Starting phenix.real_space_refine on Sat Mar 23 07:35:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcv_31897/03_2024/7vcv_31897_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcv_31897/03_2024/7vcv_31897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcv_31897/03_2024/7vcv_31897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcv_31897/03_2024/7vcv_31897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcv_31897/03_2024/7vcv_31897_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vcv_31897/03_2024/7vcv_31897_updated.pdb" } resolution = 3.21 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= 0.004 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 P 36 5.49 5 Mg 12 5.21 5 S 198 5.16 5 C 22494 2.51 5 N 6372 2.21 5 O 6924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 732": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "F ARG 225": "NH1" <-> "NH2" Residue "F ARG 239": "NH1" <-> "NH2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F ARG 453": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F ARG 560": "NH1" <-> "NH2" Residue "F ARG 599": "NH1" <-> "NH2" Residue "F ARG 662": "NH1" <-> "NH2" Residue "F PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 693": "NH1" <-> "NH2" Residue "F ARG 713": "NH1" <-> "NH2" Residue "F ARG 732": "NH1" <-> "NH2" Residue "F ARG 753": "NH1" <-> "NH2" Residue "F ARG 766": "NH1" <-> "NH2" Residue "E ARG 225": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "E ARG 453": "NH1" <-> "NH2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E ARG 560": "NH1" <-> "NH2" Residue "E ARG 599": "NH1" <-> "NH2" Residue "E ARG 662": "NH1" <-> "NH2" Residue "E PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 693": "NH1" <-> "NH2" Residue "E ARG 713": "NH1" <-> "NH2" Residue "E ARG 732": "NH1" <-> "NH2" Residue "E ARG 753": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D ARG 599": "NH1" <-> "NH2" Residue "D ARG 662": "NH1" <-> "NH2" Residue "D PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 713": "NH1" <-> "NH2" Residue "D ARG 732": "NH1" <-> "NH2" Residue "D ARG 753": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 662": "NH1" <-> "NH2" Residue "C PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 713": "NH1" <-> "NH2" Residue "C ARG 732": "NH1" <-> "NH2" Residue "C ARG 753": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 599": "NH1" <-> "NH2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 713": "NH1" <-> "NH2" Residue "B ARG 732": "NH1" <-> "NH2" Residue "B ARG 753": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36036 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5942 Classifications: {'peptide': 758} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 716} Chain: "F" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5942 Classifications: {'peptide': 758} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 716} Chain: "E" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5942 Classifications: {'peptide': 758} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 716} Chain: "D" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5942 Classifications: {'peptide': 758} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 716} Chain: "C" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5942 Classifications: {'peptide': 758} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 716} Chain: "B" Number of atoms: 5942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5942 Classifications: {'peptide': 758} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 716} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 18.82, per 1000 atoms: 0.52 Number of scatterers: 36036 At special positions: 0 Unit cell: (178.2, 173.88, 117.72, 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) S 198 16.00 P 36 15.00 Mg 12 11.99 O 6924 8.00 N 6372 7.00 C 22494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.76 Conformation dependent library (CDL) restraints added in 6.9 seconds 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8496 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 198 helices and 30 sheets defined 38.8% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.00 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 43 through 46 No H-bonds generated for 'chain 'A' and resid 43 through 46' Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 131 through 134 No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 136 through 139 No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.660A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 No H-bonds generated for 'chain 'A' and resid 222 through 225' Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 320 through 333 Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.512A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 426 removed outlier: 3.855A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 484 through 498 removed outlier: 4.649A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 501 through 505 removed outlier: 3.936A pdb=" N LYS A 505 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 removed outlier: 3.690A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 Processing helix chain 'A' and resid 557 through 568 Processing helix chain 'A' and resid 579 through 586 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 650 through 662 removed outlier: 3.542A pdb=" N LEU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 715 Processing helix chain 'A' and resid 735 through 742 Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 43 through 46 No H-bonds generated for 'chain 'F' and resid 43 through 46' Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 131 through 134 No H-bonds generated for 'chain 'F' and resid 131 through 134' Processing helix chain 'F' and resid 136 through 139 No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 191 through 195 Processing helix chain 'F' and resid 210 through 219 removed outlier: 3.659A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 225 No H-bonds generated for 'chain 'F' and resid 222 through 225' Processing helix chain 'F' and resid 227 through 233 Processing helix chain 'F' and resid 252 through 261 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 282 through 295 Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 320 through 333 Processing helix chain 'F' and resid 374 through 386 removed outlier: 3.511A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS F 386 " --> pdb=" O GLN F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 426 removed outlier: 3.854A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 484 through 498 removed outlier: 4.649A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 501 through 505 removed outlier: 3.936A pdb=" N LYS F 505 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 535 removed outlier: 3.690A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 