Starting phenix.real_space_refine on Thu Feb 15 04:34:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/02_2024/7wub_32827_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/02_2024/7wub_32827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/02_2024/7wub_32827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/02_2024/7wub_32827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/02_2024/7wub_32827_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/02_2024/7wub_32827_trim_updated.pdb" } resolution = 3.0 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= 0.083 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 348 5.16 5 C 39683 2.51 5 N 11169 2.21 5 O 12035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A ASP 669": "OD1" <-> "OD2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B ASP 669": "OD1" <-> "OD2" Residue "B PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C ASP 669": "OD1" <-> "OD2" Residue "C PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D ASP 669": "OD1" <-> "OD2" Residue "D PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 561": "OE1" <-> "OE2" Residue "E ASP 669": "OD1" <-> "OD2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 561": "OE1" <-> "OE2" Residue "F ASP 669": "OD1" <-> "OD2" Residue "F PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 30": "OE1" <-> "OE2" Residue "G PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 428": "OD1" <-> "OD2" Residue "G GLU 491": "OE1" <-> "OE2" Residue "G ASP 609": "OD1" <-> "OD2" Residue "G PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 30": "OE1" <-> "OE2" Residue "H PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 428": "OD1" <-> "OD2" Residue "H GLU 491": "OE1" <-> "OE2" Residue "H ASP 609": "OD1" <-> "OD2" Residue "H PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 30": "OE1" <-> "OE2" Residue "I PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 428": "OD1" <-> "OD2" Residue "I GLU 491": "OE1" <-> "OE2" Residue "I ASP 609": "OD1" <-> "OD2" Residue "I PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 30": "OE1" <-> "OE2" Residue "J PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 428": "OD1" <-> "OD2" Residue "J GLU 491": "OE1" <-> "OE2" Residue "J ASP 609": "OD1" <-> "OD2" Residue "J PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 30": "OE1" <-> "OE2" Residue "K PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 428": "OD1" <-> "OD2" Residue "K GLU 491": "OE1" <-> "OE2" Residue "K ASP 609": "OD1" <-> "OD2" Residue "K PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 30": "OE1" <-> "OE2" Residue "L PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 428": "OD1" <-> "OD2" Residue "L GLU 491": "OE1" <-> "OE2" Residue "L ASP 609": "OD1" <-> "OD2" Residue "L PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 63259 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4494 Classifications: {'peptide': 576} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 544} Chain: "B" Number of atoms: 4494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4494 Classifications: {'peptide': 576} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 544} Chain: "C" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4490 Classifications: {'peptide': 576} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 544} Chain: "D" Number of atoms: 4487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4487 Classifications: {'peptide': 575} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 544} Chain breaks: 1 Chain: "E" Number of atoms: 4494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4494 Classifications: {'peptide': 576} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 544} Chain: "F" Number of atoms: 4494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4494 Classifications: {'peptide': 576} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 544} Chain: "G" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 39, 'TRANS': 711} Chain: "H" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 39, 'TRANS': 711} Chain: "I" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 39, 'TRANS': 711} Chain: "J" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 39, 'TRANS': 711} Chain: "K" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 39, 'TRANS': 711} Chain: "L" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 39, 'TRANS': 711} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'Y6Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.43, per 1000 atoms: 0.37 Number of scatterers: 63259 At special positions: 0 Unit cell: (178.45, 173.47, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 348 16.00 P 24 15.00 O 12035 8.00 N 11169 7.00 C 39683 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: 18.64 Conformation dependent library (CDL) restraints added in 8.8 seconds 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14890 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 354 helices and 42 sheets defined 43.4% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.77 Creating SS restraints... Processing helix chain 'A' and resid 213 through 225 removed outlier: 5.264A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.850A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 232' Processing helix chain 'A' and resid 251 through 262 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 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 320 through 333 Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 498 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 579 through 586 removed outlier: 4.349A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 660 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 715 Processing helix chain 'A' and resid 733 through 742 removed outlier: 3.703A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 761 Processing helix chain 'B' and resid 213 through 225 removed outlier: 5.265A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.851A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 232' Processing helix chain 'B' and resid 251 through 262 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 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 320 through 333 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 397 through 403 Processing helix chain 'B' and resid 408 through 425 Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 498 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 524 through 535 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 579 through 586 removed outlier: 4.349A pdb=" N ILE B 582 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 660 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 715 Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.702A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'C' and resid 213 through 225 removed outlier: 5.266A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.850A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 232' Processing helix chain 'C' and resid 251 through 262 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 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 320 through 333 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 397 through 403 Processing helix chain 'C' and resid 408 through 425 Processing helix chain 'C' and resid 439 through 443 Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 498 Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 524 through 535 Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 568 Processing helix chain 'C' and resid 579 through 586 removed outlier: 4.349A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 660 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 715 Processing helix chain 'C' and resid 733 through 742 removed outlier: 3.703A pdb=" N PHE C 742 " --> pdb=" O GLU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 761 Processing helix chain 'D' and resid 213 through 225 removed outlier: 5.265A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.850A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 227 through 232' Processing helix chain 'D' and resid 251 through 262 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 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 320 through 333 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 408 through 425 Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 498 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 524 through 535 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 568 Processing helix chain 'D' and resid 579 through 586 removed outlier: 4.350A pdb=" N ILE D 582 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 660 Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 715 Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.702A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 761 Processing helix chain 'E' and resid 213 through 225 removed outlier: 5.265A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.850A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 227 through 232' Processing helix chain 'E' and resid 251 through 262 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 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 320 through 333 Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 397 through 403 Processing helix chain 'E' and resid 408 through 425 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 498 Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 524 through 535 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 Processing helix chain 'E' and resid 579 through 586 removed outlier: 4.349A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 660 Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 715 Processing helix chain 'E' and resid 733 through 742 removed outlier: 3.703A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 761 Processing helix chain 'F' and resid 213 through 225 removed outlier: 5.265A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.851A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA F 232 " --> pdb=" O ALA F 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 227 through 232' Processing helix chain 'F' and resid 251 through 262 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 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 320 through 333 Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 397 through 403 Processing helix chain 'F' and resid 408 through 425 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 524 through 535 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 568 Processing helix chain 'F' and resid 579 through 586 removed outlier: 4.350A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 609 Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 660 Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 712 Processing helix chain 'F' and resid 733 through 742 removed outlier: 3.702A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 761 Processing helix chain 'G' and resid 86 through 92 Processing helix chain 'G' and resid 135 through 139 Processing helix chain 'G' and resid 210 through 225 removed outlier: 3.983A pdb=" N ALA G 214 