Starting phenix.real_space_refine on Wed Sep 25 10:26:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxv_30007/09_2024/6lxv_30007.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxv_30007/09_2024/6lxv_30007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxv_30007/09_2024/6lxv_30007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxv_30007/09_2024/6lxv_30007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxv_30007/09_2024/6lxv_30007.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxv_30007/09_2024/6lxv_30007.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 16 5.49 5 S 160 5.16 5 C 32917 2.51 5 N 8896 2.21 5 O 12927 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 158 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 54924 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6472 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6521 Chain: "B" Number of atoms: 6467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6527 Chain: "C" Number of atoms: 6467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6527 Chain: "D" Number of atoms: 6467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6527 Chain: "E" Number of atoms: 6467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6527 Chain: "F" Number of atoms: 6467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6527 Chain: "G" Number of atoms: 6467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6527 Chain: "H" Number of atoms: 6467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6527 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Chain: "B" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 370 Classifications: {'water': 370} Link IDs: {None: 369} Chain: "C" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Chain: "D" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Chain: "E" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Chain: "F" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Chain: "G" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Chain: "H" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Residues with excluded nonbonded symmetry interactions: 48 residue: pdb=" N AARG A 428 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 428 " occ=0.50 residue: pdb=" N AGLN A 546 " occ=0.40 ... (16 atoms not shown) pdb=" NE2BGLN A 546 " occ=0.60 residue: pdb=" N AASP A 547 " occ=0.40 ... (14 atoms not shown) pdb=" OD2BASP A 547 " occ=0.60 residue: pdb=" N AHIS A 548 " occ=0.40 ... (18 atoms not shown) pdb=" NE2BHIS A 548 " occ=0.60 residue: pdb=" N AASN A 549 " occ=0.40 ... (14 atoms not shown) pdb=" ND2BASN A 549 " occ=0.60 residue: pdb=" N AHIS A 568 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 568 " occ=0.50 residue: pdb=" N AARG B 428 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 428 " occ=0.50 residue: pdb=" N AGLN B 546 " occ=0.40 ... (16 atoms not shown) pdb=" NE2BGLN B 546 " occ=0.60 residue: pdb=" N AASP B 547 " occ=0.40 ... (14 atoms not shown) pdb=" OD2BASP B 547 " occ=0.60 residue: pdb=" N AHIS B 548 " occ=0.40 ... (18 atoms not shown) pdb=" NE2BHIS B 548 " occ=0.60 residue: pdb=" N AASN B 549 " occ=0.40 ... (14 atoms not shown) pdb=" ND2BASN B 549 " occ=0.60 residue: pdb=" N AHIS B 568 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 568 " occ=0.50 ... (remaining 36 not shown) Time building chain proxies: 40.82, per 1000 atoms: 0.74 Number of scatterers: 54924 At special positions: 0 Unit cell: (204.45, 204.45, 113.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 160 16.00 P 16 15.00 O 12927 8.00 N 8896 7.00 C 32917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.86 Conformation dependent library (CDL) restraints added in 9.2 seconds 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12018 Finding SS restraints... Secondary structure from input PDB file: 319 helices and 48 sheets defined 52.0% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.23 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.678A pdb=" N GLY A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 122 through 133 removed outlier: 3.885A pdb=" N PHE A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 183 through 186 Processing helix chain 'A' and resid 187 through 194 removed outlier: 3.561A pdb=" N TRP A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 229 through 240 Processing helix chain 'A' and resid 255 through 282 Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 330 through 344 removed outlier: 4.012A pdb=" N TYR A 344 " --> pdb=" O TRP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.782A pdb=" N LEU A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 374 through 382 removed outlier: 4.178A pdb=" N GLY A 379 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY A 380 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 removed outlier: 6.796A pdb=" N VAL A 396 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.555A pdb=" N LEU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 503 through 507 removed outlier: 3.815A pdb=" N HIS A 506 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 526 Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 550 through 554 Processing helix chain 'A' and resid 557 through 564 removed outlier: 3.599A pdb=" N VAL A 561 " --> pdb=" O GLY A 557 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 Processing helix chain 'A' and resid 613 through 624 removed outlier: 3.658A pdb=" N LYS A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 665 removed outlier: 3.548A pdb=" N LYS A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 681 Processing helix chain 'A' and resid 691 through 699 Processing helix chain 'A' and resid 712 through 720 removed outlier: 4.091A pdb=" N VAL A 716 " --> pdb=" O TYR A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.653A pdb=" N ASN A 750 " --> pdb=" O MET A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 767 removed outlier: 3.623A pdb=" N ALA A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 792 removed outlier: 3.576A pdb=" N ASP A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 800 Processing helix chain 'B' and resid 18 through 42 Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 67 through 86 Processing helix chain 'B' and resid 98 through 110 removed outlier: 3.679A pdb=" N GLY B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 122 through 133 removed outlier: 3.885A pdb=" N PHE B 133 " --> pdb=" O PHE B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 183 through 186 Processing helix chain 'B' and resid 187 through 194 removed outlier: 3.561A pdb=" N TRP B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 229 through 240 Processing helix chain 'B' and resid 255 through 282 Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 330 through 344 removed outlier: 4.014A pdb=" N TYR B 344 " --> pdb=" O TRP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 349 Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.782A pdb=" N LEU B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 374 through 382 removed outlier: 4.178A pdb=" N GLY B 379 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY B 380 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 396 removed outlier: 6.794A pdb=" N VAL B 396 " --> pdb=" O ASP B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 403 Processing helix chain 'B' and resid 411 through 426 removed outlier: 3.554A pdb=" N LEU B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 478 through 492 Processing helix chain 'B' and resid 503 through 507 removed outlier: 3.816A pdb=" N HIS B 506 " --> pdb=" O SER B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 526 Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 550 through 554 Processing helix chain 'B' and resid 557 through 564 removed outlier: 3.599A pdb=" N VAL B 561 " --> pdb=" O GLY B 557 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 Processing helix chain 'B' and resid 613 through 624 removed outlier: 3.658A pdb=" N LYS B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 665 removed outlier: 3.548A pdb=" N LYS B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 681 Processing helix chain 'B' and resid 691 through 699 Processing helix chain 'B' and resid 712 through 720 removed outlier: 4.091A pdb=" N VAL B 716 " --> pdb=" O TYR B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 742 through 750 removed outlier: 3.653A pdb=" N ASN B 750 " --> pdb=" O MET B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 767 removed outlier: 3.636A pdb=" N ALA B 767 " --> pdb=" O ARG B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 792 removed outlier: 3.577A pdb=" N ASP B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 800 Processing helix chain 'C' and resid 18 through 42 Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 67 through 86 Processing helix chain 'C' and resid 98 through 110 removed outlier: 3.678A pdb=" N GLY C 102 " --> pdb=" O GLY C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 116 Processing helix chain 'C' and resid 122 through 133 removed outlier: 3.885A pdb=" N PHE C 133 " --> pdb=" O PHE C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 169 Processing helix chain 'C' and resid 183 through 186 Processing helix chain 'C' and resid 187 through 194 removed outlier: 3.560A pdb=" N TRP C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 199 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 229 through 240 Processing helix chain 'C' and resid 255 through 282 Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'C' and resid 330 through 344 removed outlier: 4.016A pdb=" N TYR C 344 " --> pdb=" O TRP C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 Processing helix chain 'C' and resid 357 through 362 removed outlier: 3.783A pdb=" N LEU C 361 " --> pdb=" O LYS C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 374 through 382 removed outlier: 4.178A pdb=" N GLY C 379 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY C 380 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 396 removed outlier: 6.795A pdb=" N VAL C 396 " --> pdb=" O ASP C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 403 Processing helix chain 'C' and resid 411 through 426 removed outlier: 3.556A pdb=" N LEU C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 449 Processing helix chain 'C' and resid 478 through 492 Processing helix chain 'C' and resid 503 through 507 removed outlier: 3.815A pdb=" N HIS C 506 " --> pdb=" O SER C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 526 Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 550 through 554 Processing helix chain 'C' and resid 557 through 564 removed outlier: 3.599A pdb=" N VAL C 561 " --> pdb=" O GLY C 557 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 594 Processing helix chain 'C' and resid 613 through 624 removed outlier: 3.658A pdb=" N LYS C 623 " --> pdb=" O ALA C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 665 removed outlier: 3.547A pdb=" N LYS C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 681 Processing helix chain 'C' and resid 691 through 699 Processing helix chain 'C' and resid 712 through 720 removed outlier: 4.091A pdb=" N VAL C 716 " --> pdb=" O TYR C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 727 No H-bonds generated for 'chain 'C' and resid 725 through 727' Processing helix chain 'C' and resid 742 through 750 removed outlier: 3.653A pdb=" N ASN C 750 " --> pdb=" O MET C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 