544 through 548 Processing helix chain 'F' and resid 557 through 568 Processing helix chain 'F' and resid 579 through 586 Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 650 through 662 removed outlier: 3.541A pdb=" N LEU F 661 " --> pdb=" O LEU F 657 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG F 662 " --> pdb=" O LYS F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 715 Processing helix chain 'F' and resid 735 through 742 Processing helix chain 'F' and resid 749 through 760 Processing helix chain 'F' and resid 763 through 765 No H-bonds generated for 'chain 'F' and resid 763 through 765' Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 43 through 46 No H-bonds generated for 'chain 'E' and resid 43 through 46' Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 120 through 123 No H-bonds generated for 'chain 'E' and resid 120 through 123' Processing helix chain 'E' and resid 131 through 134 No H-bonds generated for 'chain 'E' and resid 131 through 134' Processing helix chain 'E' and resid 136 through 139 No H-bonds generated for 'chain 'E' and resid 136 through 139' Processing helix chain 'E' and resid 191 through 195 Processing helix chain 'E' and resid 210 through 219 removed outlier: 3.660A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 225 No H-bonds generated for 'chain 'E' and resid 222 through 225' Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 252 through 261 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 282 through 295 Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 320 through 333 Processing helix chain 'E' and resid 374 through 386 removed outlier: 3.512A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS E 386 " --> pdb=" O GLN E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 426 removed outlier: 3.855A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 484 through 498 removed outlier: 4.649A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 501 through 505 removed outlier: 3.936A pdb=" N LYS E 505 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 535 removed outlier: 3.690A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 548 Processing helix chain 'E' and resid 557 through 568 Processing helix chain 'E' and resid 579 through 586 Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 650 through 662 removed outlier: 3.541A pdb=" N LEU E 661 " --> pdb=" O LEU E 657 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG E 662 " --> pdb=" O LYS E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 715 Processing helix chain 'E' and resid 735 through 742 Processing helix chain 'E' and resid 749 through 760 Processing helix chain 'E' and resid 763 through 765 No H-bonds generated for 'chain 'E' and resid 763 through 765' Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 43 through 46 No H-bonds generated for 'chain 'D' and resid 43 through 46' Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 120 through 123 No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 131 through 134 No H-bonds generated for 'chain 'D' and resid 131 through 134' Processing helix chain 'D' and resid 136 through 139 No H-bonds generated for 'chain 'D' and resid 136 through 139' Processing helix chain 'D' and resid 191 through 195 Processing helix chain 'D' and resid 210 through 219 removed outlier: 3.660A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 282 through 295 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 320 through 333 Processing helix chain 'D' and resid 374 through 386 removed outlier: 3.512A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS D 386 " --> pdb=" O GLN D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 426 removed outlier: 3.855A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 484 through 498 removed outlier: 4.649A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 501 through 505 removed outlier: 3.936A pdb=" N LYS D 505 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 535 removed outlier: 3.690A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 548 Processing helix chain 'D' and resid 557 through 568 Processing helix chain 'D' and resid 579 through 586 Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 650 through 662 removed outlier: 3.542A pdb=" N LEU D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG D 662 " --> pdb=" O LYS D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 715 Processing helix chain 'D' and resid 735 through 742 Processing helix chain 'D' and resid 749 through 760 Processing helix chain 'D' and resid 763 through 765 No H-bonds generated for 'chain 'D' and resid 763 through 765' Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 43 through 46 No H-bonds generated for 'chain 'C' and resid 43 through 46' Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 120 through 123 No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 131 through 134 No H-bonds generated for 'chain 'C' and resid 131 through 134' Processing helix chain 'C' and resid 136 through 139 No H-bonds generated for 'chain 'C' and resid 136 through 139' Processing helix chain 'C' and resid 191 through 195 Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.659A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 282 through 295 Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 320 through 333 Processing helix chain 'C' and resid 374 through 386 removed outlier: 3.512A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS C 386 " --> pdb=" O GLN C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 426 removed outlier: 3.855A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 443 Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 484 through 498 removed outlier: 4.650A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 501 through 505 removed outlier: 3.935A pdb=" N LYS C 505 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 535 removed outlier: 3.690A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 548 Processing helix chain 'C' and resid 557 through 568 Processing helix chain 'C' and resid 579 through 586 Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 650 through 662 removed outlier: 3.542A pdb=" N LEU C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG C 662 " --> pdb=" O LYS C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 715 Processing helix chain 'C' and resid 735 through 742 Processing helix chain 'C' and resid 749 through 760 Processing helix chain 'C' and resid 763 through 765 No H-bonds generated for 'chain 'C' and resid 763 through 765' Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 43 through 46 No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 131 through 134 No H-bonds generated for 'chain 'B' and resid 131 through 134' Processing helix chain 'B' and resid 136 through 139 No H-bonds generated for 'chain 'B' and resid 136 through 139' Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.660A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 282 through 295 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 320 through 333 Processing helix chain 'B' and resid 374 through 386 removed outlier: 3.512A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS B 386 " --> pdb=" O GLN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 426 removed outlier: 3.855A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 484 through 498 removed outlier: 4.649A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 501 through 505 removed outlier: 3.936A pdb=" N LYS B 505 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 535 removed outlier: 3.690A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 548 Processing helix chain 'B' and resid 557 through 568 Processing helix chain 'B' and resid 579 through 586 Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 650 through 662 removed outlier: 3.541A pdb=" N LEU B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ARG B 662 " --> pdb=" O LYS B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 715 Processing helix chain 'B' and resid 735 through 742 Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing sheet with id= A, first strand: chain 'A' and resid 25 through 27 removed outlier: 3.507A pdb=" N VAL A 57 " --> pdb=" O CYS A 69 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS A 69 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 113 through 115 removed outlier: 6.016A pdb=" N VAL A 181 " --> pdb=" O ILE A 114 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 116 through 118 removed outlier: 4.354A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 154 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 365 through 368 removed outlier: 3.538A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.676A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 25 through 27 removed outlier: 3.507A pdb=" N VAL F 57 " --> pdb=" O CYS F 69 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS F 69 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 113 through 115 removed outlier: 6.016A pdb=" N VAL F 181 " --> pdb=" O ILE F 114 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'F' and resid 116 through 118 removed outlier: 4.354A pdb=" N VAL F 161 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL F 154 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.538A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.676A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 25 through 27 removed outlier: 3.507A pdb=" N VAL E 57 " --> pdb=" O CYS E 69 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 113 through 115 removed outlier: 6.016A pdb=" N VAL E 181 " --> pdb=" O ILE E 114 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 116 through 118 removed outlier: 4.354A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 154 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 365 through 368 removed outlier: 3.538A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.676A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.507A pdb=" N VAL D 57 " --> pdb=" O CYS D 69 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 113 through 115 removed outlier: 6.016A pdb=" N VAL D 181 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 116 through 118 removed outlier: 4.354A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 154 " --> pdb=" O VAL D 161 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 365 through 368 removed outlier: 3.538A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.676A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.507A pdb=" N VAL C 57 " --> pdb=" O CYS C 69 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 113 through 115 removed outlier: 6.016A pdb=" N VAL C 181 " --> pdb=" O ILE C 114 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'C' and resid 116 through 118 removed outlier: 4.354A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 154 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 365 through 368 removed outlier: 3.538A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.676A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.507A pdb=" N VAL B 57 " --> pdb=" O CYS B 69 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS B 69 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 113 through 115 removed outlier: 6.016A pdb=" N VAL B 181 " --> pdb=" O ILE B 114 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'B' and resid 116 through 118 removed outlier: 4.354A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 154 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.538A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.676A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 3078 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: 13.12 Time building geometry restraints manager: 14.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 12625 1.36 - 1.50: 10709 1.50 - 1.65: 12978 1.65 - 1.79: 207 1.79 - 1.94: 105 Bond restraints: 36624 Sorted by residual: bond pdb=" N ARG D 635 " pdb=" CA ARG D 635 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.04e-02 9.25e+03 9.63e+00 bond pdb=" N ARG F 635 " pdb=" CA ARG F 635 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.04e-02 9.25e+03 9.57e+00 bond pdb=" N ARG E 635 " pdb=" CA ARG E 635 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.04e-02 9.25e+03 9.24e+00 bond pdb=" N ARG C 635 " pdb=" CA ARG C 635 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.04e-02 9.25e+03 9.05e+00 bond pdb=" C ARG F 22 " pdb=" N PRO F 23 " ideal model delta sigma weight residual 1.335 1.369 -0.034 1.19e-02 7.06e+03 8.27e+00 ... (remaining 36619 not shown) Histogram of bond angle deviations from ideal: 96.16 - 103.76: 694 103.76 - 111.35: 14766 111.35 - 118.95: 15219 118.95 - 126.55: 18433 126.55 - 134.14: 424 Bond angle restraints: 49536 Sorted by residual: angle pdb=" C ILE F 206 " pdb=" N GLY F 207 " pdb=" CA GLY F 207 " ideal model delta sigma weight residual 122.33 119.13 3.20 7.30e-01 1.88e+00 1.92e+01 angle pdb=" C ILE B 206 " pdb=" N GLY B 207 " pdb=" CA GLY B 207 " ideal model delta sigma weight residual 122.33 119.13 3.20 7.30e-01 1.88e+00 1.92e+01 angle pdb=" C ILE E 206 " pdb=" N GLY E 207 " pdb=" CA GLY E 207 " ideal model delta sigma weight residual 122.33 119.13 3.20 7.30e-01 1.88e+00 1.92e+01 angle pdb=" C ILE C 206 " pdb=" N GLY C 207 " pdb=" CA GLY C 207 " ideal model delta sigma weight residual 122.33 119.16 3.17 7.30e-01 1.88e+00 1.88e+01 angle pdb=" C ILE D 206 " pdb=" N GLY D 207 " pdb=" CA GLY D 207 " ideal model delta sigma weight residual 122.33 119.18 3.15 7.30e-01 1.88e+00 1.87e+01 ... (remaining 49531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 21519 14.84 - 29.68: 961 29.68 - 44.52: 242 44.52 - 59.36: 78 59.36 - 74.20: 18 Dihedral angle restraints: 