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU G 221 " --> pdb=" O GLU G 218 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU G 222 " --> pdb=" O MET G 219 " (cutoff:3.500A) Proline residue: G 223 - end of helix Processing helix chain 'G' and resid 227 through 232 removed outlier: 3.986A pdb=" N LYS G 231 " --> pdb=" O PRO G 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA G 232 " --> pdb=" O ALA G 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 227 through 232' Processing helix chain 'G' and resid 251 through 262 Processing helix chain 'G' and resid 271 through 275 removed outlier: 3.546A pdb=" N MET G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 271 through 275' Processing helix chain 'G' and resid 282 through 295 Processing helix chain 'G' and resid 306 through 309 No H-bonds generated for 'chain 'G' and resid 306 through 309' Processing helix chain 'G' and resid 320 through 333 Processing helix chain 'G' and resid 355 through 358 Processing helix chain 'G' and resid 374 through 384 Processing helix chain 'G' and resid 397 through 403 Processing helix chain 'G' and resid 408 through 425 Processing helix chain 'G' and resid 427 through 429 No H-bonds generated for 'chain 'G' and resid 427 through 429' Processing helix chain 'G' and resid 439 through 444 Processing helix chain 'G' and resid 449 through 458 Processing helix chain 'G' and resid 483 through 498 Proline residue: G 496 - end of helix Processing helix chain 'G' and resid 500 through 505 Processing helix chain 'G' and resid 524 through 534 Processing helix chain 'G' and resid 544 through 552 Processing helix chain 'G' and resid 557 through 568 Processing helix chain 'G' and resid 579 through 585 removed outlier: 4.384A pdb=" N ILE G 582 " --> pdb=" O LEU G 579 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 610 Processing helix chain 'G' and resid 626 through 628 No H-bonds generated for 'chain 'G' and resid 626 through 628' Processing helix chain 'G' and resid 631 through 634 Processing helix chain 'G' and resid 650 through 660 Processing helix chain 'G' and resid 672 through 678 Processing helix chain 'G' and resid 684 through 715 removed outlier: 3.768A pdb=" N THR G 715 " --> pdb=" O ARG G 711 " (cutoff:3.500A) Processing helix chain 'G' and resid 733 through 742 removed outlier: 3.995A pdb=" N PHE G 742 " --> pdb=" O GLU G 738 " (cutoff:3.500A) Processing helix chain 'G' and resid 749 through 761 Processing helix chain 'H' and resid 86 through 92 Processing helix chain 'H' and resid 135 through 139 Processing helix chain 'H' and resid 210 through 225 removed outlier: 3.983A pdb=" N ALA H 214 " --> pdb=" O LYS H 211 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU H 221 " --> pdb=" O GLU H 218 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU H 222 " --> pdb=" O MET H 219 " (cutoff:3.500A) Proline residue: H 223 - end of helix Processing helix chain 'H' and resid 227 through 232 removed outlier: 3.986A pdb=" N LYS H 231 " --> pdb=" O PRO H 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA H 232 " --> pdb=" O ALA H 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 227 through 232' Processing helix chain 'H' and resid 251 through 262 Processing helix chain 'H' and resid 271 through 275 removed outlier: 3.546A pdb=" N MET H 275 " --> pdb=" O GLY H 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 271 through 275' Processing helix chain 'H' and resid 282 through 295 Processing helix chain 'H' and resid 306 through 309 No H-bonds generated for 'chain 'H' and resid 306 through 309' Processing helix chain 'H' and resid 320 through 333 Processing helix chain 'H' and resid 355 through 358 Processing helix chain 'H' and resid 374 through 384 Processing helix chain 'H' and resid 397 through 403 Processing helix chain 'H' and resid 408 through 425 Processing helix chain 'H' and resid 427 through 429 No H-bonds generated for 'chain 'H' and resid 427 through 429' Processing helix chain 'H' and resid 439 through 444 Processing helix chain 'H' and resid 449 through 458 Processing helix chain 'H' and resid 483 through 498 Proline residue: H 496 - end of helix Processing helix chain 'H' and resid 500 through 505 Processing helix chain 'H' and resid 524 through 534 Processing helix chain 'H' and resid 544 through 552 Processing helix chain 'H' and resid 557 through 568 Processing helix chain 'H' and resid 579 through 585 removed outlier: 4.384A pdb=" N ILE H 582 " --> pdb=" O LEU H 579 " (cutoff:3.500A) Processing helix chain 'H' and resid 599 through 610 Processing helix chain 'H' and resid 626 through 628 No H-bonds generated for 'chain 'H' and resid 626 through 628' Processing helix chain 'H' and resid 631 through 634 Processing helix chain 'H' and resid 650 through 660 Processing helix chain 'H' and resid 672 through 678 Processing helix chain 'H' and resid 684 through 715 removed outlier: 3.769A pdb=" N THR H 715 " --> pdb=" O ARG H 711 " (cutoff:3.500A) Processing helix chain 'H' and resid 733 through 742 removed outlier: 3.995A pdb=" N PHE H 742 " --> pdb=" O GLU H 738 " (cutoff:3.500A) Processing helix chain 'H' and resid 749 through 761 Processing helix chain 'I' and resid 86 through 92 Processing helix chain 'I' and resid 135 through 139 Processing helix chain 'I' and resid 210 through 225 removed outlier: 3.984A pdb=" N ALA I 214 " --> pdb=" O LYS I 211 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU I 221 " --> pdb=" O GLU I 218 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU I 222 " --> pdb=" O MET I 219 " (cutoff:3.500A) Proline residue: I 223 - end of helix Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.986A pdb=" N LYS I 231 " --> pdb=" O PRO I 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA I 232 " --> pdb=" O ALA I 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 227 through 232' Processing helix chain 'I' and resid 251 through 262 Processing helix chain 'I' and resid 271 through 275 removed outlier: 3.548A pdb=" N MET I 275 " --> pdb=" O GLY I 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 271 through 275' Processing helix chain 'I' and resid 282 through 295 Processing helix chain 'I' and resid 306 through 309 No H-bonds generated for 'chain 'I' and resid 306 through 309' Processing helix chain 'I' and resid 320 through 333 Processing helix chain 'I' and resid 355 through 358 Processing helix chain 'I' and resid 374 through 384 Processing helix chain 'I' and resid 397 through 403 Processing helix chain 'I' and resid 408 through 425 Processing helix chain 'I' and resid 427 through 429 No H-bonds generated for 'chain 'I' and resid 427 through 429' Processing helix chain 'I' and resid 439 through 444 Processing helix chain 'I' and resid 449 through 458 Processing helix chain 'I' and resid 483 through 498 Proline residue: I 496 - end of helix Processing helix chain 'I' and resid 500 through 505 Processing helix chain 'I' and resid 524 through 534 Processing helix chain 'I' and resid 544 through 552 Processing helix chain 'I' and resid 557 through 568 Processing helix chain 'I' and resid 579 through 585 removed outlier: 4.384A pdb=" N ILE I 582 " --> pdb=" O LEU I 579 " (cutoff:3.500A) Processing helix chain 'I' and resid 599 through 610 Processing helix chain 'I' and resid 626 through 628 No H-bonds generated for 'chain 'I' and resid 626 through 628' Processing helix chain 'I' and resid 631 through 634 Processing helix chain 'I' and resid 650 through 660 Processing helix chain 'I' and resid 672 through 678 Processing helix chain 'I' and resid 684 through 715 removed outlier: 3.769A pdb=" N THR I 715 " --> pdb=" O ARG I 711 " (cutoff:3.500A) Processing helix chain 'I' and resid 733 through 742 removed outlier: 3.995A pdb=" N PHE I 742 " --> pdb=" O GLU I 738 " (cutoff:3.500A) Processing helix chain 'I' and resid 749 through 761 Processing helix chain 'J' and resid 86 through 92 Processing helix chain 'J' and resid 135 through 139 Processing helix chain 'J' and resid 210 through 225 removed outlier: 3.984A pdb=" N ALA J 214 " --> pdb=" O LYS J 211 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU J 221 " --> pdb=" O GLU J 218 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU J 222 " --> pdb=" O MET J 219 " (cutoff:3.500A) Proline residue: J 223 - end of helix Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.986A pdb=" N LYS J 231 " --> pdb=" O PRO J 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA J 232 " --> pdb=" O ALA J 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 227 through 232' Processing helix chain 'J' and resid 251 through 262 Processing helix chain 'J' and resid 271 through 275 removed outlier: 3.547A pdb=" N MET J 275 " --> pdb=" O GLY J 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 271 through 275' Processing helix chain 'J' and resid 282 through 295 Processing helix chain 'J' and resid 306 through 309 No H-bonds generated for 'chain 'J' and resid 306 through 309' Processing helix chain 'J' and resid 320 through 333 Processing helix chain 'J' and resid 355 through 358 Processing helix chain 'J' and resid 374 through 384 Processing helix chain 'J' and resid 397 through 403 Processing helix chain 'J' and resid 408 through 425 Processing helix chain 'J' and resid 427 through 429 No H-bonds generated for 'chain 'J' and resid 427 through 429' Processing helix chain 'J' and resid 439 through 444 Processing helix chain 'J' and resid 449 through 458 Processing helix chain 'J' and resid 483 through 498 Proline residue: J 496 - end of helix Processing helix chain 'J' and resid 500 through 505 Processing helix chain 'J' and resid 524 through 534 Processing helix chain 'J' and resid 544 through 552 Processing helix chain 'J' and resid 557 through 568 Processing helix chain 'J' and resid 579 through 585 removed outlier: 4.383A pdb=" N ILE J 582 " --> pdb=" O LEU J 579 " (cutoff:3.500A) Processing helix chain 'J' and resid 599 through 610 Processing helix chain 'J' and resid 626 through 628 No H-bonds generated for 'chain 'J' and resid 626 through 628' Processing helix chain 'J' and resid 631 through 634 Processing helix chain 'J' and resid 650 through 660 Processing helix chain 'J' and resid 672 through 678 Processing helix chain 'J' and resid 684 through 715 removed outlier: 3.768A pdb=" N THR J 715 " --> pdb=" O ARG J 711 " (cutoff:3.500A) Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.996A pdb=" N PHE J 742 " --> pdb=" O GLU J 738 " (cutoff:3.500A) Processing helix chain 'J' and resid 749 through 761 Processing helix chain 'K' and resid 86 through 92 Processing helix chain 'K' and resid 135 through 139 Processing helix chain 'K' and resid 210 through 225 removed outlier: 3.984A pdb=" N ALA K 214 " --> pdb=" O LYS K 211 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU K 221 " --> pdb=" O GLU K 218 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU K 222 " --> pdb=" O MET K 219 " (cutoff:3.500A) Proline residue: K 223 - end of helix Processing helix chain 'K' and resid 227 through 232 removed outlier: 3.986A pdb=" N LYS K 231 " --> pdb=" O PRO K 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 227 through 232' Processing helix