PHE cc_start: 0.8154 (t80) cc_final: 0.7506 (m-80) REVERT: A 424 ASP cc_start: 0.9030 (m-30) cc_final: 0.8328 (t0) REVERT: A 428 MET cc_start: 0.8810 (mtm) cc_final: 0.7547 (mtm) REVERT: A 567 ARG cc_start: 0.8516 (tpp80) cc_final: 0.8037 (tpt90) REVERT: H 236 VAL cc_start: 0.7968 (t) cc_final: 0.7667 (t) REVERT: H 260 TYR cc_start: 0.8288 (p90) cc_final: 0.8065 (p90) REVERT: H 674 LEU cc_start: 0.8052 (mt) cc_final: 0.7829 (mm) REVERT: I 342 SER cc_start: 0.8279 (m) cc_final: 0.7912 (p) REVERT: I 406 LEU cc_start: 0.8195 (mt) cc_final: 0.7897 (mp) REVERT: I 657 ASP cc_start: 0.6188 (p0) cc_final: 0.5607 (t0) REVERT: J 222 ILE cc_start: 0.8469 (tp) cc_final: 0.8107 (mt) REVERT: J 342 SER cc_start: 0.8618 (m) cc_final: 0.8197 (p) REVERT: J 357 VAL cc_start: 0.9094 (t) cc_final: 0.8832 (p) REVERT: J 465 MET cc_start: 0.7279 (tpp) cc_final: 0.6845 (tpp) REVERT: J 590 VAL cc_start: 0.8803 (m) cc_final: 0.8576 (t) REVERT: D 543 MET cc_start: 0.6166 (ptt) cc_final: 0.5785 (ptt) REVERT: D 574 SER cc_start: 0.7278 (t) cc_final: 0.7000 (t) REVERT: E 297 GLU cc_start: 0.6758 (mp0) cc_final: 0.6074 (mp0) REVERT: E 364 ASN cc_start: 0.8651 (p0) cc_final: 0.8366 (p0) REVERT: F 436 MET cc_start: 0.6340 (mmm) cc_final: 0.5912 (tpp) REVERT: F 439 ILE cc_start: 0.9363 (mt) cc_final: 0.8864 (tp) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.3865 time to fit residues: 241.6224 Evaluate side-chains 263 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 3.370 ------------------------------------------------------------------------------- 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: 3.9990 chunk 206 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 310 optimal weight: 6.9990 chunk 251 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 326 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 619 ASN ** 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 ** F 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 555 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 30014 Z= 0.271 Angle : 0.619 10.043 40638 Z= 0.316 Chirality : 0.043 0.209 4547 Planarity : 0.005 0.056 5321 Dihedral : 9.850 131.275 4305 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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: -0.51 (0.14), residues: 3732 helix: -0.22 (0.12), residues: 1927 sheet: -0.03 (0.24), residues: 422 loop : -0.36 (0.18), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 568 HIS 0.006 0.001 HIS A 259 PHE 0.028 0.002 PHE J 318 TYR 0.021 0.002 TYR E 219 ARG 0.014 0.001 ARG J 772 *********************** 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 343 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8837 (tpp) cc_final: 0.8402 (tpp) REVERT: A 258 ASP cc_start: 0.6570 (m-30) cc_final: 0.6294 (m-30) REVERT: A 377 PHE cc_start: 0.8234 (t80) cc_final: 0.7918 (m-80) REVERT: A 424 ASP cc_start: 0.8990 (m-30) cc_final: 0.8539 (t0) REVERT: A 428 MET cc_start: 0.8776 (mtm) cc_final: 0.8218 (mtp) REVERT: H 674 LEU cc_start: 0.8097 (mt) cc_final: 0.7822 (mm) REVERT: I 342 SER cc_start: 0.8518 (m) cc_final: 0.8063 (p) REVERT: I 657 ASP cc_start: 0.6444 (p0) cc_final: 0.5941 (t0) REVERT: I 758 MET cc_start: 0.6984 (mtt) cc_final: 0.5613 (tmm) REVERT: J 222 ILE cc_start: 0.8392 (tp) cc_final: 0.8101 (mt) REVERT: J 318 PHE cc_start: 0.7568 (t80) cc_final: 0.7326 (t80) REVERT: J 342 SER cc_start: 0.8702 (m) cc_final: 0.8384 (p) REVERT: J 357 VAL cc_start: 0.9208 (t) cc_final: 0.8924 (p) REVERT: J 590 VAL cc_start: 0.8843 (m) cc_final: 0.8560 (t) REVERT: D 348 MET cc_start: 0.7410 (ttt) cc_final: 0.7191 (ttm) REVERT: D 543 MET cc_start: 0.6776 (ptt) cc_final: 0.6449 (ptt) REVERT: E 297 GLU cc_start: 0.6852 (mp0) cc_final: 0.6390 (mp0) REVERT: E 360 MET cc_start: 0.6713 (mtp) cc_final: 0.6507 (mtp) REVERT: E 780 MET cc_start: 0.3333 (tpt) cc_final: 0.1845 (tpp) REVERT: F 436 MET cc_start: 0.6266 (mmm) cc_final: 0.5984 (tpp) REVERT: F 439 ILE cc_start: 0.9346 (mt) cc_final: 0.8665 (tp) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.3971 time to fit residues: 221.4430 Evaluate side-chains 228 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 3.316 ------------------------------------------------------------------------------- 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: 0.9990 chunk 327 optimal weight: 4.9990 chunk 71 optimal weight: 0.0980 chunk 213 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 363 optimal weight: 8.9990 chunk 301 optimal weight: 0.1980 chunk 168 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 619 ASN D 619 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30014 Z= 0.155 Angle : 0.538 8.797 40638 Z= 0.273 Chirality : 0.042 0.193 4547 Planarity : 0.004 0.056 5321 Dihedral : 9.597 132.632 4305 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.03 % Allowed : 1.15 % Favored : 98.82 % 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: -0.32 (0.14), residues: 3732 helix: -0.02 (0.12), residues: 1920 sheet: 0.07 (0.24), residues: 437 loop : -0.34 (0.18), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 346 HIS 0.006 0.001 HIS A 162 PHE 0.022 0.001 PHE D 569 TYR 0.017 0.002 TYR E 512 ARG 0.015 0.000 ARG J 616 *********************** 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 373 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 372 time to evaluate : 3.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8762 (tpp) cc_final: 0.8405 (tpp) REVERT: A 258 ASP cc_start: 0.6509 (m-30) cc_final: 0.6301 (m-30) REVERT: A 421 MET cc_start: 0.8233 (mpp) cc_final: 0.7774 (mpp) REVERT: A 424 ASP cc_start: 0.9012 (m-30) cc_final: 0.8493 (t70) REVERT: A 428 MET cc_start: 0.8752 (mtm) cc_final: 0.8084 (mtp) REVERT: H 217 VAL cc_start: 0.9098 (t) cc_final: 0.8756 (p) REVERT: H 758 MET cc_start: 0.6389 (tmm) cc_final: 0.6087 (tmm) REVERT: I 342 SER cc_start: 0.8387 (m) cc_final: 0.7906 (p) REVERT: I 651 CYS cc_start: 0.5944 (t) cc_final: 0.5726 (t) REVERT: I 657 ASP cc_start: 0.6137 (p0) cc_final: 0.5474 (t0) REVERT: J 342 SER cc_start: 0.8707 (m) cc_final: 0.8299 (p) REVERT: J 357 VAL cc_start: 0.9157 (t) cc_final: 0.8893 (p) REVERT: D 543 MET cc_start: 0.6711 (ptt) cc_final: 0.6400 (ptt) REVERT: E 297 GLU cc_start: 0.6663 (mp0) cc_final: 0.6268 (mp0) REVERT: F 436 MET cc_start: 0.6210 (mmm) cc_final: 0.5934 (tpp) REVERT: F 439 ILE cc_start: 0.9288 (mt) cc_final: 0.8706 (tp) outliers start: 1 outliers final: 0 residues processed: 372 average time/residue: 0.3945 time to fit residues: 240.5962 Evaluate side-chains 249 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 3.375 ------------------------------------------------------------------------------- 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: 6.9990 chunk 41 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 265 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 306 optimal weight: 0.7980 chunk 203 optimal weight: 6.9990 chunk 362 optimal weight: 0.9990 chunk 226 optimal weight: 0.0970 chunk 220 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 J 437 GLN ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN D 276 ASN ** E 467 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30014 