22818 sinusoidal: 9714 harmonic: 13104 Sorted by residual: dihedral pdb=" CA GLU C 261 " pdb=" C GLU C 261 " pdb=" N THR C 262 " pdb=" CA THR C 262 " ideal model delta harmonic sigma weight residual -180.00 -131.52 -48.48 0 5.00e+00 4.00e-02 9.40e+01 dihedral pdb=" CA GLU F 261 " pdb=" C GLU F 261 " pdb=" N THR F 262 " pdb=" CA THR F 262 " ideal model delta harmonic sigma weight residual -180.00 -131.53 -48.47 0 5.00e+00 4.00e-02 9.40e+01 dihedral pdb=" CA GLU D 261 " pdb=" C GLU D 261 " pdb=" N THR D 262 " pdb=" CA THR D 262 " ideal model delta harmonic sigma weight residual -180.00 -131.54 -48.46 0 5.00e+00 4.00e-02 9.39e+01 ... (remaining 22815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3435 0.049 - 0.099: 1522 0.099 - 0.148: 504 0.148 - 0.198: 99 0.198 - 0.247: 14 Chirality restraints: 5574 Sorted by residual: chirality pdb=" CG LEU C 642 " pdb=" CB LEU C 642 " pdb=" CD1 LEU C 642 " pdb=" CD2 LEU C 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CG LEU F 642 " pdb=" CB LEU F 642 " pdb=" CD1 LEU F 642 " pdb=" CD2 LEU F 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CG LEU D 642 " pdb=" CB LEU D 642 " pdb=" CD1 LEU D 642 " pdb=" CD2 LEU D 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 5571 not shown) Planarity restraints: 6516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 290 " 0.015 2.00e-02 2.50e+03 2.34e-02 9.62e+00 pdb=" CG PHE B 290 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE B 290 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE B 290 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 290 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 290 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 290 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 290 " -0.015 2.00e-02 2.50e+03 2.34e-02 9.62e+00 pdb=" CG PHE E 290 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE E 290 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE E 290 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE E 290 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE E 290 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE E 290 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 290 " 0.014 2.00e-02 2.50e+03 2.33e-02 9.52e+00 pdb=" CG PHE C 290 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE C 290 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE C 290 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 290 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE C 290 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 290 " 0.000 2.00e-02 2.50e+03 ... (remaining 6513 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 480 2.66 - 3.22: 31185 3.22 - 3.78: 50433 3.78 - 4.34: 69521 4.34 - 4.90: 115304 Nonbonded interactions: 266923 Sorted by model distance: nonbonded pdb=" O2G AGS A 901 " pdb="MG MG A 902 " model vdw 2.097 2.170 nonbonded pdb=" O2G AGS D 901 " pdb="MG MG D 902 " model vdw 2.097 2.170 nonbonded pdb=" O2G AGS F 901 " pdb="MG MG F 902 " model vdw 2.097 2.170 nonbonded pdb=" O2G AGS C 901 " pdb="MG MG C 902 " model vdw 2.097 2.170 nonbonded pdb=" O2G AGS B 901 " pdb="MG MG B 902 " model vdw 2.097 2.170 ... (remaining 266918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.140 Check model and map are aligned: 0.510 Set scattering table: 0.300 Process input model: 93.930 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.012 0.090 36624 Z= 0.786 Angle : 1.084 10.636 49536 Z= 0.613 Chirality : 0.061 0.247 5574 Planarity : 0.009 0.075 6516 Dihedral : 10.310 74.198 14322 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 2.44 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.10), residues: 4536 helix: -2.80 (0.09), residues: 1908 sheet: -0.92 (0.21), residues: 504 loop : -2.28 (0.11), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.006 TRP E 551 HIS 0.020 0.004 HIS F 406 PHE 0.050 0.005 PHE B 290 TYR 0.034 0.004 TYR B 755 ARG 0.018 0.001 ARG C 377 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 587 time to evaluate : 4.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6723 (tttt) cc_final: 0.6523 (mtpt) REVERT: A 502 LYS cc_start: 0.7939 (mptt) cc_final: 0.7698 (mmtm) REVERT: F 196 GLU cc_start: 0.6703 (tt0) cc_final: 0.6456 (pp20) REVERT: F 275 MET cc_start: 0.8943 (mmm) cc_final: 0.8728 (mmm) REVERT: F 499 HIS cc_start: 0.8548 (m-70) cc_final: 0.8243 (m90) REVERT: F 542 ILE cc_start: 0.9033 (mm) cc_final: 0.8748 (mt) REVERT: F 564 ASP cc_start: 0.8239 (m-30) cc_final: 0.8026 (m-30) REVERT: F 627 ASP cc_start: 0.8280 (p0) cc_final: 0.8063 (p0) REVERT: E 148 LYS cc_start: 0.6661 (tttt) cc_final: 0.6455 (mtpt) REVERT: E 190 LYS cc_start: 0.7880 (mttt) cc_final: 0.7407 (tptt) REVERT: E 288 LYS cc_start: 0.8611 (mttt) cc_final: 0.8396 (mttm) REVERT: E 580 ASP cc_start: 0.8087 (p0) cc_final: 0.7850 (p0) REVERT: E 679 THR cc_start: 0.5635 (p) cc_final: 0.5251 (p) REVERT: D 502 LYS cc_start: 0.7944 (mptt) cc_final: 0.7697 (mmtm) REVERT: C 196 GLU cc_start: 0.6703 (tt0) cc_final: 0.6443 (pp20) REVERT: C 499 HIS cc_start: 0.8545 (m-70) cc_final: 0.8234 (m90) REVERT: C 564 ASP cc_start: 0.8218 (m-30) cc_final: 0.7983 (m-30) REVERT: C 627 ASP cc_start: 0.8275 (p0) cc_final: 0.8036 (p0) REVERT: B 148 LYS cc_start: 0.6651 (tttt) cc_final: 0.6444 (mtpt) REVERT: B 190 LYS cc_start: 0.7885 (mttt) cc_final: 0.7412 (tptt) REVERT: B 288 LYS cc_start: 0.8625 (mttt) cc_final: 0.8411 (mttm) REVERT: B 580 ASP cc_start: 0.8085 (p0) cc_final: 0.7852 (p0) REVERT: B 679 THR cc_start: 0.5620 (p) cc_final: 0.5232 (p) outliers start: 0 outliers final: 0 residues processed: 587 average time/residue: 0.6508 time to fit residues: 563.7375 Evaluate side-chains 300 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 4.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 379 optimal weight: 30.0000 chunk 341 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 230 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 chunk 352 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 262 optimal weight: 1.9990 chunk 408 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 GLN A 499 HIS A 660 ASN F 421 GLN F 660 ASN E 398 GLN E 421 GLN E 499 HIS E 660 ASN D 421 GLN D 499 HIS D 660 ASN C 421 GLN C 660 ASN B 398 GLN B 421 GLN B 499 HIS B 660 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 36624 Z= 0.168 Angle : 0.530 5.689 49536 Z= 0.279 Chirality : 0.043 0.155 5574 Planarity : 0.005 0.058 6516 Dihedral : 8.664 67.596 5190 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.93 % Allowed : 4.72 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.94 (0.11), residues: 4536 helix: -0.99 (0.11), residues: 1956 sheet: -0.23 (0.23), residues: 444 loop : -1.75 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 551 HIS 0.003 0.001 HIS B 406 PHE 0.012 0.001 PHE B 290 TYR 0.010 0.001 TYR D 517 ARG 0.009 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 359 time to evaluate : 3.