chain 'K' and resid 251 through 262 Processing helix chain 'K' and resid 271 through 275 removed outlier: 3.547A pdb=" N MET K 275 " --> pdb=" O GLY K 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 271 through 275' Processing helix chain 'K' and resid 282 through 295 Processing helix chain 'K' and resid 306 through 309 No H-bonds generated for 'chain 'K' and resid 306 through 309' Processing helix chain 'K' and resid 320 through 333 Processing helix chain 'K' and resid 355 through 358 Processing helix chain 'K' and resid 374 through 384 Processing helix chain 'K' and resid 397 through 403 Processing helix chain 'K' and resid 408 through 425 Processing helix chain 'K' and resid 427 through 429 No H-bonds generated for 'chain 'K' and resid 427 through 429' Processing helix chain 'K' and resid 439 through 444 Processing helix chain 'K' and resid 449 through 458 Processing helix chain 'K' and resid 483 through 498 Proline residue: K 496 - end of helix Processing helix chain 'K' and resid 500 through 505 Processing helix chain 'K' and resid 524 through 534 Processing helix chain 'K' and resid 544 through 552 Processing helix chain 'K' and resid 557 through 568 Processing helix chain 'K' and resid 579 through 585 removed outlier: 4.383A pdb=" N ILE K 582 " --> pdb=" O LEU K 579 " (cutoff:3.500A) Processing helix chain 'K' and resid 599 through 610 Processing helix chain 'K' and resid 626 through 628 No H-bonds generated for 'chain 'K' and resid 626 through 628' Processing helix chain 'K' and resid 631 through 634 Processing helix chain 'K' and resid 650 through 660 Processing helix chain 'K' and resid 672 through 678 Processing helix chain 'K' and resid 684 through 715 removed outlier: 3.769A pdb=" N THR K 715 " --> pdb=" O ARG K 711 " (cutoff:3.500A) Processing helix chain 'K' and resid 733 through 742 removed outlier: 3.995A pdb=" N PHE K 742 " --> pdb=" O GLU K 738 " (cutoff:3.500A) Processing helix chain 'K' and resid 749 through 761 Processing helix chain 'L' and resid 86 through 92 Processing helix chain 'L' and resid 135 through 139 Processing helix chain 'L' and resid 210 through 225 removed outlier: 3.984A pdb=" N ALA L 214 " --> pdb=" O LYS L 211 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU L 221 " --> pdb=" O GLU L 218 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU L 222 " --> pdb=" O MET L 219 " (cutoff:3.500A) Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 227 through 232 removed outlier: 3.986A pdb=" N LYS L 231 " --> pdb=" O PRO L 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA L 232 " --> pdb=" O ALA L 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 227 through 232' Processing helix chain 'L' and resid 251 through 262 Processing helix chain 'L' and resid 271 through 275 removed outlier: 3.547A pdb=" N MET L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 271 through 275' Processing helix chain 'L' and resid 282 through 295 Processing helix chain 'L' and resid 306 through 309 No H-bonds generated for 'chain 'L' and resid 306 through 309' Processing helix chain 'L' and resid 320 through 333 Processing helix chain 'L' and resid 355 through 358 Processing helix chain 'L' and resid 374 through 384 Processing helix chain 'L' and resid 397 through 403 Processing helix chain 'L' and resid 408 through 425 Processing helix chain 'L' and resid 427 through 429 No H-bonds generated for 'chain 'L' and resid 427 through 429' Processing helix chain 'L' and resid 439 through 444 Processing helix chain 'L' and resid 449 through 458 Processing helix chain 'L' and resid 483 through 498 Proline residue: L 496 - end of helix Processing helix chain 'L' and resid 500 through 505 Processing helix chain 'L' and resid 524 through 534 Processing helix chain 'L' and resid 544 through 552 Processing helix chain 'L' and resid 557 through 568 Processing helix chain 'L' and resid 579 through 585 removed outlier: 4.383A pdb=" N ILE L 582 " --> pdb=" O LEU L 579 " (cutoff:3.500A) Processing helix chain 'L' and resid 599 through 610 Processing helix chain 'L' and resid 626 through 628 No H-bonds generated for 'chain 'L' and resid 626 through 628' Processing helix chain 'L' and resid 631 through 634 Processing helix chain 'L' and resid 650 through 660 Processing helix chain 'L' and resid 672 through 678 Processing helix chain 'L' and resid 684 through 715 removed outlier: 3.769A pdb=" N THR L 715 " --> pdb=" O ARG L 711 " (cutoff:3.500A) Processing helix chain 'L' and resid 733 through 742 removed outlier: 3.995A pdb=" N PHE L 742 " --> pdb=" O GLU L 738 " (cutoff:3.500A) Processing helix chain 'L' and resid 749 through 761 Processing sheet with id= A, first strand: chain 'A' and resid 365 through 368 removed outlier: 3.916A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.624A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.915A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 641 through 645 removed outlier: 3.624A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY B 518 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR B 623 " --> pdb=" O GLY B 518 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 365 through 368 removed outlier: 3.916A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.624A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 365 through 368 removed outlier: 3.916A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.625A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 365 through 368 removed outlier: 3.916A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.624A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.916A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 641 through 645 removed outlier: 3.623A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 25 through 27 removed outlier: 3.738A pdb=" N LEU G 26 " --> pdb=" O ILE G 100 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 145 through 147 Processing sheet with id= O, first strand: chain 'G' and resid 151 through 156 Processing sheet with id= P, first strand: chain 'G' and resid 365 through 368 removed outlier: 3.877A pdb=" N ARG G 365 " --> pdb=" O GLY G 240 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL G 343 " --> pdb=" O ILE G 241 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU G 243 " --> pdb=" O VAL G 343 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ALA G 345 " --> pdb=" O LEU G 243 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N PHE G 265 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE G 302 " --> pdb=" O PHE G 265 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE G 267 " --> pdb=" O PHE G 302 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP G 304 " --> pdb=" O PHE G 267 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE G 269 " --> pdb=" O ASP G 304 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 641 through 645 removed outlier: 3.706A pdb=" N GLY G 518 " --> pdb=" O THR G 623 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASN G 538 " --> pdb=" O VAL G 573 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE G 575 " --> pdb=" O ASN G 538 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE G 540 " --> pdb=" O PHE G 575 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.738A pdb=" N LEU H 26 " --> pdb=" O ILE H 100 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 145 through 147 Processing sheet with id= T, first strand: chain 'H' and resid 151 through 156 Processing sheet with id= U, first strand: chain 'H' and resid 365 through 368 removed outlier: 3.877A pdb=" N ARG H 365 " --> pdb=" O GLY H 240 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL H 343 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU H 243 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ALA H 345 " --> pdb=" O LEU H 243 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE H 265 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE H 302 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE H 267 " --> pdb=" O PHE H 302 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP H 304 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE H 269 " --> pdb=" O ASP H 304 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 641 through 645 removed outlier: 3.706A pdb=" N GLY H 518 " --> pdb=" O THR H 623 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN H 538 " --> pdb=" O VAL H 573 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE H 575 " --> pdb=" O ASN H 538 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE H 540 " --> pdb=" O PHE H 575 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 25 through 27 removed outlier: 3.737A pdb=" N LEU I 26 " --> pdb=" O ILE I 100 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 145 through 147 Processing sheet with id= Y, first strand: chain 'I' and resid 151 through 156 Processing sheet with id= Z, first strand: chain 'I' and resid 365 through 368 removed outlier: 3.877A pdb=" N ARG I 365 " --> pdb=" O GLY I 240 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL I 343 " --> pdb=" O ILE I 241 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU I 243 " --> pdb=" O VAL I 343 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ALA I 345 " --> pdb=" O LEU I 243 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N PHE I 265 " --> pdb=" O ILE I 300 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE I 302 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE I 267 " --> pdb=" O PHE I 302 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP I 304 " --> pdb=" O PHE I 267 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE I 269 " --> pdb=" O ASP I 304 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 641 through 645 removed outlier: 3.706A pdb=" N GLY I 518 " --> pdb=" O THR I 623 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN I 538 " --> pdb=" O VAL I 573 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE I 575 " --> pdb=" O ASN I 538 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE I 540 " --> pdb=" O PHE I 575 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 25 through 27 removed outlier: 3.738A pdb=" N LEU J 26 " --> pdb=" O ILE J 100 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 145 through 147 Processing sheet with id= AD, first strand: chain 'J' and resid 151 through 156 Processing sheet with id= AE, first strand: chain 'J' and resid 365 through 368 removed outlier: 3.877A pdb=" N ARG J 365 " --> pdb=" O GLY J 240 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL J 343 " --> pdb=" O ILE J 241 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU J 243 " --> pdb=" O VAL J 343 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ALA J 345 " --> pdb=" O LEU J 243 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE J 265 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE J 302 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE J 267 " --> pdb=" O PHE J 302 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP J 304 " --> pdb=" O PHE J 267 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE J 269 " --> pdb=" O ASP J 304 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 641 through 645 removed outlier: 