Z= 0.162 Angle : 0.537 10.085 40638 Z= 0.270 Chirality : 0.042 0.180 4547 Planarity : 0.004 0.058 5321 Dihedral : 9.467 132.641 4305 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.03 % Allowed : 0.89 % Favored : 99.07 % 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: -0.18 (0.14), residues: 3732 helix: 0.10 (0.12), residues: 1917 sheet: 0.20 (0.24), residues: 428 loop : -0.30 (0.18), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 133 HIS 0.004 0.001 HIS A 162 PHE 0.025 0.001 PHE J 318 TYR 0.031 0.002 TYR A 460 ARG 0.008 0.000 ARG A 459 *********************** 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 354 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 353 time to evaluate : 3.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8815 (tpp) cc_final: 0.8520 (tpp) REVERT: A 258 ASP cc_start: 0.6524 (m-30) cc_final: 0.6304 (m-30) REVERT: A 421 MET cc_start: 0.8210 (mpp) cc_final: 0.7678 (mpp) REVERT: A 424 ASP cc_start: 0.9062 (m-30) cc_final: 0.8630 (t70) REVERT: H 217 VAL cc_start: 0.9099 (t) cc_final: 0.8772 (m) REVERT: I 270 MET cc_start: 0.6752 (mtt) cc_final: 0.6501 (mtt) REVERT: I 342 SER cc_start: 0.8432 (m) cc_final: 0.7865 (p) REVERT: I 657 ASP cc_start: 0.6232 (p0) cc_final: 0.5552 (t0) REVERT: J 342 SER cc_start: 0.8734 (m) cc_final: 0.8341 (p) REVERT: J 357 VAL cc_start: 0.9166 (t) cc_final: 0.8898 (p) REVERT: D 543 MET cc_start: 0.6769 (ptt) cc_final: 0.6466 (ptt) REVERT: E 297 GLU cc_start: 0.6708 (mp0) cc_final: 0.6215 (mp0) REVERT: E 360 MET cc_start: 0.6727 (mtp) cc_final: 0.6482 (mtp) REVERT: F 270 MET cc_start: 0.8122 (mmm) cc_final: 0.7763 (mmm) REVERT: F 436 MET cc_start: 0.6247 (mmm) cc_final: 0.5915 (tpp) REVERT: F 439 ILE cc_start: 0.9330 (mt) cc_final: 0.8787 (tp) outliers start: 1 outliers final: 0 residues processed: 354 average time/residue: 0.3692 time to fit residues: 216.7864 Evaluate side-chains 238 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 3.290 ------------------------------------------------------------------------------- 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: 3.9990 chunk 144 optimal weight: 6.9990 chunk 216 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 230 optimal weight: 0.5980 chunk 246 optimal weight: 0.7980 chunk 179 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 284 optimal weight: 0.7980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 504 GLN ** D 367 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30014 Z= 0.219 Angle : 0.574 10.701 40638 Z= 0.290 Chirality : 0.042 0.172 4547 Planarity : 0.004 0.059 5321 Dihedral : 9.479 130.960 4305 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: -0.09 (0.14), residues: 3732 helix: 0.20 (0.12), residues: 1911 sheet: 0.20 (0.25), residues: 418 loop : -0.29 (0.18), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 346 HIS 0.004 0.001 HIS A 193 PHE 0.029 0.002 PHE J 318 TYR 0.031 0.002 TYR A 460 ARG 0.012 0.000 ARG I 481 *********************** 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 329 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8835 (tpp) cc_final: 0.8440 (tpp) REVERT: A 421 MET cc_start: 0.8231 (mpp) cc_final: 0.7712 (mpp) REVERT: A 424 ASP cc_start: 0.9027 (m-30) cc_final: 0.8490 (t70) REVERT: A 428 MET cc_start: 0.8600 (mtm) cc_final: 0.7762 (mtt) REVERT: A 461 ILE cc_start: 0.8512 (mm) cc_final: 0.8264 (pt) REVERT: H 217 VAL cc_start: 0.9343 (t) cc_final: 0.9058 (m) REVERT: I 270 MET cc_start: 0.6813 (mtt) cc_final: 0.6482 (mtt) REVERT: I 342 SER cc_start: 0.8528 (m) cc_final: 0.7986 (p) REVERT: I 651 CYS