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6751 (tttt) cc_final: 0.6500 (mtpt) REVERT: A 757 MET cc_start: 0.7959 (tmm) cc_final: 0.7757 (tmm) REVERT: F 18 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7292 (mtpt) REVERT: F 499 HIS cc_start: 0.8361 (m-70) cc_final: 0.8156 (m-70) REVERT: F 564 ASP cc_start: 0.8153 (m-30) cc_final: 0.7934 (m-30) REVERT: F 678 MET cc_start: 0.6632 (tmm) cc_final: 0.6333 (tmm) REVERT: E 148 LYS cc_start: 0.6710 (tttt) cc_final: 0.6437 (mtpt) REVERT: E 190 LYS cc_start: 0.7887 (mttt) cc_final: 0.7444 (tptt) REVERT: E 678 MET cc_start: 0.6799 (tmm) cc_final: 0.6421 (tmm) REVERT: E 679 THR cc_start: 0.5283 (p) cc_final: 0.5057 (p) REVERT: E 753 ARG cc_start: 0.7744 (ptp-170) cc_final: 0.6850 (mmp-170) REVERT: D 757 MET cc_start: 0.7955 (tmm) cc_final: 0.7755 (tmm) REVERT: C 18 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7243 (mtpt) REVERT: C 564 ASP cc_start: 0.8150 (m-30) cc_final: 0.7892 (m-30) REVERT: C 678 MET cc_start: 0.6731 (tmm) cc_final: 0.6413 (tmm) REVERT: B 148 LYS cc_start: 0.6697 (tttt) cc_final: 0.6426 (mtpt) REVERT: B 190 LYS cc_start: 0.7890 (mttt) cc_final: 0.7447 (tptt) REVERT: B 678 MET cc_start: 0.6805 (tmm) cc_final: 0.6429 (tmm) REVERT: B 679 THR cc_start: 0.5266 (p) cc_final: 0.5043 (p) REVERT: B 753 ARG cc_start: 0.7741 (ptp-170) cc_final: 0.6847 (mmp-170) outliers start: 36 outliers final: 22 residues processed: 383 average time/residue: 0.5251 time to fit residues: 313.9065 Evaluate side-chains 310 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 286 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 438 ASP Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 601 ILE Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 438 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 227 optimal weight: 0.0050 chunk 126 optimal weight: 2.9990 chunk 340 optimal weight: 1.9990 chunk 278 optimal weight: 0.4980 chunk 112 optimal weight: 0.2980 chunk 409 optimal weight: 0.0470 chunk 442 optimal weight: 6.9990 chunk 364 optimal weight: 9.9990 chunk 405 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 328 optimal weight: 1.9990 overall best weight: 0.5694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 660 ASN C 499 HIS C 660 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 36624 Z= 0.133 Angle : 0.464 8.971 49536 Z= 0.241 Chirality : 0.042 0.185 5574 Planarity : 0.005 0.056 6516 Dihedral : 8.083 68.036 5190 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.21 % Allowed : 6.11 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.74 (0.12), residues: 4536 helix: 0.16 (0.12), residues: 1938 sheet: 0.34 (0.25), residues: 426 loop : -1.24 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 551 HIS 0.002 0.001 HIS B 340 PHE 0.010 0.001 PHE D 516 TYR 0.010 0.001 TYR A 517 ARG 0.005 0.000 ARG D 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 314 time to evaluate : 3.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6742 (tttt) cc_final: 0.6523 (mtpt) REVERT: A 693 ARG cc_start: 0.7400 (tpp80) cc_final: 0.6966 (tpp-160) REVERT: A 744 ARG cc_start: 0.6386 (ttp-110) cc_final: 0.6176 (ttm170) REVERT: A 757 MET cc_start: 0.7773 (tmm) cc_final: 0.7402 (tmm) REVERT: F 18 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.7110 (mtpt) REVERT: F 499 HIS cc_start: 0.8351 (m-70) cc_final: 0.8099 (m-70) REVERT: F 564 ASP cc_start: 0.8090 (m-30) cc_final: 0.7858 (m-30) REVERT: F 584 LYS cc_start: 0.4558 (OUTLIER) cc_final: 0.4131 (mttt) REVERT: F 678 MET cc_start: 0.6609 (tmm) cc_final: 0.6153 (tmm) REVERT: F 693 ARG cc_start: 0.7546 (tpp80) cc_final: 0.7140 (tpp-160) REVERT: E 148 LYS cc_start: 0.6741 (tttt) cc_final: 0.6460 (mtpt) REVERT: E 190 LYS cc_start: 0.7908 (mttt) cc_final: 0.7448 (tptt) REVERT: E 678 MET cc_start: 0.6681 (tmm) cc_final: 0.6240 (tmm) REVERT: E 753 ARG cc_start: 0.7744 (ptp-170) cc_final: 0.6954 (mmp-170) REVERT: D 693 ARG cc_start: 0.7406 (tpp80) cc_final: 0.6973 (tpp-160) REVERT: D 744 ARG cc_start: 0.6394 (ttp-110) cc_final: 0.6185 (ttm170) REVERT: D 757 MET cc_start: 0.7770 (tmm) cc_final: 0.7401 (tmm) REVERT: C 18 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.7076 (mtpt) REVERT: C 564 ASP cc_start: 0.8095 (m-30) cc_final: 0.7804 (m-30) REVERT: C 584 LYS cc_start: 0.4522 (OUTLIER) cc_final: 0.4065 (mttt) REVERT: C 678 MET cc_start: 0.6636 (tmm) cc_final: 0.6146 (tmm) REVERT: C 693 ARG cc_start: 0.7554 (tpp80) cc_final: 0.7161 (tpp-160) REVERT: B 148 LYS cc_start: 0.6723 (tttt) cc_final: 0.6447 (mtpt) REVERT: B 190 LYS cc_start: 0.7910 (mttt) cc_final: 0.7452 (tptt) REVERT: B 678 MET cc_start: 0.6689 (tmm) cc_final: 0.6248 (tmm) REVERT: B 753 ARG cc_start: 0.7738 (ptp-170) cc_final: 0.6952 (mmp-170) outliers start: 47 outliers final: 28 residues processed: 348 average time/residue: 0.5222 time to fit residues: 284.3732 Evaluate side-chains 290 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 258 time to evaluate : 3.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 438 ASP Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 630 ASP Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 630 ASP Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 642 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 404 optimal weight: 0.3980 chunk 307 optimal weight: 8.9990 chunk 212 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 410 optimal weight: 0.0970 chunk 434 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 chunk 389 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 36624 Z= 0.157 Angle : 0.462 7.399 49536 Z= 0.238 Chirality : 0.042 0.157 5574 Planarity : 0.004 0.050 6516 Dihedral : 7.946 68.595 5190 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.11 % Allowed : 6.55 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.28 (0.12), residues: 4536 helix: 0.58 (0.12), residues: 1908 sheet: 1.04 (0.28), residues: 342 loop : -1.03 (0.12), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 551 HIS 0.003 0.001 HIS E 406 PHE 0.013 0.001 PHE E 516 TYR 0.009 0.001 TYR C 517 ARG 0.007 0.000 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 271 time to evaluate : 4.350 Fit side-chains REVERT: A 148 LYS cc_start: 0.6880 (tttt) cc_final: 0.6653 (mtpt) REVERT: A 693 ARG cc_start: 0.7340 (tpp80) cc_final: 0.6802 (tpp80) REVERT: A 757 MET cc_start: 0.7746 (tmm) cc_final: 0.7374 (tmm) REVERT: F 18 LYS cc_start: 0.7365 (OUTLIER) cc_final: 0.7104 (mtpt) REVERT: F 84 MET cc_start: 0.6334 (ptm) cc_final: 0.6126 (ptm) REVERT: F 275 MET cc_start: 0.8971 (mmm) cc_final: 0.8746 (mmm) REVERT: F 499 HIS cc_start: 0.8379 (m-70) cc_final: 0.8154 (m-70) REVERT: F 564 ASP cc_start: 0.8121 (m-30) cc_final: 0.7846 (m-30) REVERT: F 584 LYS cc_start: 0.4533 (OUTLIER) cc_final: 0.4203 (mttt) REVERT: F 693 ARG cc_start: 0.7273 (tpp80) cc_final: 0.6927 (tpp-160) REVERT: E 148 LYS cc_start: 0.6741 (tttt) cc_final: 0.6414 (mtmt) REVERT: E 190 LYS cc_start: 0.7851 (mttt) cc_final: 0.7464 (tptt) REVERT: E 678 MET cc_start: 0.6843 (tmm) cc_final: 0.6559 (tmm) REVERT: E 753 ARG cc_start: 0.7733 (ptp-170) cc_final: 0.6988 (mmp-170) REVERT: D 693 ARG cc_start: 0.7346 (tpp80) cc_final: 0.6808 (tpp80) REVERT: D 757 MET cc_start: 0.7744 (tmm) cc_final: 0.7369 (tmm) REVERT: C 18 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7073 (mtpt) REVERT: C 564 ASP cc_start: 0.8139 (m-30) cc_final: 0.7853 (m-30) REVERT: C 584 LYS cc_start: 0.4398 (OUTLIER) cc_final: 0.4070 (mttt) REVERT: C 678 MET cc_start: 0.6569 (tmm) cc_final: 0.6355 (tmm) REVERT: C 693 ARG cc_start: 0.7291 (tpp80) cc_final: 0.6958 (tpp-160) REVERT: B 148 LYS cc_start: 0.6728 (tttt) cc_final: 0.6402 (mtmt) REVERT: B 190 LYS cc_start: 0.7856 (mttt) cc_final: 0.7468 (tptt) REVERT: B 678 MET cc_start: 0.6850 (tmm) cc_final: 0.6564 (tmm) REVERT: B 753 ARG cc_start: 0.7729 (ptp-170) cc_final: 0.6987 (mmp-170) outliers start: 43 outliers final: 24 residues processed: 307 average time/residue: 0.5227 time to fit residues: 259.0600 Evaluate side-chains 286 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 258 time to evaluate : 4.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 438 ASP Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 642 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 362 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 323 optimal weight: 0.0570 chunk 179 optimal weight: 2.9990 chunk 371 optimal weight: 0.1980 chunk 300 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 390 optimal weight: 20.0000 chunk 109 optimal weight: 0.9990 overall best weight: 1.0504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 ASN E 660 ASN D 660 ASN B 660 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36624 Z= 0.156 Angle : 0.456 6.691 49536 Z= 0.234 Chirality : 0.042 0.151 5574 Planarity : 0.004 0.049 6516 Dihedral : 7.857 69.243 5190 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.44 % Allowed : 6.32 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.02 (0.13), residues: 4536 helix: 0.79 (0.13), residues: 1908 sheet: 1.09 (0.29), residues: 342 loop : -0.87 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 551 HIS 0.003 0.001 HIS B 406 PHE 0.013 0.001 PHE F 516 TYR 0.009 0.001 TYR C 517 ARG 0.005 0.000 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 271 time to evaluate : 3.967 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6918 (tttt) cc_final: 0.6698 (mtpt) REVERT: A 757 MET cc_start: 0.7698 (tmm) cc_final: 0.7331 (tmm) REVERT: F 18 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.7075 (mtpt) REVERT: F 84 MET cc_start: 0.6184 (OUTLIER) cc_final: 0.5984 (ptm) REVERT: F 564 ASP cc_start: 0.8152 (m-30) cc_final: 0.7878 (m-30) REVERT: F 578 GLU cc_start: 0.7332 (pt0) cc_final: 0.7068 (pt0) REVERT: F 584 LYS cc_start: 0.4510 (OUTLIER) cc_final: 0.4219 (mttt) REVERT: F 693 ARG cc_start: 0.7254 (tpp80) cc_final: 0.6959 (tpp-160) REVERT: E 148 LYS cc_start: 0.6751 (tttt) cc_final: 0.6339 (mtmt) REVERT: E 190 LYS cc_start: 0.7609 (mttt) cc_final: 0.7243 (tptt) REVERT: E 740 MET cc_start: 0.8042 (mmm) cc_final: 0.7430 (mmm) REVERT: E 753 ARG cc_start: 0.7729 (ptp-170) cc_final: 0.6991 (mmp-170) REVERT: D 757 MET cc_start: 0.7697 (tmm) cc_final: 0.7331 (tmm) REVERT: C 18 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.7039 (mtpt) REVERT: C 564 ASP cc_start: 0.8139 (m-30) cc_final: 0.7841 (m-30) REVERT: C 584 LYS cc_start: 0.4499 (OUTLIER) cc_final: 0.4186 (mttt) REVERT: B 148 LYS cc_start: 0.6742 (tttt) cc_final: 0.6332 (mtmt) REVERT: B 190 LYS cc_start: 0.7612 (mttt) cc_final: 0.7247 (tptt) REVERT: B 740 MET cc_start: 0.8047 (mmm) cc_final: 0.7433 (mmm) REVERT: B 753 ARG cc_start: 0.7724 (ptp-170) cc_final: 0.6991 (mmp-170) outliers start: 56 outliers final: 44 residues processed: 315 average time/residue: 0.4932 time to fit residues: 250.6338 Evaluate side-chains 302 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 253 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 438 ASP Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 699 ILE Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 630 ASP Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 699 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 146 optimal weight: 5.9990 chunk 391 optimal weight: 40.0000 chunk 85 optimal weight: 0.0470 chunk 255 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 435 optimal weight: 0.7980 chunk 361 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 36 optimal weight: 0.0770 chunk 144 optimal weight: 10.0000 chunk 228 optimal weight: 40.0000 overall best weight: 2.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 36624 Z= 0.287 Angle : 0.531 8.584 49536 Z= 0.271 Chirality : 0.045 0.143 5574 Planarity : 0.004 0.048 6516 Dihedral : 8.045 74.840 5190 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.83 % Allowed : 6.40 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.11 (0.12), residues: 4536 helix: 0.67 (0.12), residues: 1908 sheet: 0.98 (0.28), residues: 342 loop : -0.86 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 551 HIS 0.004 0.001 HIS C 406 PHE 0.022 0.002 PHE F 516 TYR 0.011 0.001 TYR C 517 ARG 0.006 0.000 ARG F 359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 271 time to evaluate : 4.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6858 (tttt) cc_final: 0.6626 (mtpt) REVERT: A 757 MET cc_start: 0.7658 (tmm) cc_final: 0.7285 (tmm) REVERT: F 18 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.7024 (mtpt) REVERT: F 219 MET cc_start: 0.8161 (mtt) cc_final: 0.7888 (mtm) REVERT: F 564 ASP cc_start: 0.8221 (m-30) cc_final: 0.7909 (m-30) REVERT: F 584 LYS cc_start: 0.4582 (OUTLIER) cc_final: 0.4278 (mttt) REVERT: F 693 ARG cc_start: 0.7433 (tpp80) cc_final: 0.7142 (tpp-160) REVERT: E 148 LYS cc_start: 0.6788 (tttt) cc_final: 0.6386 (mtmt) REVERT: E 190 LYS cc_start: 0.7643 (mttt) cc_final: 0.7255 (tptt) REVERT: E 753 ARG cc_start: 0.7759 (ptp-170) cc_final: 0.6992 (mmp-170) REVERT: D 757 MET cc_start: 0.7664 (tmm) cc_final: 0.7287 (tmm) REVERT: C 18 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6994 (mtpt) REVERT: C 219 MET cc_start: 0.8164 (mtt) cc_final: 0.7890 (mtm) REVERT: C 564 ASP cc_start: 0.8204 (m-30) cc_final: 0.7883 (m-30) REVERT: C 584 LYS cc_start: 0.4600 (OUTLIER) cc_final: 0.4315 (mttt) REVERT: B 148 LYS cc_start: 0.6771 (tttt) cc_final: 0.6377 (mtmt) REVERT: B 190 LYS cc_start: 0.7646 (mttt) cc_final: 0.7257 (tptt) REVERT: B 753 ARG cc_start: 0.7754 (ptp-170) cc_final: 0.6992 (mmp-170) outliers start: 71 outliers final: 49 residues processed: 324 average time/residue: 0.5174 time to fit residues: 277.3138 Evaluate side-chains 304 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 251 time to evaluate : 4.