3.706A pdb=" N GLY J 518 " --> pdb=" O THR J 623 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN J 538 " --> pdb=" O VAL J 573 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE J 575 " --> pdb=" O ASN J 538 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE J 540 " --> pdb=" O PHE J 575 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 25 through 27 removed outlier: 3.738A pdb=" N LEU K 26 " --> pdb=" O ILE K 100 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'K' and resid 145 through 147 Processing sheet with id= AI, first strand: chain 'K' and resid 151 through 156 Processing sheet with id= AJ, first strand: chain 'K' and resid 365 through 368 removed outlier: 3.878A pdb=" N ARG K 365 " --> pdb=" O GLY K 240 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL K 343 " --> pdb=" O ILE K 241 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU K 243 " --> pdb=" O VAL K 343 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ALA K 345 " --> pdb=" O LEU K 243 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE K 265 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE K 302 " --> pdb=" O PHE K 265 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE K 267 " --> pdb=" O PHE K 302 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP K 304 " --> pdb=" O PHE K 267 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE K 269 " --> pdb=" O ASP K 304 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'K' and resid 641 through 645 removed outlier: 3.706A pdb=" N GLY K 518 " --> pdb=" O THR K 623 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASN K 538 " --> pdb=" O VAL K 573 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE K 575 " --> pdb=" O ASN K 538 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE K 540 " --> pdb=" O PHE K 575 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.737A pdb=" N LEU L 26 " --> pdb=" O ILE L 100 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 145 through 147 Processing sheet with id= AN, first strand: chain 'L' and resid 151 through 156 Processing sheet with id= AO, first strand: chain 'L' and resid 365 through 368 removed outlier: 3.877A pdb=" N ARG L 365 " --> pdb=" O GLY L 240 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL L 343 " --> pdb=" O ILE L 241 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU L 243 " --> pdb=" O VAL L 343 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ALA L 345 " --> pdb=" O LEU L 243 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE L 265 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE L 302 " --> pdb=" O PHE L 265 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE L 267 " --> pdb=" O PHE L 302 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP L 304 " --> pdb=" O PHE L 267 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE L 269 " --> pdb=" O ASP L 304 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'L' and resid 641 through 645 removed outlier: 3.707A pdb=" N GLY L 518 " --> pdb=" O THR L 623 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASN L 538 " --> pdb=" O VAL L 573 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE L 575 " --> pdb=" O ASN L 538 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE L 540 " --> pdb=" O PHE L 575 " (cutoff:3.500A) 2331 hydrogen bonds defined for protein. 6219 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: 23.60 Time building geometry restraints manager: 20.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 21782 1.35 - 1.48: 13346 1.48 - 1.61: 28609 1.61 - 1.74: 60 1.74 - 1.87: 582 Bond restraints: 64379 Sorted by residual: bond pdb=" C3' ADP L 801 " pdb=" C4' ADP L 801 " ideal model delta sigma weight residual 1.524 1.302 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C3' ADP G 801 " pdb=" C4' ADP G 801 " ideal model delta sigma weight residual 1.524 1.302 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C3' ADP H 801 " pdb=" C4' ADP H 801 " ideal model delta sigma weight residual 1.524 1.302 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C3' ADP I 801 " pdb=" C4' ADP I 801 " ideal model delta sigma weight residual 1.524 1.303 0.221 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C3' ADP J 801 " pdb=" C4' ADP J 801 " ideal model delta sigma weight residual 1.524 1.303 0.221 2.00e-02 2.50e+03 1.22e+02 ... (remaining 64374 not shown) Histogram of bond angle deviations from ideal: 95.07 - 102.87: 558 102.87 - 110.66: 19571 110.66 - 118.45: 30512 118.45 - 126.24: 35590 126.24 - 134.03: 780 Bond angle restraints: 87011 Sorted by residual: angle pdb=" C ARG C 711 " pdb=" CA ARG C 711 " pdb=" CB ARG C 711 " ideal model delta sigma weight residual 110.79 95.53 15.26 1.66e+00 3.63e-01 8.45e+01 angle pdb=" C ARG E 711 " pdb=" CA ARG E 711 " pdb=" CB ARG E 711 " ideal model delta sigma weight residual 110.79 95.53 15.26 1.66e+00 3.63e-01 8.45e+01 angle pdb=" C ARG A 711 " pdb=" CA ARG A 711 " pdb=" CB ARG A 711 " ideal model delta sigma weight residual 110.79 95.53 15.26 1.66e+00 3.63e-01 8.45e+01 angle pdb=" C ARG D 711 " pdb=" CA ARG D 711 " pdb=" CB ARG D 711 " ideal model delta sigma weight residual 110.79 95.53 15.26 1.66e+00 3.63e-01 8.45e+01 angle pdb=" C ARG B 711 " pdb=" CA ARG B 711 " pdb=" CB ARG B 711 " ideal model delta sigma weight residual 110.79 95.56 15.23 1.66e+00 3.63e-01 8.42e+01 ... (remaining 87006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.39: 38502 30.39 - 60.77: 1240 60.77 - 91.15: 207 91.15 - 121.54: 30 121.54 - 151.92: 6 Dihedral angle restraints: 39985 sinusoidal: 17021 harmonic: 22964 Sorted by residual: dihedral pdb=" CD ARG G 741 " pdb=" NE ARG G 741 " pdb=" CZ ARG G 741 " pdb=" NH1 ARG G 741 " ideal model delta sinusoidal sigma weight residual 0.00 85.62 -85.62 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CD ARG H 741 " pdb=" NE ARG H 741 " pdb=" CZ ARG H 741 " pdb=" NH1 ARG H 741 " ideal model delta sinusoidal sigma weight residual 0.00 85.61 -85.61 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CD ARG K 741 " pdb=" NE ARG K 741 " pdb=" CZ ARG K 741 " pdb=" NH1 ARG K 741 " ideal model delta sinusoidal sigma weight residual 0.00 85.61 -85.61 1 1.00e+01 1.00e-02 8.86e+01 ... (remaining 39982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 7428 0.049 - 0.098: 1579 0.098 - 0.148: 545 0.148 - 0.197: 66 0.197 - 0.246: 18 Chirality restraints: 9636 Sorted by residual: chirality pdb=" C17 Y6Y I 802 " pdb=" C18 Y6Y I 802 " pdb=" C21 Y6Y I 802 " pdb=" S1 Y6Y I 802 " both_signs ideal model delta sigma weight residual False 3.51 3.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C17 Y6Y G 802 " pdb=" C18 Y6Y G 802 " pdb=" C21 Y6Y G 802 " pdb=" S1 Y6Y G 802 " both_signs ideal model delta sigma weight residual False 3.51 3.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C17 Y6Y J 802 " pdb=" C18 Y6Y J 802 " pdb=" C21 Y6Y J 802 " pdb=" S1 Y6Y J 802 " both_signs ideal model delta sigma weight residual False 3.51 3.26 0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 9633 not shown) Planarity restraints: 11498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 741 " -0.992 9.50e-02 1.11e+02 4.45e-01 1.22e+02 pdb=" NE ARG K 741 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG K 741 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG K 741 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 741 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 741 " -0.992 9.50e-02 1.11e+02 4.45e-01 1.22e+02 pdb=" NE ARG H 741 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG H 741 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 741 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 741 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 741 " -0.992 9.50e-02 1.11e+02 4.45e-01 1.22e+02 pdb=" NE ARG G 741 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG G 741 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 741 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 741 " -0.009 2.00e-02 2.50e+03 ... (remaining 11495 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 568 2.47 - 3.08: 48129 3.08 - 3.68: 96228 3.68 - 4.29: 142176 4.29 - 4.90: 233479 Nonbonded interactions: 520580 Sorted by model distance: nonbonded pdb=" O VAL A 399 " pdb=" OG1 THR A 403 " model vdw 1.859 2.440 nonbonded pdb=" O VAL E 399 " pdb=" OG1 THR E 403 " model vdw 1.859 2.440 nonbonded pdb=" O VAL F 399 " pdb=" OG1 THR F 403 " model vdw 1.859 2.440 nonbonded pdb=" O VAL D 399 " pdb=" OG1 THR D 403 " model vdw 1.859 2.440 nonbonded pdb=" O VAL C 399 " pdb=" OG1 THR C 403 " model vdw 1.860 2.440 ... (remaining 520575 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' and (resid 200 through 519 or resid 521 through 711 or resid 714 thro \ ugh 775 or resid 801 through 802)) selection = (chain 'B' and (resid 200 through 519 or resid 521 through 711 or resid 714 thro \ ugh 775 or resid 801 through 802)) selection = (chain 'C' and (resid 200 through 519 or resid 521 through 711 or resid 714 thro \ ugh 775 or resid 801 through 802)) selection = (chain 'D' and (resid 200 through 711 or resid 714 through 775 or resid 801 thro \ ugh 802)) selection = (chain 'E' and (resid 200 through 519 or resid 521 through 711 or resid 714 thro \ ugh 775 or resid 801 through 802)) selection = (chain 'F' and (resid 200 through 519 or resid 521 through 711 or resid 714 thro \ ugh 775 or resid 801 through 802)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 11.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 51.330 Check model and map are aligned: 0.690 Set scattering table: 0.430 Process input model: 132.890 Find NCS groups from input model: 4.500 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 213.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 0.222 64379 Z= 0.796 Angle : 0.948 24.573 87011 Z= 0.476 Chirality : 0.047 0.246 9636 Planarity : 0.013 0.445 11498 Dihedral : 15.238 151.925 25095 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 45.64 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.42 % Favored : 94.21 % Rotamer: Outliers : 1.96 % Allowed : 1.69 % Favored : 96.35 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.49 % Cis-general : 0.08 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.10), residues: 7959 helix: 2.23 (0.09), residues: 3456 sheet: -0.63 (0.18), residues: 894 loop : -0.53 (0.11), residues: 3609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 454 HIS 0.008 0.001 HIS A 406 PHE 0.062 0.002 PHE K 360 TYR 0.026 0.001 TYR D 495 ARG 0.073 0.002 ARG B 732 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1313 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1181 time to evaluate : 5.