cc_start: 0.6019 (t) cc_final: 0.5789 (t) REVERT: J 318 PHE cc_start: 0.7774 (t80) cc_final: 0.7470 (t80) REVERT: J 342 SER cc_start: 0.8739 (m) cc_final: 0.8418 (p) REVERT: J 357 VAL cc_start: 0.9199 (t) cc_final: 0.8945 (p) REVERT: D 543 MET cc_start: 0.7029 (ptt) cc_final: 0.6694 (ptt) REVERT: E 297 GLU cc_start: 0.6802 (mp0) cc_final: 0.6431 (mp0) REVERT: E 360 MET cc_start: 0.6813 (mtp) cc_final: 0.6608 (mtp) REVERT: E 780 MET cc_start: 0.4431 (mmm) cc_final: 0.3265 (tpt) REVERT: F 270 MET cc_start: 0.8101 (mmm) cc_final: 0.7744 (mmm) REVERT: F 439 ILE cc_start: 0.9274 (mt) cc_final: 0.9026 (tp) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.3697 time to fit residues: 201.6234 Evaluate side-chains 232 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 3.370 ------------------------------------------------------------------------------- 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: 8.9990 chunk 347 optimal weight: 0.0770 chunk 316 optimal weight: 0.8980 chunk 337 optimal weight: 3.9990 chunk 203 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 305 optimal weight: 50.0000 chunk 319 optimal weight: 3.9990 chunk 336 optimal weight: 0.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** J 619 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30014 Z= 0.173 Angle : 0.554 9.812 40638 Z= 0.279 Chirality : 0.042 0.198 4547 Planarity : 0.004 0.071 5321 Dihedral : 9.392 131.702 4305 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.03 % Allowed : 0.45 % Favored : 99.52 % 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: -0.04 (0.14), residues: 3732 helix: 0.26 (0.12), residues: 1899 sheet: 0.10 (0.24), residues: 448 loop : -0.26 (0.18), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 346 HIS 0.004 0.001 HIS A 162 PHE 0.025 0.001 PHE J 318 TYR 0.023 0.002 TYR A 460 ARG 0.010 0.000 ARG I 616 *********************** 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 327 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 326 time to evaluate : 3.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 MET cc_start: 0.8788 (tpp) cc_final: 0.8454 (tpp) REVERT: A 421 MET cc_start: 0.8230 (mpp) cc_final: 0.7686 (mpp) REVERT: A 424 ASP cc_start: 0.9038 (m-30) cc_final: 0.8432 (t70) REVERT: A 428 MET cc_start: 0.8588 (mtm) cc_final: 0.7854 (mtt) REVERT: H 217 VAL cc_start: 0.9348 (t) cc_final: 0.9014 (m) REVERT: I 270 MET cc_start: 0.6805 (mtt) cc_final: 0.6497 (mtt) REVERT: I 342 SER cc_start: 0.8471 (m) cc_final: 0.7874 (p) REVERT: J 342 SER cc_start: 0.8762 (m) cc_final: 0.8343 (p) REVERT: J 357 VAL cc_start: 0.9145 (t) cc_final: 0.8909 (p) REVERT: D 543 MET cc_start: 0.7277 (ptt) cc_final: 0.6986 (ptt) REVERT: E 297 GLU cc_start: 0.6753 (mp0) cc_final: 0.6366 (mp0) REVERT: E 360 MET cc_start: 0.6785 (mtp) cc_final: 0.6544 (mtp) REVERT: E 780 MET cc_start: 0.4353 (mmm) cc_final: 0.3240 (tpt) REVERT: F 439 ILE cc_start: 0.9277 (mt) cc_final: 0.8993 (tp) REVERT: F 625 MET cc_start: 0.6750 (ttp) cc_final: 0.6509 (ttp) outliers start: 1 outliers final: 0 residues processed: 326 average time/residue: 0.3845 time to fit residues: 207.4554 Evaluate side-chains 231 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 3.297 ------------------------------------------------------------------------------- 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: 0.8980 chunk 357 optimal weight: 0.8980 chunk 217 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 374 optimal weight: 5.9990 chunk 344 optimal weight: 1.9990 chunk 298 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 230 