767 removed outlier: 3.637A pdb=" N ALA C 767 " --> pdb=" O ARG C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 792 removed outlier: 3.579A pdb=" N ASP C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 800 Processing helix chain 'D' and resid 18 through 42 Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 67 through 86 Processing helix chain 'D' and resid 98 through 110 removed outlier: 3.678A pdb=" N GLY D 102 " --> pdb=" O GLY D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 116 Processing helix chain 'D' and resid 122 through 133 removed outlier: 3.885A pdb=" N PHE D 133 " --> pdb=" O PHE D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 169 Processing helix chain 'D' and resid 183 through 186 Processing helix chain 'D' and resid 187 through 194 removed outlier: 3.560A pdb=" N TRP D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 199 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 229 through 240 Processing helix chain 'D' and resid 255 through 282 Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 330 through 344 removed outlier: 4.013A pdb=" N TYR D 344 " --> pdb=" O TRP D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 Processing helix chain 'D' and resid 357 through 362 removed outlier: 3.783A pdb=" N LEU D 361 " --> pdb=" O LYS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 370 Processing helix chain 'D' and resid 374 through 382 removed outlier: 4.179A pdb=" N GLY D 379 " --> pdb=" O ASN D 376 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY D 380 " --> pdb=" O ALA D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 396 removed outlier: 6.796A pdb=" N VAL D 396 " --> pdb=" O ASP D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 411 through 426 removed outlier: 3.555A pdb=" N LEU D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 449 Processing helix chain 'D' and resid 478 through 492 Processing helix chain 'D' and resid 503 through 507 removed outlier: 3.815A pdb=" N HIS D 506 " --> pdb=" O SER D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 526 Processing helix chain 'D' and resid 542 through 546 Processing helix chain 'D' and resid 550 through 554 Processing helix chain 'D' and resid 557 through 564 removed outlier: 3.599A pdb=" N VAL D 561 " --> pdb=" O GLY D 557 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 594 Processing helix chain 'D' and resid 613 through 624 removed outlier: 3.658A pdb=" N LYS D 623 " --> pdb=" O ALA D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 665 removed outlier: 3.547A pdb=" N LYS D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 681 Processing helix chain 'D' and resid 691 through 699 Processing helix chain 'D' and resid 712 through 720 removed outlier: 4.091A pdb=" N VAL D 716 " --> pdb=" O TYR D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 727 No H-bonds generated for 'chain 'D' and resid 725 through 727' Processing helix chain 'D' and resid 742 through 750 removed outlier: 3.654A pdb=" N ASN D 750 " --> pdb=" O MET D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 767 removed outlier: 3.637A pdb=" N ALA D 767 " --> pdb=" O ARG D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 792 removed outlier: 3.579A pdb=" N ASP D 782 " --> pdb=" O GLU D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 800 Processing helix chain 'E' and resid 18 through 42 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 67 through 86 Processing helix chain 'E' and resid 98 through 110 removed outlier: 3.678A pdb=" N GLY E 102 " --> pdb=" O GLY E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 116 Processing helix chain 'E' and resid 122 through 133 removed outlier: 3.885A pdb=" N PHE E 133 " --> pdb=" O PHE E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 169 Processing helix chain 'E' and resid 183 through 186 Processing helix chain 'E' and resid 187 through 194 removed outlier: 3.561A pdb=" N TRP E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 199 Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 229 through 240 Processing helix chain 'E' and resid 255 through 282 Processing helix chain 'E' and resid 316 through 320 Processing helix chain 'E' and resid 330 through 344 removed outlier: 4.013A pdb=" N TYR E 344 " --> pdb=" O TRP E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 362 removed outlier: 3.782A pdb=" N LEU E 361 " --> pdb=" O LYS E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 370 Processing helix chain 'E' and resid 374 through 382 removed outlier: 4.178A pdb=" N GLY E 379 " --> pdb=" O ASN E 376 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY E 380 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 396 removed outlier: 6.797A pdb=" N VAL E 396 " --> pdb=" O ASP E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 411 through 426 removed outlier: 3.555A pdb=" N LEU E 415 " --> pdb=" O ALA E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 449 Processing helix chain 'E' and resid 478 through 492 Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.815A pdb=" N HIS E 506 " --> pdb=" O SER E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 526 Processing helix chain 'E' and resid 542 through 546 Processing helix chain 'E' and resid 550 through 554 Processing helix chain 'E' and resid 557 through 564 removed outlier: 3.599A pdb=" N VAL E 561 " --> pdb=" O GLY E 557 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN E 564 " --> pdb=" O SER E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 594 Processing helix chain 'E' and resid 613 through 624 removed outlier: 3.658A pdb=" N LYS E 623 " --> pdb=" O ALA E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 665 removed outlier: 3.547A pdb=" N LYS E 661 " --> pdb=" O ALA E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 681 Processing helix chain 'E' and resid 691 through 699 Processing helix chain 'E' and resid 712 through 720 removed outlier: 4.091A pdb=" N VAL E 716 " --> pdb=" O TYR E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 727 No H-bonds generated for 'chain 'E' and resid 725 through 727' Processing helix chain 'E' and resid 742 through 750 removed outlier: 3.653A pdb=" N ASN E 750 " --> pdb=" O MET E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 753 through 767 removed outlier: 3.637A pdb=" N ALA E 767 " --> pdb=" O ARG E 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 792 removed outlier: 3.577A pdb=" N ASP E 782 " --> pdb=" O GLU E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 795 through 800 Processing helix chain 'F' and resid 18 through 42 Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 67 through 86 Processing helix chain 'F' and resid 98 through 110 removed outlier: 3.678A pdb=" N GLY F 102 " --> pdb=" O GLY F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 116 Processing helix chain 'F' and resid 122 through 133 removed outlier: 3.885A pdb=" N PHE F 133 " --> pdb=" O PHE F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 169 Processing helix chain 'F' and resid 183 through 186 Processing helix chain 'F' and resid 187 through 194 removed outlier: 3.561A pdb=" N TRP F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 199 Processing helix chain 'F' and resid 223 through 228 Processing helix chain 'F' and resid 229 through 240 Processing helix chain 'F' and resid 255 through 282 Processing helix chain 'F' and resid 316 through 320 Processing helix chain 'F' and resid 330 through 344 removed outlier: 4.012A pdb=" N TYR F 344 " --> pdb=" O TRP F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 349 Processing helix chain 'F' and resid 357 through 362 removed outlier: 3.782A pdb=" N LEU F 361 " --> pdb=" O LYS F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 370 Processing helix chain 'F' and resid 374 through 382 removed outlier: 4.179A pdb=" N GLY F 379 " --> pdb=" O ASN F 376 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY F 380 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 396 removed outlier: 6.800A pdb=" N VAL F 396 " --> pdb=" O ASP F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 403 Processing helix chain 'F' and resid 411 through 426 removed outlier: 3.555A pdb=" N LEU F 415 " --> pdb=" O ALA F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 449 Processing helix chain 'F' and resid 478 through 492 Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.815A pdb=" N HIS F 506 " --> pdb=" O SER F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 526 Processing helix chain 'F' and resid 542 through 546 Processing helix chain 'F' and resid 550 through 554 Processing helix chain 'F' and resid 557 through 564 removed outlier: 3.599A pdb=" N VAL F 561 " --> pdb=" O GLY F 557 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN F 564 " --> pdb=" O SER F 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 594 Processing helix chain 'F' and resid 613 through 624 removed outlier: 3.658A pdb=" N LYS F 623 " --> pdb=" O ALA F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 665 removed outlier: 3.549A pdb=" N LYS F 661 " --> pdb=" O ALA F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 681 Processing helix chain 'F' and resid 691 through 699 Processing helix chain 'F' and resid 712 through 720 removed outlier: 4.091A pdb=" N VAL F 716 " --> pdb=" O TYR F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 727 No H-bonds generated for 'chain 'F' and resid 725 through 727' Processing helix chain 'F' and resid 742 through 750 removed outlier: 3.653A pdb=" N ASN F 750 " --> pdb=" O MET F 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 753 through 767 removed outlier: 3.637A pdb=" N ALA F 767 " --> pdb=" O ARG F 763 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 792 removed outlier: 3.580A pdb=" N ASP F 782 " --> pdb=" O GLU F 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 795 through 800 Processing helix chain 'G' and resid 18 through 42 Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 67 through 86 Processing helix chain 'G' and resid 98 through 110 removed outlier: 3.679A pdb=" N GLY G 102 " --> pdb=" O GLY G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 116 Processing helix chain 'G' and resid 122 through 133 removed outlier: 3.885A pdb=" N PHE G 133 " --> pdb=" O PHE G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 169 Processing helix chain 'G' and resid 183 through 186 Processing helix chain 'G' and resid 187 through 194 removed outlier: 3.560A pdb=" N TRP G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 199 Processing helix chain 'G' and resid 223 through 228 Processing helix chain 'G' and resid 229 through 240 Processing helix chain 'G' and resid 255 through 282 Processing helix chain 'G' and resid 316 through 320 Processing helix chain 'G' and resid 330 through 344 removed outlier: 4.012A pdb=" N TYR G 344 " --> pdb=" O TRP G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 349 Processing helix chain 'G' and resid 357 through 362 removed outlier: 3.783A pdb=" N LEU G 361 " --> pdb=" O LYS G 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 370 Processing helix chain 'G' and resid 374 through 382 removed outlier: 4.179A pdb=" N GLY G 379 " --> pdb=" O ASN G 376 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY G 380 " --> pdb=" O ALA G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 396 removed outlier: 6.796A pdb=" N VAL G 396 " --> pdb=" O ASP G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 403 Processing helix chain 'G' and