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.8022 (mm) REVERT: A 709 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6968 (ttm170) REVERT: C 678 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8176 (mmm) REVERT: D 359 ARG cc_start: 0.7401 (ttt-90) cc_final: 0.6936 (ttm170) REVERT: D 678 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7964 (mmm) REVERT: F 709 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.6260 (ttm170) REVERT: G 723 GLU cc_start: 0.3484 (OUTLIER) cc_final: 0.3144 (tm-30) REVERT: H 723 GLU cc_start: 0.3175 (OUTLIER) cc_final: 0.2785 (tm-30) REVERT: I 669 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7590 (OUTLIER) REVERT: I 723 GLU cc_start: 0.3098 (OUTLIER) cc_final: 0.2655 (tm-30) REVERT: K 598 ASP cc_start: 0.7478 (p0) cc_final: 0.7256 (p0) REVERT: L 194 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6503 (tm-30) REVERT: L 723 GLU cc_start: 0.2986 (OUTLIER) cc_final: 0.2617 (tm-30) outliers start: 132 outliers final: 33 residues processed: 1228 average time/residue: 1.4989 time to fit residues: 2331.6159 Evaluate side-chains 737 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 694 time to evaluate : 5.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain D residue 221 GLU Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 706 GLU Chi-restraints excluded: chain E residue 678 MET Chi-restraints excluded: chain E residue 706 GLU Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 706 GLU Chi-restraints excluded: chain F residue 709 ARG Chi-restraints excluded: chain F residue 749 ASP Chi-restraints excluded: chain G residue 706 GLU Chi-restraints excluded: chain G residue 723 GLU Chi-restraints excluded: chain G residue 738 GLU Chi-restraints excluded: chain H residue 706 GLU Chi-restraints excluded: chain H residue 707 ILE Chi-restraints excluded: chain H residue 723 GLU Chi-restraints excluded: chain H residue 738 GLU Chi-restraints excluded: chain I residue 669 ASP Chi-restraints excluded: chain I residue 706 GLU Chi-restraints excluded: chain I residue 723 GLU Chi-restraints excluded: chain I residue 738 GLU Chi-restraints excluded: chain J residue 706 GLU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 738 GLU Chi-restraints excluded: chain K residue 706 GLU Chi-restraints excluded: chain K residue 707 ILE Chi-restraints excluded: chain K residue 738 GLU Chi-restraints excluded: chain L residue 194 GLU Chi-restraints excluded: chain L residue 706 GLU Chi-restraints excluded: chain L residue 723 GLU Chi-restraints excluded: chain L residue 738 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 668 optimal weight: 0.8980 chunk 600 optimal weight: 3.9990 chunk 333 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 chunk 404 optimal weight: 0.6980 chunk 320 optimal weight: 1.9990 chunk 620 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 377 optimal weight: 0.9990 chunk 462 optimal weight: 3.9990 chunk 719 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN B 285 ASN C 285 ASN D 285 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN F 285 ASN G 24 ASN ** G 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 499 HIS ** H 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 602 ASN I 24 ASN ** I 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 ASN ** J 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 499 HIS K 215 GLN ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 499 HIS K 602 ASN ** L 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 602 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 64379 Z= 0.271 Angle : 0.720 10.738 87011 Z= 0.349 Chirality : 0.046 0.201 9636 Planarity : 0.005 0.073 11498 Dihedral : 9.568 129.502 9283 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.31 % Favored : 94.23 % Rotamer: Outliers : 3.53 % Allowed : 10.10 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.10), residues: 7959 helix: 1.62 (0.09), residues: 3483 sheet: -0.20 (0.17), residues: 960 loop : -0.65 (0.11), residues: 3516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 454 HIS 0.009 0.001 HIS K 317 PHE 0.017 0.002 PHE A 363 TYR 0.023 0.002 TYR I 755 ARG 0.013 0.001 ARG B 732 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 778 time to evaluate : 5.429 Fit side-chains REVERT: A 561 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7440 (mt-10) REVERT: A 564 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: B 283 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6492 (mt-10) REVERT: B 564 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7412 (m-30) REVERT: B 749 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6776 (t0) REVERT: D 359 ARG cc_start: 0.7332 (ttt-90) cc_final: 0.6905 (ttm110) REVERT: E 283 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6266 (mt-10) REVERT: E 504 LEU cc_start: 0.8793 (tt) cc_final: 0.8416 (mt) REVERT: E 508 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8339 (ttt) REVERT: F 427 MET cc_start: 0.3949 (tmt) cc_final: 0.3296 (ttm) REVERT: F 564 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: G 420 LEU cc_start: 0.7727 (mm) cc_final: 0.7516 (mt) REVERT: G 427 MET cc_start: 0.6485 (tpt) cc_final: 0.6232 (ttt) REVERT: G 672 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8109 (mp) REVERT: I 713 ARG cc_start: 0.7918 (tmm160) cc_final: 0.7616 (ttp80) REVERT: J 672 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8168 (mp) REVERT: J 713 ARG cc_start: 0.7959 (tmm160) cc_final: 0.7503 (ttp80) REVERT: K 278 LEU cc_start: 0.8185 (tt) cc_final: 0.7981 (tp) REVERT: K 423 ILE cc_start: 0.7861 (mt) cc_final: 0.7652 (mt) REVERT: K 508 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8608 (ttt) REVERT: L 62 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7275 (mttm) REVERT: L 278 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8156 (tp) REVERT: L 427 MET cc_start: 0.6361 (tpt) cc_final: 0.6143 (ttt) outliers start: 238 outliers final: 85 residues processed: 913 average time/residue: 1.3923 time to fit residues: 1676.5587 Evaluate side-chains 758 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 662 time to evaluate : 5.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 564 ASP Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 749 ASP Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 283 GLU Chi-restraints excluded: chain E residue 285 ASN Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 484 ASP Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 709 ARG Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 564 ASP Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 749 ASP Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 387 ASN Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 627 ASP Chi-restraints excluded: chain G residue 629 ILE Chi-restraints excluded: chain G residue 640 ASP Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain G residue 734 ASP Chi-restraints excluded: chain G residue 752 ILE Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 387 ASN Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 627 ASP Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 640 ASP Chi-restraints excluded: chain H residue 734 ASP Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 218 GLU Chi-restraints excluded: chain I residue 365 ARG Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 669 ASP Chi-restraints excluded: chain I residue 734 ASP Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 448 THR Chi-restraints excluded: chain J residue 627 ASP Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 640 ASP Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 707 ILE Chi-restraints excluded: chain J residue 734 ASP Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 387 ASN Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 508 MET Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 707 ILE Chi-restraints excluded: chain K residue 734 ASP Chi-restraints excluded: chain L residue 218 GLU Chi-restraints excluded: chain L residue 278 LEU Chi-restraints excluded: chain L residue 387 ASN Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 672 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 399 optimal weight: 7.9990 chunk 223 optimal weight: 7.9990 chunk 598 optimal weight: 2.9990 chunk 489 optimal weight: 4.9990 chunk 198 optimal weight: 0.9990 chunk 720 optimal weight: 0.9980 chunk 778 optimal weight: 0.6980 chunk 641 optimal weight: 6.9990 chunk 714 optimal weight: 0.6980 chunk 245 optimal weight: 1.9990 chunk 578 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN C 285 ASN C 401 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN D 401 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 ASN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 760 GLN ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 ASN I 760 GLN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 ASN ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 ASN ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 458 GLN L 760 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 64379 Z= 0.223 Angle : 0.649 10.270 87011 Z= 0.318 Chirality : 0.044 0.166 9636 Planarity : 0.005 0.071 11498 Dihedral : 7.715 117.337 9177 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.63 % Favored : 93.99 % Rotamer: Outliers : 3.38 % Allowed : 11.85 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.39 (0.09), residues: 7959 helix: 1.38 (0.09), residues: 3513 sheet: -0.06 (0.17), residues: 960 loop : -0.79 (0.11), residues: 3486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 454 HIS 0.009 0.001 HIS I 317 PHE 0.013 0.001 PHE L 230 TYR 0.026 0.001 TYR I 244 ARG 0.010 0.001 ARG J 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 713 time to evaluate : 5.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6653 (mm-30) REVERT: A 365 ARG cc_start: 0.7708 (ptp-110) cc_final: 0.7379 (ptp-110) REVERT: A 561 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: A 564 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: C 218 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6729 (mt-10) REVERT: D 359 ARG cc_start: 0.7269 (ttt-90) cc_final: 0.6971 (ttm110) REVERT: D 564 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: E 564 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: F 365 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7714 (ptp-110) REVERT: F 427 MET cc_start: 0.3868 (tmt) cc_final: 0.3331 (ttm) REVERT: G 672 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8214 (mp) REVERT: H 198 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7407 (tt) REVERT: H 427 MET cc_start: 0.6493 (tpt) cc_final: 0.6188 (ttt) REVERT: H 672 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8156 (mp) REVERT: I 323 ARG cc_start: 0.7773 (mtp-110) cc_final: 0.7497 (mtp180) REVERT: I 389 LYS cc_start: 0.6919 (mppt) cc_final: 0.6611 (mmtt) REVERT: I 420 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7654 (mt) REVERT: I 427 MET cc_start: 0.6111 (tpt) cc_final: 0.5817 (ttt) REVERT: I 713 ARG cc_start: 0.7946 (tmm160) cc_final: 0.7695 (ttp80) REVERT: J 672 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8275 (mp) REVERT: J 713 ARG cc_start: 0.7928 (tmm160) cc_final: 0.7598 (ttp80) REVERT: K 198 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7426 (tt) REVERT: K 427 MET cc_start: 0.6118 (tpt) cc_final: 0.5905 (ttt) REVERT: K 508 MET cc_start: 0.8964 (ttt) cc_final: 0.8649 (ttt) REVERT: K 713 ARG cc_start: 0.8007 (tmm160) cc_final: 0.7657 (ttp80) outliers start: 228 outliers final: 99 residues processed: 853 average time/residue: 1.3107 time to fit residues: 1468.0141 Evaluate side-chains 737 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 626 time to evaluate : 5.