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 438 ASP Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 598 ASP Chi-restraints excluded: chain D residue 679 THR Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 699 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 419 optimal weight: 5.9990 chunk 49 optimal weight: 0.0170 chunk 248 optimal weight: 0.9990 chunk 317 optimal weight: 40.0000 chunk 246 optimal weight: 0.8980 chunk 366 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 433 optimal weight: 3.9990 chunk 271 optimal weight: 0.0570 chunk 264 optimal weight: 7.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 327 GLN B 421 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 36624 Z= 0.126 Angle : 0.446 7.041 49536 Z= 0.230 Chirality : 0.042 0.147 5574 Planarity : 0.004 0.046 6516 Dihedral : 7.696 73.078 5190 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.32 % Allowed : 7.43 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.29 (0.13), residues: 4536 helix: 1.08 (0.13), residues: 1878 sheet: 1.13 (0.29), residues: 342 loop : -0.68 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 551 HIS 0.002 0.000 HIS F 499 PHE 0.008 0.001 PHE F 516 TYR 0.009 0.001 TYR A 517 ARG 0.006 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 280 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6918 (tttt) cc_final: 0.6691 (mtpt) REVERT: A 757 MET cc_start: 0.7549 (tmm) cc_final: 0.7190 (tmm) REVERT: F 18 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6959 (mtpt) REVERT: F 564 ASP cc_start: 0.8190 (m-30) cc_final: 0.7908 (m-30) REVERT: F 584 LYS cc_start: 0.4594 (OUTLIER) cc_final: 0.4263 (mttt) REVERT: F 693 ARG cc_start: 0.7224 (tpp80) cc_final: 0.6985 (tpp-160) REVERT: E 148 LYS cc_start: 0.6760 (tttt) cc_final: 0.6374 (mtmt) REVERT: E 190 LYS cc_start: 0.7680 (mttt) cc_final: 0.7284 (tptt) REVERT: E 550 MET cc_start: 0.4084 (ttp) cc_final: 0.3601 (tpt) REVERT: E 753 ARG cc_start: 0.7682 (ptp-170) cc_final: 0.6978 (mmp-170) REVERT: D 757 MET cc_start: 0.7600 (tmm) cc_final: 0.7244 (tmm) REVERT: C 18 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6931 (mtpt) REVERT: C 564 ASP cc_start: 0.8173 (m-30) cc_final: 0.7834 (m-30) REVERT: C 584 LYS cc_start: 0.4589 (OUTLIER) cc_final: 0.4252 (mttt) REVERT: B 148 LYS cc_start: 0.6748 (tttt) cc_final: 0.6366 (mtmt) REVERT: B 190 LYS cc_start: 0.7683 (mttt) cc_final: 0.7286 (tptt) REVERT: B 550 MET cc_start: 0.4095 (ttp) cc_final: 0.3614 (tpt) REVERT: B 753 ARG cc_start: 0.7677 (ptp-170) cc_final: 0.6977 (mmp-170) outliers start: 51 outliers final: 37 residues processed: 324 average time/residue: 0.4965 time to fit residues: 257.2587 Evaluate side-chains 299 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 258 time to evaluate : 4.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 438 ASP Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 601 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 268 optimal weight: 0.3980 chunk 173 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 85 optimal weight: 50.0000 chunk 84 optimal weight: 0.0020 chunk 275 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 340 optimal weight: 2.9990 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 421 GLN D 421 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36624 Z= 0.188 Angle : 0.471 7.601 49536 Z= 0.240 Chirality : 0.043 0.155 5574 Planarity : 0.004 0.047 6516 Dihedral : 7.700 74.222 5190 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.44 % Allowed : 7.30 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.29 (0.13), residues: 4536 helix: 1.07 (0.13), residues: 1884 sheet: 0.75 (0.26), residues: 396 loop : -0.63 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 551 HIS 0.002 0.001 HIS B 384 PHE 0.015 0.001 PHE C 516 TYR 0.009 0.001 TYR C 517 ARG 0.006 0.000 ARG C 359 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 273 time to evaluate : 4.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6873 (tttt) cc_final: 0.6643 (mtpt) REVERT: A 757 MET cc_start: 0.7599 (tmm) cc_final: 0.7239 (tmm) REVERT: F 18 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6965 (mtpt) REVERT: F 564 ASP cc_start: 0.8150 (m-30) cc_final: 0.7883 (m-30) REVERT: F 584 LYS cc_start: 0.4570 (OUTLIER) cc_final: 0.4239 (mttt) REVERT: F 693 ARG cc_start: 0.7321 (tpp80) cc_final: 0.7087 (tpp-160) REVERT: E 148 LYS cc_start: 0.6746 (tttt) cc_final: 0.6383 (mtmt) REVERT: E 190 LYS cc_start: 0.7682 (mttt) cc_final: 0.7279 (tptt) REVERT: E 550 MET cc_start: 0.4237 (ttp) cc_final: 0.3685 (tpt) REVERT: E 753 ARG cc_start: 0.7705 (ptp-170) cc_final: 0.6990 (mmp-170) REVERT: D 757 MET cc_start: 0.7604 (tmm) cc_final: 0.7242 (tmm) REVERT: C 18 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6929 (mtpt) REVERT: C 564 ASP cc_start: 0.8193 (m-30) cc_final: 0.7854 (m-30) REVERT: C 584 LYS cc_start: 0.4592 (OUTLIER) cc_final: 0.4268 (mttt) REVERT: B 148 LYS cc_start: 0.6736 (tttt) cc_final: 0.6374 (mtmt) REVERT: B 190 LYS cc_start: 0.7684 (mttt) cc_final: 0.7281 (tptt) REVERT: B 550 MET cc_start: 0.4252 (ttp) cc_final: 0.3697 (tpt) REVERT: B 753 ARG cc_start: 0.7700 (ptp-170) cc_final: 0.6988 (mmp-170) outliers start: 56 outliers final: 47 residues processed: 318 average time/residue: 0.4844 time to fit residues: 249.3025 Evaluate side-chains 315 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 264 time to evaluate : 4.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 630 ASP Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 438 ASP Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 630 ASP Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 699 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 394 optimal weight: 4.9990 chunk 415 optimal weight: 1.9990 chunk 379 optimal weight: 9.9990 chunk 404 optimal weight: 3.9990 chunk 243 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 317 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 365 optimal weight: 8.9990 chunk 382 optimal weight: 8.9990 chunk 402 optimal weight: 0.6980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 421 GLN E 421 GLN D 421 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36624 Z= 0.201 Angle : 0.478 8.053 49536 Z= 0.243 Chirality : 0.043 0.169 5574 Planarity : 0.004 0.046 6516 Dihedral : 7.700 75.580 5190 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.47 % Allowed : 7.51 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.28 (0.13), residues: 4536 helix: 1.05 (0.13), residues: 1884 sheet: 0.72 (0.26), residues: 396 loop : -0.63 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 551 HIS 0.002 0.001 HIS C 406 PHE 0.015 0.001 PHE C 516 TYR 0.010 0.001 TYR C 517 ARG 0.006 0.000 ARG C 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 273 time to evaluate : 4.