resid 411 through 426 removed outlier: 3.554A pdb=" N LEU G 415 " --> pdb=" O ALA G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 443 through 449 Processing helix chain 'G' and resid 478 through 492 Processing helix chain 'G' and resid 503 through 507 removed outlier: 3.815A pdb=" N HIS G 506 " --> pdb=" O SER G 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 526 Processing helix chain 'G' and resid 542 through 546 Processing helix chain 'G' and resid 550 through 554 Processing helix chain 'G' and resid 557 through 564 removed outlier: 3.599A pdb=" N VAL G 561 " --> pdb=" O GLY G 557 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN G 564 " --> pdb=" O SER G 560 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 594 Processing helix chain 'G' and resid 613 through 624 removed outlier: 3.658A pdb=" N LYS G 623 " --> pdb=" O ALA G 619 " (cutoff:3.500A) Processing helix chain 'G' and resid 648 through 665 removed outlier: 3.548A pdb=" N LYS G 661 " --> pdb=" O ALA G 657 " (cutoff:3.500A) Processing helix chain 'G' and resid 676 through 681 Processing helix chain 'G' and resid 691 through 699 Processing helix chain 'G' and resid 712 through 720 removed outlier: 4.091A pdb=" N VAL G 716 " --> pdb=" O TYR G 712 " (cutoff:3.500A) Processing helix chain 'G' and resid 725 through 727 No H-bonds generated for 'chain 'G' and resid 725 through 727' Processing helix chain 'G' and resid 742 through 750 removed outlier: 3.654A pdb=" N ASN G 750 " --> pdb=" O MET G 746 " (cutoff:3.500A) Processing helix chain 'G' and resid 753 through 767 removed outlier: 3.637A pdb=" N ALA G 767 " --> pdb=" O ARG G 763 " (cutoff:3.500A) Processing helix chain 'G' and resid 770 through 792 removed outlier: 3.579A pdb=" N ASP G 782 " --> pdb=" O GLU G 778 " (cutoff:3.500A) Processing helix chain 'G' and resid 795 through 800 Processing helix chain 'H' and resid 18 through 42 Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 67 through 86 Processing helix chain 'H' and resid 98 through 110 removed outlier: 3.678A pdb=" N GLY H 102 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 116 Processing helix chain 'H' and resid 122 through 133 removed outlier: 3.886A pdb=" N PHE H 133 " --> pdb=" O PHE H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 169 Processing helix chain 'H' and resid 183 through 186 Processing helix chain 'H' and resid 187 through 194 removed outlier: 3.561A pdb=" N TRP H 194 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 199 Processing helix chain 'H' and resid 223 through 228 Processing helix chain 'H' and resid 229 through 240 Processing helix chain 'H' and resid 255 through 282 Processing helix chain 'H' and resid 316 through 320 Processing helix chain 'H' and resid 330 through 344 removed outlier: 4.012A pdb=" N TYR H 344 " --> pdb=" O TRP H 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 349 Processing helix chain 'H' and resid 357 through 362 removed outlier: 3.782A pdb=" N LEU H 361 " --> pdb=" O LYS H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 370 Processing helix chain 'H' and resid 374 through 382 removed outlier: 4.179A pdb=" N GLY H 379 " --> pdb=" O ASN H 376 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY H 380 " --> pdb=" O ALA H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 396 removed outlier: 6.794A pdb=" N VAL H 396 " --> pdb=" O ASP H 393 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 403 Processing helix chain 'H' and resid 411 through 426 removed outlier: 3.555A pdb=" N LEU H 415 " --> pdb=" O ALA H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 449 Processing helix chain 'H' and resid 478 through 492 Processing helix chain 'H' and resid 503 through 507 removed outlier: 3.816A pdb=" N HIS H 506 " --> pdb=" O SER H 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 508 through 526 Processing helix chain 'H' and resid 542 through 546 Processing helix chain 'H' and resid 550 through 554 Processing helix chain 'H' and resid 557 through 564 removed outlier: 3.599A pdb=" N VAL H 561 " --> pdb=" O GLY H 557 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN H 564 " --> pdb=" O SER H 560 " (cutoff:3.500A) Processing helix chain 'H' and resid 580 through 594 Processing helix chain 'H' and resid 613 through 624 removed outlier: 3.658A pdb=" N LYS H 623 " --> pdb=" O ALA H 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 648 through 665 removed outlier: 3.548A pdb=" N LYS H 661 " --> pdb=" O ALA H 657 " (cutoff:3.500A) Processing helix chain 'H' and resid 676 through 681 Processing helix chain 'H' and resid 691 through 699 Processing helix chain 'H' and resid 712 through 720 removed outlier: 4.091A pdb=" N VAL H 716 " --> pdb=" O TYR H 712 " (cutoff:3.500A) Processing helix chain 'H' and resid 725 through 727 No H-bonds generated for 'chain 'H' and resid 725 through 727' Processing helix chain 'H' and resid 742 through 750 removed outlier: 3.653A pdb=" N ASN H 750 " --> pdb=" O MET H 746 " (cutoff:3.500A) Processing helix chain 'H' and resid 753 through 767 removed outlier: 3.636A pdb=" N ALA H 767 " --> pdb=" O ARG H 763 " (cutoff:3.500A) Processing helix chain 'H' and resid 770 through 792 removed outlier: 3.578A pdb=" N ASP H 782 " --> pdb=" O GLU H 778 " (cutoff:3.500A) Processing helix chain 'H' and resid 795 through 800 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 removed outlier: 6.495A pdb=" N ILE A 92 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLY A 181 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AA3, first strand: chain 'A' and resid 406 through 410 removed outlier: 3.815A pdb=" N GLN A 408 " --> pdb=" O ALA A 608 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA A 608 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 475 removed outlier: 8.508A pdb=" N VAL A 474 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 432 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLY A 496 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU A 538 " --> pdb=" O GLY A 496 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP A 498 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER A 540 " --> pdb=" O TRP A 498 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER A 500 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY A 574 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE A 602 " --> pdb=" O GLY A 574 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR A 576 " --> pdb=" O ILE A 602 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 452 through 453 removed outlier: 5.551A pdb=" N LYS A 452 " --> pdb=" O HIS A 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 625 through 627 Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 93 removed outlier: 6.493A pdb=" N ILE B 92 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLY B 181 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AA9, first strand: chain 'B' and resid 406 through 410 removed outlier: 3.816A pdb=" N GLN B 408 " --> pdb=" O ALA B 608 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 608 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 475 removed outlier: 8.509A pdb=" N VAL B 474 " --> pdb=" O PHE B 430 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 432 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLY B 496 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU B 538 " --> pdb=" O GLY B 496 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP B 498 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N SER B 540 " --> pdb=" O TRP B 498 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N SER B 500 " --> pdb=" O SER B 540 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY B 574 " --> pdb=" O ALA B 600 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE B 602 " --> pdb=" O GLY B 574 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR B 576 " --> pdb=" O ILE B 602 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 452 through 453 removed outlier: 5.552A pdb=" N LYS B 452 " --> pdb=" O HIS B 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 625 through 627 Processing sheet with id=AB4, first strand: chain 'C' and resid 92 through 93 removed outlier: 6.492A pdb=" N ILE C 92 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLY C 181 " --> pdb=" O ILE C 92 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 307 through 308 Processing sheet with id=AB6, first strand: chain 'C' and resid 406 through 410 removed outlier: 3.815A pdb=" N GLN C 408 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA C 608 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 473 through 475 removed outlier: 8.507A pdb=" N VAL C 474 " --> pdb=" O PHE C 430 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE C 432 " --> pdb=" O VAL C 474 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLY C 496 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU C 538 " --> pdb=" O GLY C 496 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP C 498 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER C 540 " --> pdb=" O TRP C 498 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N SER C 500 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY C 574 " --> pdb=" O ALA C 600 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE C 602 " --> pdb=" O GLY C 574 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR C 576 " --> pdb=" O ILE C 602 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 452 through 453 removed outlier: 5.551A pdb=" N LYS C 452 " --> pdb=" O HIS C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 625 through 627 Processing sheet with id=AC1, first strand: chain 'D' and resid 92 through 93 removed outlier: 6.492A pdb=" N ILE D 92 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLY D 181 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 307 through 308 Processing sheet with id=AC3, first strand: chain 'D' and resid 406 through 410 removed outlier: 3.816A pdb=" N GLN D 408 " --> pdb=" O ALA D 608 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA D 608 " --> pdb=" O GLN D 408 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 473 through 475 removed outlier: 8.508A pdb=" N VAL D 474 " --> pdb=" O PHE D 430 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE D 432 " --> pdb=" O VAL D 474 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLY D 496 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU D 538 " --> pdb=" O GLY D 496 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP D 498 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER D 540 " --> pdb=" O TRP D 498 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER D 500 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY D 574 " --> pdb=" O ALA D 600 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE D 602 " --> pdb=" O GLY D 574 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR D 576 " --> pdb=" O ILE D 602 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 452 through 453 removed outlier: 5.551A pdb=" N LYS D 452 " --> pdb=" O HIS D 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 625 through 627 Processing sheet with id=AC7, first strand: chain 'E' and resid 92 through 93 removed outlier: 6.492A pdb=" N ILE E 92 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLY E 181 " --> pdb=" O ILE E 92 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 307 through 308 Processing sheet with id=AC9, first strand: chain 'E' and resid 406 through 410 removed outlier: 3.816A pdb=" N GLN E 408 " --> pdb=" O ALA E 608 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA E 608 " --> pdb=" O GLN E 408 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 473 through 475 removed outlier: 8.508A pdb=" N VAL E 474 " --> pdb=" O PHE E 430 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE E 432 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLY E 496 " --> pdb=" O ASN E 536 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU E 538 " --> pdb=" O GLY E 496 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP E 498 " --> pdb=" O LEU E 538 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER E 540 " --> pdb=" O TRP E 498 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N SER E 500 " --> pdb=" O SER E 540 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY E 574 " --> pdb=" O ALA E 600 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE E 602 " --> pdb=" O GLY E 574 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR E 576 " --> pdb=" O ILE E 602 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 452 through 453 removed outlier: 5.552A pdb=" N LYS E 452 " --> pdb=" O HIS E 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 625 through 627 Processing sheet with id=AD4, first strand: chain 'F' and resid 92 through 93 removed outlier: 6.492A pdb=" N ILE F 92 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLY F 181 " --> pdb=" O ILE F 92 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 307 through 308 Processing sheet with id=AD6, first strand: chain 'F' and resid 406 through 410 removed outlier: 3.816A pdb=" N GLN F 408 " --> pdb=" O ALA F 608 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA F 608 " --> pdb=" O GLN F 408 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 473 through 475 removed outlier: 8.509A pdb=" N VAL F 474 " --> pdb=" O PHE F 430 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE F 432 " --> pdb=" O VAL F 474 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLY F 496 " --> pdb=" O ASN F 536 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU F 538 " --> pdb=" O GLY F 496 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP F 498 " --> pdb=" O LEU F 538 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER F 540 " --> pdb=" O TRP F 498 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER F 500 " --> pdb=" O SER F 540 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY F 574 " --> pdb=" O ALA F 600 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE F 602 " --> pdb=" O GLY F 574 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR F 576 " --> pdb=" O ILE F 602 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 452 through 453 removed outlier: 5.551A pdb=" N LYS F 452 " --> pdb=" O HIS F 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'F' and resid 625 through 627 Processing sheet with id=AE1, first strand: chain 'G' and resid 92 through 93 removed outlier: 6.492A pdb=" N ILE G 92 " --> pdb=" O ILE G 179 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N GLY G 181 " --> pdb=" O ILE G 92 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 307 through 308 Processing sheet with id=AE3, first strand: chain 'G' and resid 406 through 410 removed outlier: 3.815A pdb=" N GLN G 408 " --> pdb=" O ALA G 608 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA G 608 " --> pdb=" O GLN G 408 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 473 through 475 removed outlier: 8.508A pdb=" N VAL G 474 " --> pdb=" O PHE G 430 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE G 432 " --> pdb=" O VAL G 474 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLY G 496 " --> pdb=" O ASN G 536 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU G 538 " --> pdb=" O GLY G 496 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP G 498 " --> pdb=" O LEU G 538 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER G 540 " --> pdb=" O TRP G 498 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N SER G 500 " --> pdb=" O SER G 540 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY G 574 " --> pdb=" O ALA G 600 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE G 602 " --> pdb=" O GLY G 574 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR G 576 " --> pdb=" O ILE G 602 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 452 through 453 removed outlier: 5.550A pdb=" N LYS G 452 " --> pdb=" O HIS G 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'G' and resid 625 through 627 Processing sheet with id=AE7, first strand: chain 'H' and resid 92 through 93 removed outlier: 6.492A pdb=" N ILE H 92 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLY H 181 " --> pdb=" O ILE H 92 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 307 through 308 Processing sheet with id=AE9, first strand: chain 'H' and resid 406 through 410 removed outlier: 3.816A pdb=" N GLN H 408 " --> pdb=" O ALA H 608 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA H 608 " --> pdb=" O GLN H 408 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 473 through 475 removed outlier: 8.507A pdb=" N VAL H 474 " --> pdb=" O PHE H 430 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE H 432 " --> pdb=" O VAL H 474 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLY H 496 " --> pdb=" O ASN H 536 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU H 538 " --> pdb=" O GLY H 496 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP H 498 " --> pdb=" O LEU H 538 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER H 540 " --> pdb=" O TRP H 498 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N SER H 500 " --> pdb=" O SER H 540 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY H 574 " --> pdb=" O ALA H 600 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE H 602 " --> pdb=" O GLY H 574 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR H 576 " --> pdb=" O ILE H 602 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 452 through 453 removed outlier: 5.550A pdb=" N LYS H 452 " --> pdb=" O HIS H 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'H' and resid 625 through 627 2398 hydrogen bonds defined for protein. 6408 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: 22.11 Time building geometry restraints manager: 12.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 9039 1.27 - 1.41: 14776 1.41 - 1.54: 28355 1.54 - 1.68: 972 1.68 - 1.82: 272 Bond restraints: 53414 Sorted by residual: bond pdb=" C5 TPP H 900 " pdb=" S1 TPP H 900 " ideal model delta sigma weight residual 1.727 1.587 0.140 1.00e-02 1.00e+04 1.95e+02 bond pdb=" C5 TPP B 900 " pdb=" S1 TPP B 900 " ideal model delta sigma weight residual 1.727 1.588 0.139 1.00e-02 1.00e+04 1.94e+02 bond pdb=" C5 TPP E 900 " pdb=" S1 TPP E 900 " ideal model delta sigma weight residual 1.727 1.588 0.139 1.00e-02 1.00e+04 1.94e+02 bond pdb=" C5 TPP G 900 " pdb=" S1 TPP G 900 " ideal model delta sigma weight residual 1.727 1.588 0.139 1.00e-02 1.00e+04 1.93e+02 bond pdb=" C5 TPP C 900 " pdb=" S1 TPP C 900 " ideal model delta sigma weight residual 1.727 1.588 0.139 1.00e-02 1.00e+04 1.93e+02 ... (remaining 53409 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 70708 4.18 - 8.36: 1822 8.36 - 12.55: 140 12.55 - 16.73: 24 16.73 - 20.91: 12 Bond angle restraints: 72706 Sorted by residual: angle pdb=" N3 TPP A 900 " pdb=" C2 TPP A 900 " pdb=" S1 TPP A 900 " ideal model delta sigma weight residual 112.34 122.29 -9.95 1.00e+00 1.00e+00 9.89e+01 angle pdb=" N3 TPP C 900 " pdb=" C2 TPP C 900 " pdb=" S1 TPP C 900 " ideal model delta sigma weight residual 112.34 122.11 -9.77 1.00e+00 1.00e+00 9.54e+01 angle pdb=" N3 TPP F 900 " pdb=" C2 TPP F 900 " pdb=" S1 TPP F 900 " ideal model delta sigma weight residual 112.34 122.07 -9.73 1.00e+00 1.00e+00 9.47e+01 angle pdb=" N3 TPP D 900 " pdb=" C2 TPP D 900 " pdb=" S1 TPP D 900 " ideal model delta sigma weight residual 112.34 122.04 -9.70 1.00e+00 1.00e+00 9.40e+01 angle pdb=" N3 TPP B 900 " pdb=" C2 TPP B 900 " pdb=" S1 TPP B 900 " ideal model delta sigma weight residual 112.34 122.00 -9.66 1.00e+00 1.00e+00 9.34e+01 ... (remaining 72701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 27924 17.84 - 35.67: 2535 35.67 - 53.51: 522 53.51 - 71.34: 205 71.34 - 89.18: 92 Dihedral angle restraints: 31278 sinusoidal: 12482 harmonic: 18796 Sorted by residual: dihedral pdb=" CA PHE F 699 " pdb=" C PHE F 699 " pdb=" N THR F 700 " pdb=" CA THR F 700 " ideal model delta harmonic sigma weight residual 180.00 143.07 36.93 0 5.00e+00 4.00e-02 5.46e+01 dihedral pdb=" CA PHE C 699 " pdb=" C PHE C 699 " pdb=" N THR C 700 " pdb=" CA THR C 700 " ideal model delta harmonic sigma weight residual 180.00 143.07 36.93 0 5.00e+00 4.00e-02 5.45e+01 dihedral pdb=" CA PHE G 699 " pdb=" C PHE G 699 " pdb=" N THR G 700 " pdb=" CA THR G 700 " ideal model delta harmonic sigma weight residual 180.00 143.07 36.93 0 5.00e+00 4.00e-02 5.45e+01 ... (remaining 31275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 6357 0.154 - 0.308: 1141 0.308 - 0.461: 88 0.461 - 0.615: 8 0.615 - 0.769: 8 Chirality restraints: 7602 Sorted by residual: chirality pdb=" CG LEU F 477 " pdb=" CB LEU F 477 " pdb=" CD1 LEU F 477 " pdb=" CD2 LEU F 477 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CG LEU C 477 " pdb=" CB LEU C 477 " pdb=" CD1 LEU C 477 " pdb=" CD2 LEU C 477 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CG LEU H 477 " pdb=" CB LEU H 477 " pdb=" CD1 LEU H 477 " pdb=" CD2 LEU H 477 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.77 2.00e-01 2.50e+01 1.47e+01 ... (remaining 7599 not shown) Planarity restraints: 9577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 217 " -0.072 2.00e-02 2.50e+03 3.74e-02 2.80e+01 pdb=" CG TYR D 217 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR D 217 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR D 217 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR D 217 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR D 217 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR D 217 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR D 217 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 217 " -0.072 2.00e-02 2.50e+03 3.74e-02 2.80e+01 pdb=" CG TYR G 217 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR G 217 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR G 217 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR G 217 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR G 217 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR G 217 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR G 217 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 217 " 0.071 2.00e-02 2.50e+03 3.73e-02 2.79e+01 pdb=" CG TYR C 217 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR C 217 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR C 217 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR C 217 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 217 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR C 217 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR C 217 " 0.032 2.00e-02 2.50e+03 ... (remaining 9574 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 7842 2.74 - 3.28: 56452 3.28 - 3.82: 115050 3.82 - 4.36: 141154 4.36 - 4.90: 219911 Nonbonded interactions: 540409 Sorted by model distance: nonbonded pdb=" OE1 GLU E 153 " pdb=" O HOH E1001 " model vdw 2.196 3.040 nonbonded pdb=" OE1 GLU H 153 " pdb=" O HOH H1001 " model vdw 2.196 3.040 nonbonded pdb=" OE1 GLU A 153 " pdb=" O HOH A1001 " model