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 564 ASP Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 365 ARG Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 387 ASN Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 627 ASP Chi-restraints excluded: chain G residue 629 ILE Chi-restraints excluded: chain G residue 672 LEU Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain G residue 728 VAL Chi-restraints excluded: chain G residue 734 ASP Chi-restraints excluded: chain G residue 752 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 387 ASN Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 672 LEU Chi-restraints excluded: chain H residue 728 VAL Chi-restraints excluded: chain H residue 734 ASP Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 669 ASP Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 734 ASP Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 448 THR Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 627 ASP Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 734 ASP Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 387 ASN Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 663 LYS Chi-restraints excluded: chain K residue 728 VAL Chi-restraints excluded: chain K residue 734 ASP Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 387 ASN Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 711 optimal weight: 0.0030 chunk 541 optimal weight: 1.9990 chunk 373 optimal weight: 0.0570 chunk 79 optimal weight: 0.0270 chunk 343 optimal weight: 9.9990 chunk 483 optimal weight: 1.9990 chunk 723 optimal weight: 5.9990 chunk 765 optimal weight: 0.0000 chunk 377 optimal weight: 0.5980 chunk 685 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 overall best weight: 0.1370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS F 226 HIS F 401 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 348 ASN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 348 ASN ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 64379 Z= 0.156 Angle : 0.602 13.296 87011 Z= 0.295 Chirality : 0.043 0.161 9636 Planarity : 0.004 0.068 11498 Dihedral : 6.954 105.070 9169 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.50 % Favored : 94.18 % Rotamer: Outliers : 3.17 % Allowed : 13.85 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.45 (0.09), residues: 7959 helix: 1.46 (0.09), residues: 3486 sheet: 0.06 (0.17), residues: 970 loop : -0.80 (0.10), residues: 3503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.000 TRP D 454 HIS 0.008 0.001 HIS I 317 PHE 0.012 0.001 PHE B 363 TYR 0.025 0.001 TYR I 244 ARG 0.009 0.001 ARG F 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 708 time to evaluate : 5.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6665 (mm-30) REVERT: A 365 ARG cc_start: 0.7669 (ptp-110) cc_final: 0.7389 (ptp-110) REVERT: A 373 ASP cc_start: 0.6651 (p0) cc_final: 0.6450 (p0) REVERT: D 359 ARG cc_start: 0.7224 (ttt-90) cc_final: 0.6958 (ttm110) REVERT: D 373 ASP cc_start: 0.6786 (p0) cc_final: 0.6557 (p0) REVERT: E 508 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8495 (ttt) REVERT: H 198 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7309 (tt) REVERT: H 378 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8166 (tt) REVERT: I 323 ARG cc_start: 0.7770 (mtp-110) cc_final: 0.7535 (mtp180) REVERT: I 389 LYS cc_start: 0.6774 (mppt) cc_final: 0.6516 (mmtt) REVERT: I 713 ARG cc_start: 0.7924 (tmm160) cc_final: 0.7660 (ttp80) REVERT: J 423 ILE cc_start: 0.7865 (mt) cc_final: 0.7563 (mt) REVERT: K 158 MET cc_start: 0.7792 (mtt) cc_final: 0.7481 (mtt) REVERT: K 198 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7327 (tt) REVERT: K 427 MET cc_start: 0.5989 (tpt) cc_final: 0.5772 (ttt) REVERT: K 508 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8678 (ttt) REVERT: K 713 ARG cc_start: 0.7926 (tmm160) cc_final: 0.7647 (ttp80) REVERT: L 198 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7537 (tt) REVERT: L 244 TYR cc_start: 0.8303 (p90) cc_final: 0.8056 (p90) REVERT: L 479 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8340 (mm) outliers start: 214 outliers final: 83 residues processed: 836 average time/residue: 1.2999 time to fit residues: 1426.6949 Evaluate side-chains 728 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 637 time to evaluate : 5.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 387 ASN Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 734 ASP Chi-restraints excluded: chain G residue 752 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 378 LEU Chi-restraints excluded: chain H residue 387 ASN Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 728 VAL Chi-restraints excluded: chain H residue 734 ASP Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 734 ASP Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 448 THR Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 734 ASP Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 387 ASN Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 508 MET Chi-restraints excluded: chain K residue 629 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 728 VAL Chi-restraints excluded: chain K residue 734 ASP Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 387 ASN Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 479 ILE Chi-restraints excluded: chain L residue 633 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 637 optimal weight: 3.9990 chunk 434 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 570 optimal weight: 4.9990 chunk 315 optimal weight: 1.9990 chunk 653 optimal weight: 0.9980 chunk 529 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 390 optimal weight: 0.8980 chunk 687 optimal weight: 0.0770 chunk 193 optimal weight: 0.8980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 401 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN E 226 HIS F 226 HIS F 285 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 ASN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 602 ASN ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 ASN ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 64379 Z= 0.238 Angle : 0.620 10.250 87011 Z= 0.303 Chirality : 0.044 0.196 9636 Planarity : 0.005 0.070 11498 Dihedral : 6.723 93.762 9165 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.68 % Favored : 93.96 % Rotamer: Outliers : 3.74 % Allowed : 14.86 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.39 (0.09), residues: 7959 helix: 1.33 (0.09), residues: 3518 sheet: 0.08 (0.17), residues: 990 loop : -0.77 (0.11), residues: 3451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 551 HIS 0.015 0.001 HIS J 317 PHE 0.021 0.001 PHE C 363 TYR 0.025 0.002 TYR I 244 ARG 0.012 0.001 ARG L 323 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 685 time to evaluate : 5.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6710 (mm-30) REVERT: A 349 ARG cc_start: 0.7697 (mtp-110) cc_final: 0.7476 (mtp-110) REVERT: A 365 ARG cc_start: 0.7797 (ptp-110) cc_final: 0.7535 (ptp-110) REVERT: B 373 ASP cc_start: 0.6681 (p0) cc_final: 0.6453 (p0) REVERT: D 564 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: D 720 MET cc_start: 0.5216 (ppp) cc_final: 0.3048 (tpt) REVERT: F 304 ASP cc_start: 0.8025 (t0) cc_final: 0.7663 (t70) REVERT: F 720 MET cc_start: 0.5727 (ppp) cc_final: 0.5291 (pmm) REVERT: H 198 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7392 (tt) REVERT: H 378 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8274 (tt) REVERT: H 663 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.8023 (mtmm) REVERT: H 672 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8292 (mp) REVERT: I 323 ARG cc_start: 0.7827 (mtp-110) cc_final: 0.7593 (mtp180) REVERT: I 389 LYS cc_start: 0.6900 (mppt) cc_final: 0.6690 (mmtt) REVERT: I 420 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7704 (mt) REVERT: I 427 MET cc_start: 0.6106 (tpt) cc_final: 0.5791 (ttt) REVERT: I 713 ARG cc_start: 0.7899 (tmm160) cc_final: 0.7653 (ttp80) REVERT: J 672 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8207 (mp) REVERT: K 198 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7402 (tt) REVERT: K 663 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8050 (mtmm) REVERT: L 198 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7637 (tt) REVERT: L 244 TYR cc_start: 0.8317 (p90) cc_final: 0.8110 (p90) REVERT: L 479 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8349 (mm) outliers start: 252 outliers final: 117 residues processed: 856 average time/residue: 1.3127 time to fit residues: 1478.9312 Evaluate side-chains 759 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 630 time to evaluate : 5.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 387 ASN Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 627 ASP Chi-restraints excluded: chain G residue 629 ILE Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain G residue 734 ASP Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 378 LEU Chi-restraints excluded: chain H residue 387 ASN Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 627 ASP Chi-restraints excluded: chain H residue 629 ILE Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 663 LYS Chi-restraints excluded: chain H residue 672 LEU Chi-restraints excluded: chain H residue 728 VAL Chi-restraints excluded: chain H residue 734 ASP Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 420 LEU Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 728 VAL Chi-restraints excluded: chain I residue 734 ASP Chi-restraints excluded: chain J residue 278 LEU Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 448 THR Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 627 ASP Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 734 ASP Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 387 ASN Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 629 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 663 LYS Chi-restraints excluded: chain K residue 728 VAL Chi-restraints excluded: chain K residue 734 ASP Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 229 LEU Chi-restraints excluded: chain L residue 364 ASP Chi-restraints excluded: chain L residue 387 ASN Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 479 ILE Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 670 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 257 optimal weight: 0.9990 chunk 689 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 449 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 766 optimal weight: 0.6980 chunk 636 optimal weight: 6.9990 chunk 354 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 402 optimal weight: 0.0670 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 401 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS F 226 HIS F 285 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 458 GLN ** I 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 458 GLN ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 64379 Z= 0.200 Angle : 0.603 10.400 87011 Z= 0.293 Chirality : 0.043 0.292 9636 Planarity : 0.004 0.069 11498 Dihedral : 6.568 91.978 9165 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.48 % Favored : 94.27 % Rotamer: Outliers : 3.41 % Allowed : 16.24 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.37 (0.09), residues: 7959 helix: 1.28 (0.09), residues: 3518 sheet: 0.14 (0.17), residues: 984 loop : -0.77 (0.11), residues: 3457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 551 HIS 0.012 0.001 HIS I 317 PHE 0.018 0.001 PHE E 363 TYR 0.026 0.001 TYR I 244 ARG 0.009 0.000 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 658 time to evaluate : 5.