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6873 (tttt) cc_final: 0.6641 (mtpt) REVERT: A 720 MET cc_start: 0.3876 (mtp) cc_final: 0.3617 (mtt) REVERT: A 757 MET cc_start: 0.7549 (tmm) cc_final: 0.7194 (tmm) REVERT: F 18 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6955 (mtpt) REVERT: F 219 MET cc_start: 0.8156 (mtt) cc_final: 0.7856 (mtm) REVERT: F 564 ASP cc_start: 0.8152 (m-30) cc_final: 0.7886 (m-30) REVERT: F 584 LYS cc_start: 0.4498 (OUTLIER) cc_final: 0.4185 (mttt) REVERT: F 693 ARG cc_start: 0.7324 (tpp80) cc_final: 0.7093 (tpp-160) REVERT: E 148 LYS cc_start: 0.6755 (tttt) cc_final: 0.6404 (mtmt) REVERT: E 190 LYS cc_start: 0.7705 (mttt) cc_final: 0.7307 (tptt) REVERT: E 550 MET cc_start: 0.4155 (ttp) cc_final: 0.3588 (tpt) REVERT: E 753 ARG cc_start: 0.7698 (ptp-170) cc_final: 0.6990 (mmp-170) REVERT: D 720 MET cc_start: 0.3866 (mtp) cc_final: 0.3611 (mtt) REVERT: D 757 MET cc_start: 0.7601 (tmm) cc_final: 0.7238 (tmm) REVERT: C 219 MET cc_start: 0.8158 (mtt) cc_final: 0.7856 (mtm) REVERT: C 564 ASP cc_start: 0.8148 (m-30) cc_final: 0.7847 (m-30) REVERT: C 584 LYS cc_start: 0.4620 (OUTLIER) cc_final: 0.4287 (mttt) REVERT: B 148 LYS cc_start: 0.6741 (tttt) cc_final: 0.6395 (mtmt) REVERT: B 190 LYS cc_start: 0.7707 (mttt) cc_final: 0.7309 (tptt) REVERT: B 550 MET cc_start: 0.4170 (ttp) cc_final: 0.3601 (tpt) REVERT: B 753 ARG cc_start: 0.7692 (ptp-170) cc_final: 0.6987 (mmp-170) outliers start: 57 outliers final: 48 residues processed: 318 average time/residue: 0.4794 time to fit residues: 246.5549 Evaluate side-chains 311 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 260 time to evaluate : 4.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 438 ASP Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 630 ASP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 699 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 265 optimal weight: 0.8980 chunk 427 optimal weight: 3.9990 chunk 260 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 448 optimal weight: 20.0000 chunk 412 optimal weight: 0.9990 chunk 356 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 421 GLN F 421 GLN D 33 ASN D 421 GLN C 33 ASN C 421 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36624 Z= 0.198 Angle : 0.479 8.299 49536 Z= 0.243 Chirality : 0.043 0.169 5574 Planarity : 0.004 0.046 6516 Dihedral : 7.665 76.815 5190 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.37 % Allowed : 7.87 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.29 (0.13), residues: 4536 helix: 1.05 (0.13), residues: 1884 sheet: 0.71 (0.26), residues: 396 loop : -0.62 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 551 HIS 0.002 0.001 HIS B 384 PHE 0.018 0.001 PHE C 516 TYR 0.011 0.001 TYR C 517 ARG 0.006 0.000 ARG C 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9072 Ramachandran restraints generated. 4536 Oldfield, 0 Emsley, 4536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 268 time to evaluate : 4.139 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.6872 (tttt) cc_final: 0.6639 (mtpt) REVERT: A 720 MET cc_start: 0.3871 (mtp) cc_final: 0.3604 (mtt) REVERT: A 757 MET cc_start: 0.7549 (tmm) cc_final: 0.7193 (tmm) REVERT: F 18 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6943 (mtpt) REVERT: F 219 MET cc_start: 0.8180 (mtt) cc_final: 0.7886 (mtm) REVERT: F 564 ASP cc_start: 0.8155 (m-30) cc_final: 0.7889 (m-30) REVERT: F 584 LYS cc_start: 0.4479 (OUTLIER) cc_final: 0.4166 (mttt) REVERT: F 693 ARG cc_start: 0.7315 (tpp80) cc_final: 0.7091 (tpp-160) REVERT: E 148 LYS cc_start: 0.6755 (tttt) cc_final: 0.6397 (mtmt) REVERT: E 190 LYS cc_start: 0.7639 (mttt) cc_final: 0.7264 (tptt) REVERT: E 550 MET cc_start: 0.4215 (ttp) cc_final: 0.3609 (tpt) REVERT: E 753 ARG cc_start: 0.7690 (ptp-170) cc_final: 0.6990 (mmp-170) REVERT: D 720 MET cc_start: 0.3857 (mtp) cc_final: 0.3593 (mtt) REVERT: D 757 MET cc_start: 0.7549 (tmm) cc_final: 0.7192 (tmm) REVERT: C 219 MET cc_start: 0.8179 (mtt) cc_final: 0.7889 (mtm) REVERT: C 564 ASP cc_start: 0.8148 (m-30) cc_final: 0.7846 (m-30) REVERT: C 584 LYS cc_start: 0.4554 (OUTLIER) cc_final: 0.4211 (mttt) REVERT: B 148 LYS cc_start: 0.6743 (tttt) cc_final: 0.6389 (mtmt) REVERT: B 190 LYS cc_start: 0.7642 (mttt) cc_final: 0.7268 (tptt) REVERT: B 550 MET cc_start: 0.4225 (ttp) cc_final: 0.3621 (tpt) REVERT: B 753 ARG cc_start: 0.7685 (ptp-170) cc_final: 0.6987 (mmp-170) outliers start: 53 outliers final: 49 residues processed: 310 average time/residue: 0.4970 time to fit residues: 248.8076 Evaluate side-chains 314 residues out of total 3876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 262 time to evaluate : 4.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 314 GLU Chi-restraints excluded: chain F residue 344 MET Chi-restraints excluded: chain F residue 364 ASP Chi-restraints excluded: chain F residue 438 ASP Chi-restraints excluded: chain F residue 535 CYS Chi-restraints excluded: chain F residue 584 LYS Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 314 GLU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 438 ASP Chi-restraints excluded: chain E residue 535 CYS Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain E residue 647 LEU Chi-restraints excluded: chain E residue 679 THR Chi-restraints excluded: chain E residue 699 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 364 ASP Chi-restraints excluded: chain D residue 438 ASP Chi-restraints excluded: chain D residue 535 CYS Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 535 CYS Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 314 GLU Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 535 CYS Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 679 THR Chi-restraints excluded: chain B residue 699 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 283 optimal weight: 2.9990 chunk 380 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 329 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 357 optimal weight: 0.0020 chunk 149 optimal weight: 4.9990 chunk 367 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 421 GLN D 33 ASN D 421 GLN C 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.193517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128009 restraints weight = 47144.441| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.67 r_work: 0.3253 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36624 Z= 0.215 Angle : 0.490 7.975 49536 Z= 0.248 Chirality : 0.044 0.164 5574 Planarity : 0.004 0.046 6516 Dihedral : 7.687 77.893 5190 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.37 % Allowed : 8.02 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.27 (0.13), residues: 4536 helix: 1.03 (0.13), residues: 1878 sheet: 0.70 (0.26), residues: 396 loop : -0.61 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 551 HIS 0.003 0.001 HIS F 406 PHE 0.017 0.001 PHE C 516 TYR 0.010 0.001 TYR D 517 ARG 0.006 0.000 ARG C 359 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7812.15 seconds wall clock time: 140 minutes 40.52 seconds (8440.52 seconds total)