vdw 2.196 3.040 nonbonded pdb=" OE1 GLU F 153 " pdb=" O HOH F1001 " model vdw 2.196 3.040 nonbonded pdb=" OE1 GLU C 153 " pdb=" O HOH C1001 " model vdw 2.196 3.040 ... (remaining 540404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ selection = (chain 'B' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ selection = (chain 'C' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ selection = (chain 'D' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ selection = (chain 'E' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ selection = (chain 'F' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ selection = (chain 'G' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ selection = (chain 'H' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.590 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 121.980 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.270 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: 0.020 Load rotamer database and sin/cos tables:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 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 : 0.025 0.198 53414 Z= 1.665 Angle : 1.662 20.909 72706 Z= 0.963 Chirality : 0.120 0.769 7602 Planarity : 0.011 0.055 9577 Dihedral : 16.134 89.175 19260 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.93 % Favored : 95.94 % Rotamer: Outliers : 2.81 % Allowed : 4.96 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.79 (0.09), residues: 6529 helix: -1.54 (0.08), residues: 2736 sheet: -1.45 (0.17), residues: 801 loop : -0.53 (0.11), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.010 TRP D 65 HIS 0.028 0.008 HIS B 320 PHE 0.045 0.009 PHE B 237 TYR 0.072 0.011 TYR G 217 ARG 0.022 0.003 ARG D 494 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 584 time to evaluate : 4.526 Fit side-chains REVERT: A 23 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: A 60 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8018 (ttm170) REVERT: A 123 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: A 635 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7086 (mmtm) REVERT: B 60 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8031 (ttm170) REVERT: B 123 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: B 635 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7084 (mmtm) REVERT: C 60 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8031 (ttm170) REVERT: C 123 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: C 635 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7092 (mmtm) REVERT: D 60 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8030 (ttm170) REVERT: D 123 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: D 635 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7084 (mmtm) REVERT: E 60 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8032 (ttm170) REVERT: E 123 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: E 635 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7090 (mmtm) REVERT: F 23 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7427 (mm-30) REVERT: F 60 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8023 (ttm170) REVERT: F 123 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: F 635 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7093 (mmtm) REVERT: G 60 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8027 (ttm170) REVERT: G 123 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: G 635 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7089 (mmtm) REVERT: H 23 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7423 (mm-30) REVERT: H 60 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8019 (ttm170) REVERT: H 123 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: H 635 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7092 (mmtm) outliers start: 137 outliers final: 93 residues processed: 671 average time/residue: 1.7824 time to fit residues: 1458.5448 Evaluate side-chains 687 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 567 time to evaluate : 4.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 635 LYS Chi-restraints excluded: chain A residue 735 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 735 GLU Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 768 ASP Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 635 LYS Chi-restraints excluded: chain C residue 735 GLU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 387 LYS Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 635 LYS Chi-restraints excluded: chain D residue 735 GLU Chi-restraints excluded: chain D residue 752 ILE Chi-restraints excluded: chain D residue 768 ASP Chi-restraints excluded: chain D residue 769 LYS Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain E residue 635 LYS Chi-restraints excluded: chain E residue 735 GLU Chi-restraints excluded: chain E residue 752 ILE Chi-restraints excluded: chain E residue 768 ASP Chi-restraints excluded: chain E residue 769 LYS Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 387 LYS Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain F residue 635 LYS Chi-restraints excluded: chain F residue 735 GLU Chi-restraints excluded: chain F residue 752 ILE Chi-restraints excluded: chain F residue 768 ASP Chi-restraints excluded: chain F residue 769 LYS Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 60 ARG Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 387 LYS Chi-restraints excluded: chain G residue 525 GLU Chi-restraints excluded: chain G residue 635 LYS Chi-restraints excluded: chain G residue 735 GLU Chi-restraints excluded: chain G residue 752 ILE Chi-restraints excluded: chain G residue 768 ASP Chi-restraints excluded: chain G residue 769 LYS Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 60 ARG Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 387 LYS Chi-restraints excluded: chain H residue 525 GLU Chi-restraints excluded: chain H residue 635 LYS Chi-restraints excluded: chain H residue 735 GLU Chi-restraints excluded: chain H residue 752 ILE Chi-restraints excluded: chain H residue 768 ASP Chi-restraints excluded: chain H residue 769 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 540 optimal weight: 5.9990 chunk 485 optimal weight: 0.7980 chunk 269 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 327 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 501 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 305 optimal weight: 5.9990 chunk 373 optimal weight: 2.9990 chunk 581 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 39 GLN A 105 GLN A 321 GLN A 408 GLN A 546 GLN B A 549 ASN B A 653 GLN B 14 ASN B 39 GLN B 105 GLN B 321 GLN B 408 GLN B 546 GLN B B 549 ASN B B 653 GLN C 14 ASN C 39 GLN C 105 GLN C 321 GLN C 408 GLN C 546 GLN B C 549 ASN B C 653 GLN C 673 ASN D 14 ASN D 39 GLN D 105 GLN D 321 GLN D 408 GLN D 546 GLN B D 549 ASN B D 653 GLN D 673 ASN E 14 ASN E 39 GLN E 105 GLN E 321 GLN E 408 GLN E 546 GLN B E 549 ASN B E 653 GLN F 14 ASN F 39 GLN F 105 GLN F 321 GLN F 408 GLN F 546 GLN B F 549 ASN B F 653 GLN F 673 ASN G 14 ASN G 39 GLN G 105 GLN G 321 GLN G 408 GLN G 546 GLN B G 549 ASN B G 653 GLN H 14 ASN H 39 GLN H 105 GLN H 321 GLN H 408 GLN H 546 GLN B H 549 ASN B H 653 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 53414 Z= 0.198 Angle : 0.621 8.100 72706 Z= 0.338 Chirality : 0.046 0.232 7602 Planarity : 0.005 0.037 9577 Dihedral : 9.376 89.042 7416 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.69 % Allowed : 7.58 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.10), residues: 6529 helix: 0.56 (0.09), residues: 2768 sheet: -0.99 (0.17), residues: 873 loop : 0.08 (0.12), residues: 2888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 302 HIS 0.006 0.001 HIS F 260 PHE 0.019 0.002 PHE E 334 TYR 0.020 0.002 TYR F 744 ARG 0.003 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 658 time to evaluate : 4.555 Fit side-chains REVERT: A 60 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7911 (ttm170) REVERT: A 123 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: A 331 GLU cc_start: 0.7390 (tp30) cc_final: 0.7012 (tp30) REVERT: A 392 GLU cc_start: 0.7493 (mp0) cc_final: 0.7150 (mm-30) REVERT: B 60 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7895 (ttm170) REVERT: B 123 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: B 331 GLU cc_start: 0.7392 (tp30) cc_final: 0.7019 (tp30) REVERT: B 392 GLU cc_start: 0.7491 (mp0) cc_final: 0.7151 (mm-30) REVERT: B 769 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7628 (pttt) REVERT: C 60 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7916 (ttm170) REVERT: C 123 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: C 331 GLU cc_start: 0.7396 (tp30) cc_final: 0.7021 (tp30) REVERT: C 392 GLU cc_start: 0.7490 (mp0) cc_final: 0.7148 (mm-30) REVERT: C 769 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7626 (pttt) REVERT: D 60 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7891 (ttm170) REVERT: D 123 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: D 331 GLU cc_start: 0.7395 (tp30) cc_final: 0.7020 (tp30) REVERT: D 769 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7631 (pttt) REVERT: E 60 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7916 (ttm170) REVERT: E 123 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: E 331 GLU cc_start: 0.7391 (tp30) cc_final: 0.7018 (tp30) REVERT: E 392 GLU cc_start: 0.7496 (mp0) cc_final: 0.7152 (mm-30) REVERT: E 769 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7630 (pttt) REVERT: F 60 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7915 (ttm170) REVERT: F 123 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: F 331 GLU cc_start: 0.7394 (tp30) cc_final: 0.7017 (tp30) REVERT: F 392 GLU cc_start: 0.7492 (mp0) cc_final: 0.7149 (mm-30) REVERT: F 769 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7629 (pttt) REVERT: G 60 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7912 (ttm170) REVERT: G 123 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: G 331 GLU cc_start: 0.7394 (tp30) cc_final: 0.7017 (tp30) REVERT: G 392 GLU cc_start: 0.7492 (mp0) cc_final: 0.7152 (mm-30) REVERT: G 769 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7627 (pttt) REVERT: H 60 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7969 (ttm170) REVERT: H 123 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: H 331 GLU cc_start: 0.7389 (tp30) cc_final: 0.7018 (tp30) REVERT: H 392 GLU cc_start: 0.7486 (mp0) cc_final: 0.7147 (mm-30) REVERT: H 769 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7630 (pttt) outliers start: 92 outliers final: 17 residues processed: 710 average time/residue: 1.8498 time to fit residues: 1587.3382 Evaluate side-chains 621 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 581 time to evaluate : 4.