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6767 (mm-30) REVERT: A 365 ARG cc_start: 0.7777 (ptp-110) cc_final: 0.7531 (ptp-110) REVERT: C 283 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.5953 (mt-10) REVERT: C 324 ILE cc_start: 0.8481 (tp) cc_final: 0.8258 (tp) REVERT: D 564 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: D 720 MET cc_start: 0.5036 (ppp) cc_final: 0.2902 (tpt) REVERT: F 304 ASP cc_start: 0.8000 (t0) cc_final: 0.7628 (t70) REVERT: F 373 ASP cc_start: 0.6618 (p0) cc_final: 0.6375 (p0) REVERT: F 720 MET cc_start: 0.5696 (ppp) cc_final: 0.5325 (pmm) REVERT: H 198 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7348 (tt) REVERT: H 663 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8087 (mtmm) REVERT: H 672 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8329 (mp) REVERT: I 198 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7394 (tt) REVERT: I 360 PHE cc_start: 0.8494 (m-80) cc_final: 0.8256 (m-80) REVERT: I 378 LEU cc_start: 0.8061 (tm) cc_final: 0.7846 (tt) REVERT: J 82 ILE cc_start: 0.5623 (OUTLIER) cc_final: 0.5400 (tt) REVERT: J 427 MET cc_start: 0.6249 (tpt) cc_final: 0.5592 (ttt) REVERT: J 672 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8223 (mp) REVERT: K 198 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7319 (tt) REVERT: K 663 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8039 (mtmm) REVERT: K 672 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8256 (mp) REVERT: L 62 LYS cc_start: 0.7971 (mtpt) cc_final: 0.7322 (mttm) REVERT: L 198 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7601 (tt) REVERT: L 244 TYR cc_start: 0.8304 (p90) cc_final: 0.8094 (p90) REVERT: L 479 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8371 (mm) outliers start: 230 outliers final: 123 residues processed: 822 average time/residue: 1.2869 time to fit residues: 1397.1351 Evaluate side-chains 765 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 628 time to evaluate : 7.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 203 TYR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 285 ASN Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 464 LEU Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 203 TYR Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 285 ASN Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 387 ASN Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 627 ASP Chi-restraints excluded: chain G residue 629 ILE Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain G residue 734 ASP Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 387 ASN Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 627 ASP Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 663 LYS Chi-restraints excluded: chain H residue 672 LEU Chi-restraints excluded: chain H residue 734 ASP Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 442 MET Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain J residue 82 ILE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 448 THR Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 627 ASP Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 387 ASN Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 468 VAL Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 629 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 663 LYS Chi-restraints excluded: chain K residue 672 LEU Chi-restraints excluded: chain K residue 734 ASP Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 364 ASP Chi-restraints excluded: chain L residue 425 LYS Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 479 ILE Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 738 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 436 optimal weight: 2.9990 chunk 559 optimal weight: 0.9980 chunk 433 optimal weight: 10.0000 chunk 645 optimal weight: 0.7980 chunk 427 optimal weight: 0.6980 chunk 763 optimal weight: 0.9990 chunk 477 optimal weight: 2.9990 chunk 465 optimal weight: 0.9980 chunk 352 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS F 226 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 ASN ** H 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 ASN ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 ASN ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 ASN ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 64379 Z= 0.219 Angle : 0.610 10.615 87011 Z= 0.295 Chirality : 0.044 0.253 9636 Planarity : 0.004 0.069 11498 Dihedral : 6.470 97.870 9165 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.67 % Favored : 94.08 % Rotamer: Outliers : 3.19 % Allowed : 17.08 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.35 (0.09), residues: 7959 helix: 1.28 (0.09), residues: 3523 sheet: 0.13 (0.17), residues: 984 loop : -0.79 (0.11), residues: 3452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 454 HIS 0.008 0.001 HIS H 317 PHE 0.015 0.001 PHE F 363 TYR 0.024 0.001 TYR I 244 ARG 0.010 0.000 ARG I 323 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 643 time to evaluate : 5.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6736 (mm-30) REVERT: A 464 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.7993 (pt) REVERT: B 304 ASP cc_start: 0.8045 (t0) cc_final: 0.7668 (t0) REVERT: B 722 VAL cc_start: 0.4551 (OUTLIER) cc_final: 0.4333 (m) REVERT: C 365 ARG cc_start: 0.7790 (ptp-110) cc_final: 0.7571 (ptp-110) REVERT: C 427 MET cc_start: 0.4917 (OUTLIER) cc_final: 0.4440 (tmm) REVERT: D 720 MET cc_start: 0.5070 (ppp) cc_final: 0.2972 (tpt) REVERT: F 720 MET cc_start: 0.5653 (ppp) cc_final: 0.5140 (pmm) REVERT: H 198 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7340 (tt) REVERT: H 427 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.6185 (ttt) REVERT: H 663 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8087 (mtmm) REVERT: H 672 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8361 (mp) REVERT: I 198 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7425 (tt) REVERT: I 378 LEU cc_start: 0.8105 (tm) cc_final: 0.7869 (tt) REVERT: I 745 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6650 (mtp85) REVERT: J 427 MET cc_start: 0.6155 (tpt) cc_final: 0.5495 (ttt) REVERT: J 672 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8234 (mp) REVERT: K 198 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7334 (tt) REVERT: K 663 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8071 (mtmm) REVERT: K 672 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8296 (mp) REVERT: L 198 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7590 (tt) REVERT: L 479 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8380 (mm) REVERT: L 745 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6686 (mtp85) outliers start: 215 outliers final: 124 residues processed: 795 average time/residue: 1.3101 time to fit residues: 1374.4861 Evaluate side-chains 748 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 607 time to evaluate : 5.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 203 TYR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 203 TYR Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 387 ASN Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain G residue 427 MET Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 627 ASP Chi-restraints excluded: chain G residue 629 ILE Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain G residue 734 ASP Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 387 ASN Chi-restraints excluded: chain H residue 427 MET Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 627 ASP Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 663 LYS Chi-restraints excluded: chain H residue 672 LEU Chi-restraints excluded: chain H residue 734 ASP Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 442 MET Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 745 ARG Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 448 THR Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 627 ASP Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 387 ASN Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 468 VAL Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 629 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 663 LYS Chi-restraints excluded: chain K residue 672 LEU Chi-restraints excluded: chain K residue 734 ASP Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 387 ASN Chi-restraints excluded: chain L residue 425 LYS Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 479 ILE Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 745 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 472 optimal weight: 2.9990 chunk 304 optimal weight: 9.9990 chunk 455 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 485 optimal weight: 1.9990 chunk 520 optimal weight: 0.6980 chunk 377 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 600 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS F 226 HIS F 285 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 ASN ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 ASN ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 760 GLN ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 64379 Z= 0.283 Angle : 0.641 10.676 87011 Z= 0.310 Chirality : 0.045 0.291 9636 Planarity : 0.005 0.071 11498 Dihedral : 6.490 107.935 9165 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.67 % Favored : 94.04 % Rotamer: Outliers : 3.38 % Allowed : 17.37 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.25 (0.09), residues: 7959 helix: 1.16 (0.09), residues: 3530 sheet: 0.01 (0.17), residues: 990 loop : -0.79 (0.11), residues: 3439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 551 HIS 0.011 0.001 HIS D 406 PHE 0.015 0.001 PHE F 363 TYR 0.025 0.002 TYR I 244 ARG 0.010 0.001 ARG A 753 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 641 time to evaluate : 5.