optimal weight: 0.4980 chunk 182 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 403 ASN ** J 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 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 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7171 moved from start: 0.5967 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= 0.165 Angle : 0.556 10.681 40638 Z= 0.277 Chirality : 0.042 0.181 4547 Planarity : 0.004 0.059 5321 Dihedral : 9.282 132.054 4305 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.01 (0.14), residues: 3732 helix: 0.26 (0.12), residues: 1911 sheet: 0.16 (0.24), residues: 448 loop : -0.17 (0.18), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 346 HIS 0.005 0.001 HIS I 420 PHE 0.026 0.001 PHE J 318 TYR 0.036 0.002 TYR E 512 ARG 0.009 0.000 ARG I 481 ********************** 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 339 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 3.202 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: A 196 MET cc_start: 0.8737 (tpp) cc_final: 0.8372 (tpp) REVERT: A 421 MET cc_start: 0.8261 (mpp) cc_final: 0.7759 (mpp) REVERT: A 424 ASP cc_start: 0.9114 (m-30) cc_final: 0.8769 (p0) REVERT: H 217 VAL cc_start: 0.9328 (t) cc_final: 0.9003 (m) REVERT: I 270 MET cc_start: 0.6766 (mtt) cc_final: 0.6554 (mtt) REVERT: I 342 SER cc_start: 0.8422 (m) cc_final: 0.7814 (p) REVERT: J 342 SER cc_start: 0.8755 (m) cc_final: 0.8306 (p) REVERT: J 357 VAL cc_start: 0.9158 (t) cc_final: 0.8899 (p) REVERT: J 399 ILE cc_start: 0.7773 (tp) cc_final: 0.7527 (tp) REVERT: D 543 MET cc_start: 0.7270 (ptt) cc_final: 0.6928 (ptt) REVERT: D 567 MET cc_start: 0.6388 (ppp) cc_final: 0.5726 (ptm) REVERT: E 297 GLU cc_start: 0.6776 (mp0) cc_final: 0.6438 (mp0) REVERT: E 625 MET cc_start: 0.6693 (mtp) cc_final: 0.6294 (mtp) REVERT: E 780 MET cc_start: 0.4084 (mmm) cc_final: 0.3004 (tpt) REVERT: F 439 ILE cc_start: 0.9257 (mt) cc_final: 0.8684 (tp) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.3796 time to fit residues: 213.3047 Evaluate side-chains 230 residues out of total 3131 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 3.334 ------------------------------------------------------------------------------- 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: 2.9990 chunk 317 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 275 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 298 optimal weight: 0.0270 chunk 125 optimal weight: 10.0000 chunk 306 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 677 GLN ** E 467 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.073695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.061082 restraints weight = 129652.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.062800 restraints weight = 81071.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.064021 restraints weight = 57670.999| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.6157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30014 Z= 0.200 Angle : 0.565 9.686 40638 Z= 0.283 Chirality : 0.042 0.170 4547 Planarity : 0.004 0.058 5321 Dihedral : 9.218 130.396 4305 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.07 (0.14), residues: 3732 helix: 0.35 (0.12), residues: 1869 sheet: -0.00 (0.24), residues: 456 loop : -0.14 (0.18), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 346 HIS 0.004 0.001 HIS A 162 PHE 0.031 0.002 PHE J 318 TYR 0.036 0.002 TYR A 472 ARG 0.004 0.000 ARG I 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5764.55 seconds wall clock time: 106 minutes 14.50 seconds (6374.50 seconds total)