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 60 ARG Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain D residue 769 LYS Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 769 LYS Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 769 LYS Chi-restraints excluded: chain G residue 60 ARG Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 769 LYS Chi-restraints excluded: chain H residue 60 ARG Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 769 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 322 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 483 optimal weight: 9.9990 chunk 395 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 582 optimal weight: 0.7980 chunk 628 optimal weight: 1.9990 chunk 518 optimal weight: 0.9990 chunk 577 optimal weight: 4.9990 chunk 198 optimal weight: 0.9980 chunk 467 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS A 546 GLN B A 549 ASN B ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS B 546 GLN B B 549 ASN B ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 HIS C 546 GLN B C 549 ASN B ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS D 546 GLN B D 549 ASN B ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS E 546 GLN B E 549 ASN B ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS F 546 GLN B F 549 ASN B ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 333 HIS G 546 GLN B G 549 ASN B ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 HIS H 546 GLN B H 549 ASN B Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 53414 Z= 0.233 Angle : 0.632 7.054 72706 Z= 0.344 Chirality : 0.048 0.263 7602 Planarity : 0.005 0.051 9577 Dihedral : 7.830 88.284 7233 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.41 % Allowed : 10.04 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.10), residues: 6529 helix: 1.10 (0.10), residues: 2768 sheet: -0.93 (0.17), residues: 817 loop : 0.25 (0.12), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 544 HIS 0.005 0.001 HIS F 260 PHE 0.016 0.002 PHE A 296 TYR 0.021 0.002 TYR C 112 ARG 0.003 0.000 ARG E 723 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 606 time to evaluate : 4.548 Fit side-chains REVERT: A 123 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: A 273 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6755 (tm-30) REVERT: A 331 GLU cc_start: 0.7404 (tp30) cc_final: 0.7081 (tp30) REVERT: A 776 GLU cc_start: 0.7259 (tt0) cc_final: 0.7017 (tt0) REVERT: B 123 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: B 273 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: B 331 GLU cc_start: 0.7403 (tp30) cc_final: 0.7085 (tp30) REVERT: B 776 GLU cc_start: 0.7255 (tt0) cc_final: 0.7013 (tt0) REVERT: C 123 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: C 273 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6773 (tm-30) REVERT: C 331 GLU cc_start: 0.7407 (tp30) cc_final: 0.7087 (tp30) REVERT: D 123 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: D 273 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6773 (tm-30) REVERT: D 328 ARG cc_start: 0.8504 (ttt90) cc_final: 0.8298 (ttt180) REVERT: D 331 GLU cc_start: 0.7410 (tp30) cc_final: 0.7092 (tp30) REVERT: E 123 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: E 273 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: E 331 GLU cc_start: 0.7404 (tp30) cc_final: 0.7087 (tp30) REVERT: E 776 GLU cc_start: 0.7275 (tt0) cc_final: 0.7035 (tt0) REVERT: F 123 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: F 273 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: F 331 GLU cc_start: 0.7404 (tp30) cc_final: 0.7084 (tp30) REVERT: G 123 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7428 (tm-30) REVERT: G 273 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: G 331 GLU cc_start: 0.7406 (tp30) cc_final: 0.7086 (tp30) REVERT: H 123 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: H 273 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6766 (tm-30) REVERT: H 328 ARG cc_start: 0.8504 (ttt90) cc_final: 0.8296 (ttt180) REVERT: H 331 GLU cc_start: 0.7405 (tp30) cc_final: 0.7060 (tp30) outliers start: 69 outliers final: 26 residues processed: 627 average time/residue: 1.9592 time to fit residues: 1473.0252 Evaluate side-chains 615 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 573 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 525 GLU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 525 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 575 optimal weight: 4.9990 chunk 437 optimal weight: 3.9990 chunk 302 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 277 optimal weight: 3.9990 chunk 390 optimal weight: 0.6980 chunk 584 optimal weight: 6.9990 chunk 618 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 553 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS A 546 GLN B A 549 ASN B ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS B 546 GLN B B 549 ASN B ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 HIS C 466 HIS C 546 GLN B C 549 ASN B ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS D 466 HIS D 546 GLN B D 549 ASN B ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS E 546 GLN B E 549 ASN B ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS F 546 GLN B F 549 ASN B ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 333 HIS G 546 GLN B G 549 ASN B ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 HIS H 546 GLN B H 549 ASN B Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 53414 Z= 0.314 Angle : 0.684 6.431 72706 Z= 0.374 Chirality : 0.050 0.193 7602 Planarity : 0.005 0.061 9577 Dihedral : 7.462 87.859 7173 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.05 % Allowed : 10.74 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.62 (0.10), residues: 6529 helix: 1.19 (0.10), residues: 2720 sheet: -0.96 (0.17), residues: 817 loop : 0.25 (0.12), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 65 HIS 0.007 0.002 HIS G 320 PHE 0.022 0.003 PHE G 237 TYR 0.024 0.003 TYR G 217 ARG 0.003 0.001 ARG H 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 578 time to evaluate : 4.584 Fit side-chains REVERT: A 123 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: A 273 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: A 776 GLU cc_start: 0.7313 (tt0) cc_final: 0.7107 (tt0) REVERT: B 123 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: B 273 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: B 776 GLU cc_start: 0.7260 (tt0) cc_final: 0.7053 (tt0) REVERT: C 123 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: C 273 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6721 (tm-30) REVERT: D 123 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: D 273 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6720 (tm-30) REVERT: E 123 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: E 273 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: E 776 GLU cc_start: 0.7256 (tt0) cc_final: 0.7044 (tt0) REVERT: F 123 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7426 (tm-30) REVERT: F 273 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: G 123 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7428 (tm-30) REVERT: G 273 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: H 123 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: H 273 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6716 (tm-30) outliers start: 57 outliers final: 33 residues processed: 595 average time/residue: 1.8915 time to fit residues: 1355.3894 Evaluate side-chains 603 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 554 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 401 GLU Chi-restraints excluded: chain G residue 525 GLU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 401 GLU Chi-restraints excluded: chain H residue 525 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 515 optimal weight: 10.0000 chunk 351 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 460 optimal weight: 5.9990 chunk 255 optimal weight: 3.9990 chunk 527 optimal weight: 7.9990 chunk 427 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 315 optimal weight: 4.9990 chunk 555 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS A 546 GLN B A 549 ASN B ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS B 546 GLN B B 549 ASN B ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 HIS C 546 GLN B C 549 ASN B ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS D 546 GLN B D 549 ASN B ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS E 546 GLN B E 549 ASN B ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS F 546 GLN B F 549 ASN B ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 333 HIS G 546 GLN B G 549 ASN B ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 HIS H 546 GLN B H 549 ASN B Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 53414 Z= 0.316 Angle : 0.681 6.247 72706 Z= 0.373 Chirality : 0.050 0.168 7602 Planarity : 0.005 0.061 9577 Dihedral : 7.423 87.954 7173 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.32 % Allowed : 10.39 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.60 (0.10), residues: 6529 helix: 1.18 (0.10), residues: 2720 sheet: -0.97 (0.17), residues: 817 loop : 0.23 (0.12), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 65 HIS 0.006 0.002 HIS F 287 PHE 0.022 0.003 PHE H 237 TYR 0.024 0.003 TYR E 217 ARG 0.003 0.001 ARG B 494 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 571 time to evaluate : 4.531 Fit side-chains REVERT: A 123 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: A 273 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6717 (tm-30) REVERT: A 331 GLU cc_start: 0.7508 (tp30) cc_final: 0.7120 (tp30) REVERT: A 776 GLU cc_start: 0.7323 (tt0) cc_final: 0.7106 (tt0) REVERT: B 123 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: B 273 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: B 331 GLU cc_start: 0.7506 (tp30) cc_final: 0.7119 (tp30) REVERT: B 776 GLU cc_start: 0.7278 (tt0) cc_final: 0.7064 (tt0) REVERT: C 123 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: C 273 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6732 (tm-30) REVERT: C 331 GLU cc_start: 0.7490 (tp30) cc_final: 0.7122 (tp30) REVERT: D 123 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: D 273 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6731 (tm-30) REVERT: D 331 GLU cc_start: 0.7513 (tp30) cc_final: 0.7138 (tp30) REVERT: E 123 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: E 273 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: E 331 GLU cc_start: 0.7510 (tp30) cc_final: 0.7125 (tp30) REVERT: E 776 GLU cc_start: 0.7274 (tt0) cc_final: 0.7060 (tt0) REVERT: F 123 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: F 273 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: F 331 GLU cc_start: 0.7507 (tp30) cc_final: 0.7121 (tp30) REVERT: G 123 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7439 (tm-30) REVERT: G 273 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6726 (tm-30) REVERT: G 331 GLU cc_start: 0.7511 (tp30) cc_final: 0.7123 (tp30) REVERT: H 123 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: H 273 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: H 331 GLU cc_start: 0.7483 (tp30) cc_final: 0.7117 (tp30) outliers start: 64 outliers final: 33 residues processed: 588 average time/residue: 1.9257 time to fit residues: 1357.6470 Evaluate side-chains 608 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 559 time to evaluate : 4.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 401 GLU Chi-restraints excluded: chain G residue 525 GLU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 401 GLU Chi-restraints excluded: chain H residue 525 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 208 optimal weight: 7.9990 chunk 557 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 363 optimal weight: 0.9980 chunk 152 optimal weight: 0.0070 chunk 619 optimal weight: 5.9990 chunk 514 optimal weight: 0.9980 chunk 286 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 325 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 333 HIS A 546 GLN B A 549 ASN B A 673 ASN B 321 GLN B 333 HIS B 546 GLN B B 549 ASN B B 673 ASN C 321 GLN C 333 HIS C 546 GLN B C 549 ASN B D 321 GLN D 333 HIS D 546 GLN B D 549 ASN B E 321 GLN E 333 HIS E 546 GLN B E 549 ASN B E 673 ASN F 321 GLN F 333 HIS F 546 GLN B F 549 ASN B G 321 GLN G 333 HIS G 546 GLN B G 549 ASN B G 673 ASN H 321 GLN H 333 HIS H 546 GLN B H 549 ASN B H 673 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 53414 Z= 0.175 Angle : 0.565 7.516 72706 Z= 0.306 Chirality : 0.045 0.272 7602 Planarity : 0.004 0.037 9577 Dihedral : 6.959 88.023 7173 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.23 % Allowed : 10.39 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.85 (0.11), residues: 6529 helix: 1.38 (0.10), residues: 2768 sheet: -0.73 (0.17), residues: 857 loop : 0.34 (0.12), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 498 HIS 0.005 0.001 HIS F 152 PHE 0.017 0.002 PHE A 236 TYR 0.017 0.002 TYR C 744 ARG 0.002 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 616 time to evaluate : 4.600 Fit side-chains REVERT: A 123 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: A 273 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: A 331 GLU cc_start: 0.7422 (tp30) cc_final: 0.7050 (tp30) REVERT: A 641 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7621 (mt-10) REVERT: B 123 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: B 273 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6790 (tm-30) REVERT: B 331 GLU cc_start: 0.7420 (tp30) cc_final: 0.7051 (tp30) REVERT: C 123 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: C 273 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6800 (tm-30) REVERT: C 331 GLU cc_start: 0.7425 (tp30) cc_final: 0.7056 (tp30) REVERT: C 641 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7619 (mt-10) REVERT: D 123 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: D 273 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6798 (tm-30) REVERT: D 331 GLU cc_start: 0.7430 (tp30) cc_final: 0.7060 (tp30) REVERT: E 123 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: E 273 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6798 (tm-30) REVERT: E 331 GLU cc_start: 0.7422 (tp30) cc_final: 0.7055 (tp30) REVERT: E 345 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8143 (mtmt) REVERT: F 123 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: F 273 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6796 (tm-30) REVERT: F 331 GLU cc_start: 0.7422 (tp30) cc_final: 0.7052 (tp30) REVERT: F 641 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7620 (mt-10) REVERT: G 123 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: G 273 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6788 (tm-30) REVERT: G 331 GLU cc_start: 0.7423 (tp30) cc_final: 0.7052 (tp30) REVERT: H 123 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: H 273 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6794 (tm-30) REVERT: H 331 GLU cc_start: 0.7415 (tp30) cc_final: 0.6750 (tt0) REVERT: H 641 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7620 (mt-10) outliers start: 67 outliers final: 32 residues processed: 633 average time/residue: 1.8485 time to fit residues: 1415.5152 Evaluate side-chains 638 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 590 time to evaluate : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 401 GLU Chi-restraints excluded: chain G residue 525 GLU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 401 GLU Chi-restraints excluded: chain H residue 525 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 597 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 352 optimal weight: 9.9990 chunk 452 optimal weight: 7.9990 chunk 350 optimal weight: 4.9990 chunk 521 optimal weight: 9.9990 chunk 345 optimal weight: 1.9990 chunk 616 optimal weight: 6.9990 chunk 386 optimal weight: 0.7980 chunk 376 optimal weight: 6.9990 chunk 284 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN B A 549 ASN B A 636 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 GLN B B 549 ASN B B 636 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 HIS C 546 GLN B C 549 ASN B C 636 ASN ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS D 546 GLN B D 549 ASN B D 636 ASN ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 GLN B E 549 ASN B E 636 ASN ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 GLN B F 549 ASN B F 636 ASN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 333 HIS ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 546 GLN B G 549 ASN B G 636 ASN ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 HIS ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 546 GLN B H 549 ASN B H 636 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 53414 Z= 0.275 Angle : 0.651 7.927 72706 Z= 0.354 Chirality : 0.049 0.306 7602 Planarity : 0.005 0.054 9577 Dihedral : 7.112 87.498 7173 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.90 % Allowed : 11.12 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.77 (0.11), residues: 6529 helix: 1.26 (0.10), residues: 2768 sheet: -0.91 (0.18), residues: 817 loop : 0.39 (0.12), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 65 HIS 0.006 0.002 HIS E 287 PHE 0.020 0.003 PHE F 237 TYR 0.021 0.002 TYR B 112 ARG 0.003 0.000 ARG A 494 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 588 time to evaluate : 4.567 Fit side-chains REVERT: A 123 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: A 273 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: A 331 GLU cc_start: 0.7556 (tp30) cc_final: 0.7170 (tp30) REVERT: B 123 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: B 273 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: B 331 GLU cc_start: 0.7554 (tp30) cc_final: 0.7171 (tp30) REVERT: C 123 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7417 (tm-30) REVERT: C 273 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: C 331 GLU cc_start: 0.7555 (tp30) cc_final: 0.7173 (tp30) REVERT: D 123 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: D 273 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: D 331 GLU cc_start: 0.7560 (tp30) cc_final: 0.7152 (tp30) REVERT: E 123 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7424 (tm-30) REVERT: E 273 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6765 (tm-30) REVERT: E 331 GLU cc_start: 0.7553 (tp30) cc_final: 0.7171 (tp30) REVERT: E 722 ASP cc_start: 0.8544 (p0) cc_final: 0.8341 (p0) REVERT: F 123 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: F 273 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: F 331 GLU cc_start: 0.7555 (tp30) cc_final: 0.7171 (tp30) REVERT: G 123 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: G 273 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6756 (tm-30) REVERT: G 331 GLU cc_start: 0.7554 (tp30) cc_final: 0.7170 (tp30) REVERT: H 123 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: H 273 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6761 (tm-30) REVERT: H 331 GLU cc_start: 0.7495 (tp30) cc_final: 0.7085 (tp30) outliers start: 41 outliers final: 24 residues processed: 605 average time/residue: 1.9344 time to fit residues: 1402.0242 Evaluate side-chains 626 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 586 time to evaluate : 4.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 401 GLU Chi-restraints excluded: chain G residue 525 GLU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 401 GLU Chi-restraints excluded: chain H residue 525 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 381 optimal weight: 10.0000 chunk 246 optimal weight: 0.8980 chunk 368 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 121 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 392 optimal weight: 0.1980 chunk 420 optimal weight: 7.9990 chunk 304 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 484 optimal weight: 8.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN B A 549 ASN B A 636 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 GLN B B 549 ASN B B 636 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 HIS C 546 GLN B C 549 ASN B C 636 ASN ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS D 546 GLN B D 549 ASN B D 636 ASN ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 GLN B E 549 ASN B E 636 ASN ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 GLN B F 549 ASN B F 636 ASN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 333 HIS ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 546 GLN B G 549 ASN B G 636 ASN ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 HIS ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 546 GLN B H 549 ASN B H 636 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 53414 Z= 0.248 Angle : 0.634 7.768 72706 Z= 0.343 Chirality : 0.048 0.282 7602 Planarity : 0.005 0.051 9577 Dihedral : 7.024 87.915 7165 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.88 % Allowed : 11.19 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.85 (0.11), residues: 6529 helix: 1.38 (0.10), residues: 2720 sheet: -0.91 (0.18), residues: 817 loop : 0.39 (0.12), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 65 HIS 0.005 0.001 HIS G 287 PHE 0.018 0.002 PHE A 237 TYR 0.020 0.002 TYR D 112 ARG 0.002 0.000 ARG C 494 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 589 time to evaluate : 4.526 Fit side-chains REVERT: A 123 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: A 273 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6747 (tm-30) REVERT: A 331 GLU cc_start: 0.7541 (tp30) cc_final: 0.7162 (tp30) REVERT: A 333 HIS cc_start: 0.7783 (m90) cc_final: 0.7456 (m90) REVERT: B 123 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: B 273 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: B 331 GLU cc_start: 0.7540 (tp30) cc_final: 0.7161 (tp30) REVERT: B 333 HIS cc_start: 0.7788 (m90) cc_final: 0.7458 (m90) REVERT: C 123 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: C 273 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: C 331 GLU cc_start: 0.7541 (tp30) cc_final: 0.7164 (tp30) REVERT: C 333 HIS cc_start: 0.7788 (m90) cc_final: 0.7461 (m90) REVERT: D 123 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: D 273 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6759 (tm-30) REVERT: D 331 GLU cc_start: 0.7549 (tp30) cc_final: 0.7101 (tp30) REVERT: D 333 HIS cc_start: 0.7787 (m90) cc_final: 0.7456 (m90) REVERT: E 123 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: E 273 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: E 331 GLU cc_start: 0.7538 (tp30) cc_final: 0.7161 (tp30) REVERT: E 333 HIS cc_start: 0.7847 (m90) cc_final: 0.7459 (m170) REVERT: F 123 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: F 273 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: F 331 GLU cc_start: 0.7540 (tp30) cc_final: 0.7162 (tp30) REVERT: F 333 HIS cc_start: 0.7784 (m90) cc_final: 0.7456 (m90) REVERT: G 123 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: G 273 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: G 331 GLU cc_start: 0.7543 (tp30) cc_final: 0.7163 (tp30) REVERT: G 333 HIS cc_start: 0.7787 (m90) cc_final: 0.7459 (m90) REVERT: H 123 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: H 273 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6756 (tm-30) REVERT: H 331 GLU cc_start: 0.7479 (tp30) cc_final: 0.7114 (tp30) REVERT: H 333 HIS cc_start: 0.7788 (m90) cc_final: 0.7454 (m90) outliers start: 48 outliers final: 24 residues processed: 605 average time/residue: 1.9430 time to fit residues: 1409.2717 Evaluate side-chains 612 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 572 time to evaluate : 4.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 401 GLU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 401 GLU Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 401 GLU Chi-restraints excluded: chain G residue 525 GLU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 401 GLU Chi-restraints excluded: chain H residue 525 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 561 optimal weight: 3.9990 chunk 590 optimal weight: 4.9990 chunk 539 optimal weight: 2.9990 chunk 574 optimal weight: 2.9990 chunk 345 optimal weight: 0.9980 chunk 250 optimal weight: 10.0000 chunk 451 optimal weight: 0.8980 chunk 176 optimal weight: 10.0000 chunk 519 optimal weight: 8.9990 chunk 543 optimal weight: 0.0270 chunk 572 optimal weight: 8.9990 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN B A 549 ASN B A 636 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 GLN B B 549 ASN B B 636 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 GLN B C 549 ASN B C 636 ASN ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 GLN B D 549 ASN B D 636 ASN ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 GLN B E 549 ASN B E 636 ASN ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 GLN B F 549 ASN B F 636 ASN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 546 GLN B G 549 ASN B G 636 ASN ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 546 GLN B H 549 ASN B H 636 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 53414 Z= 0.203 Angle : 0.595 7.901 72706 Z= 0.321 Chirality : 0.046 0.285 7602 Planarity : 0.004 0.041 9577 Dihedral : 6.859 88.449 7165 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.97 % Allowed : 10.97 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.88 (0.11), residues: 6529 helix: 1.36 (0.10), residues: 2768 sheet: -0.89 (0.18), residues: 817 loop : 0.45 (0.12), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 65 HIS 0.005 0.001 HIS B 152 PHE 0.017 0.002 PHE C 236 TYR 0.018 0.002 TYR A 112 ARG 0.002 0.000 ARG C 494 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 600 time to evaluate : 4.494 Fit side-chains REVERT: A 123 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: A 273 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6753 (tm-30) REVERT: A 331 GLU cc_start: 0.7516 (tp30) cc_final: 0.7172 (tp30) REVERT: A 333 HIS cc_start: 0.7814 (m90) cc_final: 0.7446 (m90) REVERT: A 345 LYS cc_start: 0.8435 (mtmm) cc_final: 0.8162 (mtmt) REVERT: B 123 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: B 273 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: B 331 GLU cc_start: 0.7514 (tp30) cc_final: 0.7173 (tp30) REVERT: B 333 HIS cc_start: 0.7816 (m90) cc_final: 0.7447 (m90) REVERT: B 345 LYS cc_start: 0.8435 (mtmm) cc_final: 0.8162 (mtmt) REVERT: C 123 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: C 273 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: C 331 GLU cc_start: 0.7516 (tp30) cc_final: 0.7173 (tp30) REVERT: C 333 HIS cc_start: 0.7816 (m90) cc_final: 0.7448 (m90) REVERT: D 123 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: D 273 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6766 (tm-30) REVERT: D 331 GLU cc_start: 0.7518 (tp30) cc_final: 0.7173 (tp30) REVERT: D 333 HIS cc_start: 0.7816 (m90) cc_final: 0.7445 (m90) REVERT: D 345 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8147 (mtmt) REVERT: E 123 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: E 273 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: E 331 GLU cc_start: 0.7513 (tp30) cc_final: 0.7176 (tp30) REVERT: E 345 LYS cc_start: 0.8363 (mtmm) cc_final: 0.8160 (mtmt) REVERT: F 123 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: F 273 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: F 331 GLU cc_start: 0.7516 (tp30) cc_final: 0.7175 (tp30) REVERT: F 333 HIS cc_start: 0.7814 (m90) cc_final: 0.7447 (m90) REVERT: F 345 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8161 (mtmt) REVERT: G 123 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: G 273 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6758 (tm-30) REVERT: G 331 GLU cc_start: 0.7517 (tp30) cc_final: 0.7176 (tp30) REVERT: G 333 HIS cc_start: 0.7815 (m90) cc_final: 0.7447 (m90) REVERT: G 345 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8162 (mtmt) REVERT: H 123 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: H 273 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6760 (tm-30) REVERT: H 331 GLU cc_start: 0.7463 (tp30) cc_final: 0.7137 (tp30) REVERT: H 333 HIS cc_start: 0.7819 (m90) cc_final: 0.7442 (m90) REVERT: H 345 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8164 (mtmt) outliers start: 45 outliers final: 17 residues processed: 608 average time/residue: 1.9474 time to fit residues: 1418.3014 Evaluate side-chains 627 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 594 time to evaluate : 4.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 525 GLU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 525 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 377 optimal weight: 10.0000 chunk 607 optimal weight: 9.9990 chunk 371 optimal weight: 9.9990 chunk 288 optimal weight: 0.8980 chunk 422 optimal weight: 6.9990 chunk 637 optimal weight: 4.9990 chunk 586 optimal weight: 0.7980 chunk 507 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 392 optimal weight: 0.2980 chunk 311 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN B A 549 ASN B A 636 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 GLN B B 549 ASN B B 636 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 GLN B C 549 ASN B C 636 ASN ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 GLN B D 549 ASN B D 636 ASN ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS E 546 GLN B E 549 ASN B E 636 ASN ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 GLN B F 549 ASN B F 636 ASN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 546 GLN B G 549 ASN B G 636 ASN ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 546 GLN B H 549 ASN B H 636 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 53414 Z= 0.161 Angle : 0.554 8.134 72706 Z= 0.297 Chirality : 0.045 0.387 7602 Planarity : 0.004 0.036 9577 Dihedral : 6.563 89.663 7165 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.73 % Allowed : 11.23 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.01 (0.11), residues: 6529 helix: 1.49 (0.10), residues: 2768 sheet: -0.64 (0.18), residues: 833 loop : 0.43 (0.12), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 498 HIS 0.005 0.001 HIS B 152 PHE 0.018 0.002 PHE A 236 TYR 0.016 0.002 TYR E 744 ARG 0.002 0.000 ARG G 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 619 time to evaluate : 4.497 Fit side-chains REVERT: A 273 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6800 (tm-30) REVERT: A 331 GLU cc_start: 0.7384 (tp30) cc_final: 0.7030 (tp30) REVERT: A 345 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8132 (mtmt) REVERT: A 684 LYS cc_start: 0.7699 (mmtt) cc_final: 0.7432 (mmpt) REVERT: B 273 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6801 (tm-30) REVERT: B 331 GLU cc_start: 0.7385 (tp30) cc_final: 0.7033 (tp30) REVERT: B 345 LYS cc_start: 0.8387 (mtmm) cc_final: 0.8128 (mtmt) REVERT: B 684 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7433 (mmpt) REVERT: C 273 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: C 331 GLU cc_start: 0.7386 (tp30) cc_final: 0.7033 (tp30) REVERT: C 684 LYS cc_start: 0.7699 (mmtt) cc_final: 0.7431 (mmpt) REVERT: D 273 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: D 331 GLU cc_start: 0.7400 (tp30) cc_final: 0.7048 (tp30) REVERT: D 345 LYS cc_start: 0.8388 (mtmm) cc_final: 0.8119 (mtmt) REVERT: D 684 LYS cc_start: 0.7700 (mmtt) cc_final: 0.7432 (mmpt) REVERT: E 273 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6812 (tm-30) REVERT: E 331 GLU cc_start: 0.7451 (tp30) cc_final: 0.7054 (tp30) REVERT: E 345 LYS cc_start: 0.8357 (mtmm) cc_final: 0.8153 (mtmt) REVERT: E 684 LYS cc_start: 0.7709 (mmtt) cc_final: 0.7434 (mmpt) REVERT: F 273 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6809 (tm-30) REVERT: F 331 GLU cc_start: 0.7386 (tp30) cc_final: 0.7034 (tp30) REVERT: F 345 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8130 (mtmt) REVERT: F 684 LYS cc_start: 0.7708 (mmtt) cc_final: 0.7438 (mmpt) REVERT: G 273 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6805 (tm-30) REVERT: G 331 GLU cc_start: 0.7387 (tp30) cc_final: 0.7033 (tp30) REVERT: G 345 LYS cc_start: 0.8398 (mtmm) cc_final: 0.8131 (mtmt) REVERT: G 684 LYS cc_start: 0.7704 (mmtt) cc_final: 0.7429 (mmpt) REVERT: H 273 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6807 (tm-30) REVERT: H 331 GLU cc_start: 0.7374 (tp30) cc_final: 0.7024 (tp30) REVERT: H 345 LYS cc_start: 0.8399 (mtmm) cc_final: 0.8135 (mtmt) REVERT: H 684 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7435 (mmpt) outliers start: 40 outliers final: 16 residues processed: 627 average time/residue: 1.8951 time to fit residues: 1429.5215 Evaluate side-chains 628 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 604 time to evaluate : 4.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 525 GLU Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain D residue 273 GLU Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 525 GLU Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 525 GLU Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 525 GLU Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 381 VAL Chi-restraints excluded: chain G residue 525 GLU Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 381 VAL Chi-restraints excluded: chain H residue 525 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 403 optimal weight: 5.9990 chunk 540 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 468 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 508 optimal weight: 0.7980 chunk 212 optimal weight: 0.0570 chunk 522 optimal weight: 0.0770 chunk 64 optimal weight: 5.9990 chunk 93 optimal weight: 0.0070 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS A 636 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 ASN ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 ASN ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS E 636 ASN ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS F 636 ASN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 333 HIS G 636 ASN ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 HIS H 636 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.102233 restraints weight = 136928.878| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.50 r_work: 0.2915 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 53414 Z= 0.143 Angle : 0.527 9.345 72706 Z= 0.279 Chirality : 0.044 0.396 7602 Planarity : 0.004 0.034 9577 Dihedral : 5.811 84.565 7141 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.59 % Allowed : 11.84 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.21 (0.11), residues: 6529 helix: 1.75 (0.10), residues: 2712 sheet: -0.59 (0.18), residues: 849 loop : 0.48 (0.12), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 498 HIS 0.005 0.001 HIS B 152 PHE 0.019 0.001 PHE H 236 TYR 0.015 0.001 TYR E 744 ARG 0.002 0.000 ARG G 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21537.50 seconds wall clock time: 369 minutes 19.93 seconds (22159.93 seconds total)