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 ASP cc_start: 0.6829 (p0) cc_final: 0.6571 (p0) REVERT: B 304 ASP cc_start: 0.8084 (t0) cc_final: 0.7737 (t0) REVERT: B 722 VAL cc_start: 0.4584 (OUTLIER) cc_final: 0.4294 (m) REVERT: C 283 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6006 (mt-10) REVERT: C 365 ARG cc_start: 0.7916 (ptp-110) cc_final: 0.7704 (ptp-110) REVERT: C 427 MET cc_start: 0.4958 (OUTLIER) cc_final: 0.4537 (tmm) REVERT: D 373 ASP cc_start: 0.6653 (p0) cc_final: 0.6449 (p0) REVERT: D 449 MET cc_start: 0.7560 (tpt) cc_final: 0.7272 (tpt) REVERT: D 720 MET cc_start: 0.4900 (ppp) cc_final: 0.2863 (tpt) REVERT: F 467 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8532 (p) REVERT: F 720 MET cc_start: 0.5551 (ppp) cc_final: 0.4624 (pmm) REVERT: G 663 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8153 (mtmm) REVERT: H 198 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7324 (tt) REVERT: H 427 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.6171 (ttt) REVERT: H 663 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8154 (mtmm) REVERT: I 198 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7582 (tt) REVERT: I 663 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8164 (mtmm) REVERT: I 672 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8235 (mp) REVERT: J 487 ARG cc_start: 0.7395 (ttp80) cc_final: 0.7119 (mtm110) REVERT: J 672 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8279 (mp) REVERT: J 720 MET cc_start: 0.4139 (ptt) cc_final: 0.3801 (ptt) REVERT: K 198 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7372 (tt) REVERT: K 426 LYS cc_start: 0.7708 (tmtt) cc_final: 0.7349 (tmtt) REVERT: K 663 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8148 (mtmm) REVERT: K 672 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8361 (mp) REVERT: L 62 LYS cc_start: 0.7919 (mtpt) cc_final: 0.7252 (mttm) REVERT: L 198 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7616 (tt) REVERT: L 244 TYR cc_start: 0.8377 (p90) cc_final: 0.8142 (p90) REVERT: L 420 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7769 (mt) REVERT: L 479 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8385 (mm) outliers start: 228 outliers final: 135 residues processed: 812 average time/residue: 1.2930 time to fit residues: 1381.1378 Evaluate side-chains 755 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 602 time to evaluate : 5.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 627 ASP Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 633 ILE Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 464 LEU Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 387 ASN Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain G residue 427 MET Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 627 ASP Chi-restraints excluded: chain G residue 629 ILE Chi-restraints excluded: chain G residue 663 LYS Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 387 ASN Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 427 MET Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 627 ASP Chi-restraints excluded: chain H residue 629 ILE Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 663 LYS Chi-restraints excluded: chain H residue 734 ASP Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 672 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 448 THR Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 627 ASP Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 663 LYS Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 387 ASN Chi-restraints excluded: chain K residue 394 VAL Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 468 VAL Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 629 ILE Chi-restraints excluded: chain K residue 633 ILE Chi-restraints excluded: chain K residue 663 LYS Chi-restraints excluded: chain K residue 672 LEU Chi-restraints excluded: chain K residue 720 MET Chi-restraints excluded: chain K residue 734 ASP Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 387 ASN Chi-restraints excluded: chain L residue 420 LEU Chi-restraints excluded: chain L residue 425 LYS Chi-restraints excluded: chain L residue 448 THR Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 479 ILE Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 694 optimal weight: 0.9990 chunk 731 optimal weight: 4.9990 chunk 667 optimal weight: 1.9990 chunk 711 optimal weight: 7.9990 chunk 428 optimal weight: 0.9980 chunk 309 optimal weight: 7.9990 chunk 558 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 642 optimal weight: 4.9990 chunk 672 optimal weight: 0.5980 chunk 708 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS F 226 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 ASN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 ASN ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 64379 Z= 0.223 Angle : 0.621 10.870 87011 Z= 0.300 Chirality : 0.044 0.234 9636 Planarity : 0.004 0.071 11498 Dihedral : 6.330 117.334 9165 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.91 % Favored : 93.93 % Rotamer: Outliers : 2.92 % Allowed : 17.99 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.26 (0.09), residues: 7959 helix: 1.17 (0.09), residues: 3533 sheet: 0.04 (0.16), residues: 1086 loop : -0.82 (0.11), residues: 3340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 551 HIS 0.011 0.001 HIS A 406 PHE 0.021 0.001 PHE A 363 TYR 0.022 0.001 TYR I 244 ARG 0.012 0.001 ARG J 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 634 time to evaluate : 5.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 464 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.7943 (pt) REVERT: B 304 ASP cc_start: 0.8085 (t0) cc_final: 0.7735 (t0) REVERT: B 709 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6159 (ptp-170) REVERT: C 283 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.5978 (mt-10) REVERT: C 427 MET cc_start: 0.5057 (ttm) cc_final: 0.4751 (tmm) REVERT: C 720 MET cc_start: 0.5395 (ppp) cc_final: 0.2993 (OUTLIER) REVERT: D 720 MET cc_start: 0.4795 (ppp) cc_final: 0.2750 (tpt) REVERT: F 720 MET cc_start: 0.5452 (ppp) cc_final: 0.5051 (pmm) REVERT: G 210 ARG cc_start: 0.7689 (ttm-80) cc_final: 0.7487 (mmp80) REVERT: H 198 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7171 (tt) REVERT: H 487 ARG cc_start: 0.7394 (ttp-110) cc_final: 0.7181 (mtp85) REVERT: H 663 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8175 (mtmm) REVERT: H 746 SER cc_start: 0.8374 (m) cc_final: 0.8167 (m) REVERT: I 198 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7527 (tt) REVERT: I 378 LEU cc_start: 0.8057 (tm) cc_final: 0.7815 (tt) REVERT: I 672 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8236 (mp) REVERT: J 487 ARG cc_start: 0.7356 (ttp80) cc_final: 0.6954 (mtm110) REVERT: J 672 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8301 (mp) REVERT: J 720 MET cc_start: 0.4093 (ptt) cc_final: 0.3783 (ptt) REVERT: K 198 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7310 (tt) REVERT: K 426 LYS cc_start: 0.7470 (tmtt) cc_final: 0.7159 (tmtt) REVERT: K 663 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8152 (mtmm) REVERT: L 62 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7228 (mttm) REVERT: L 198 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7604 (tt) REVERT: L 244 TYR cc_start: 0.8371 (p90) cc_final: 0.8106 (p90) REVERT: L 467 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8689 (p) REVERT: L 479 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8425 (mm) REVERT: L 487 ARG cc_start: 0.7377 (mtp85) cc_final: 0.7138 (ttp-110) outliers start: 197 outliers final: 124 residues processed: 784 average time/residue: 1.3001 time to fit residues: 1342.4062 Evaluate side-chains 737 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 601 time to evaluate : 5.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 275 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 387 ASN Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain G residue 427 MET Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 627 ASP Chi-restraints excluded: chain G residue 629 ILE Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 387 ASN Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 627 ASP Chi-restraints excluded: chain H residue 629 ILE Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 663 LYS Chi-restraints excluded: chain H residue 734 ASP Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 672 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 448 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 627 ASP Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 663 LYS Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 448 THR Chi-restraints excluded: chain K residue 468 VAL Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 629 ILE Chi-restraints excluded: chain K residue 663 LYS Chi-restraints excluded: chain K residue 720 MET Chi-restraints excluded: chain K residue 734 ASP Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 387 ASN Chi-restraints excluded: chain L residue 467 THR Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 479 ILE Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 670 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 467 optimal weight: 0.5980 chunk 752 optimal weight: 0.7980 chunk 459 optimal weight: 3.9990 chunk 356 optimal weight: 3.9990 chunk 522 optimal weight: 1.9990 chunk 789 optimal weight: 2.9990 chunk 726 optimal weight: 0.6980 chunk 628 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 485 optimal weight: 4.9990 chunk 385 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN E 226 HIS F 226 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 64379 Z= 0.193 Angle : 0.614 11.876 87011 Z= 0.295 Chirality : 0.044 0.222 9636 Planarity : 0.004 0.070 11498 Dihedral : 6.187 117.502 9165 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.73 % Favored : 94.13 % Rotamer: Outliers : 2.42 % Allowed : 18.63 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.10), residues: 7959 helix: 1.23 (0.09), residues: 3533 sheet: 0.11 (0.16), residues: 1098 loop : -0.79 (0.11), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 454 HIS 0.012 0.001 HIS F 406 PHE 0.015 0.001 PHE A 363 TYR 0.022 0.001 TYR I 244 ARG 0.011 0.000 ARG I 713 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 631 time to evaluate : 5.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.4310 (tmt) cc_final: 0.3820 (ttt) REVERT: A 470 GLU cc_start: 0.7397 (pt0) cc_final: 0.6957 (pm20) REVERT: B 304 ASP cc_start: 0.8075 (t0) cc_final: 0.7731 (t0) REVERT: B 709 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6093 (ptp-170) REVERT: B 722 VAL cc_start: 0.4856 (OUTLIER) cc_final: 0.4614 (m) REVERT: C 283 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.5952 (mt-10) REVERT: C 427 MET cc_start: 0.5001 (ttm) cc_final: 0.4716 (tmm) REVERT: C 720 MET cc_start: 0.5154 (ppp) cc_final: 0.2991 (tpt) REVERT: D 449 MET cc_start: 0.7532 (tpt) cc_final: 0.7247 (tpt) REVERT: D 720 MET cc_start: 0.4766 (ppp) cc_final: 0.2724 (tpt) REVERT: E 720 MET cc_start: 0.5019 (ppp) cc_final: 0.2955 (tpt) REVERT: F 401 ASN cc_start: 0.7657 (m110) cc_final: 0.7452 (m110) REVERT: F 720 MET cc_start: 0.5387 (ppp) cc_final: 0.4729 (pmm) REVERT: H 198 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7168 (tt) REVERT: H 487 ARG cc_start: 0.7389 (ttp-110) cc_final: 0.7176 (mtp85) REVERT: H 663 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8166 (mtmm) REVERT: H 746 SER cc_start: 0.8317 (m) cc_final: 0.8109 (m) REVERT: I 198 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7334 (tt) REVERT: I 378 LEU cc_start: 0.8057 (tm) cc_final: 0.7791 (tt) REVERT: I 479 ILE cc_start: 0.8158 (mm) cc_final: 0.7885 (mm) REVERT: I 487 ARG cc_start: 0.7327 (mtp85) cc_final: 0.7076 (ttp-110) REVERT: I 672 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8208 (mp) REVERT: J 487 ARG cc_start: 0.7362 (ttp80) cc_final: 0.6983 (mtm110) REVERT: J 672 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8271 (mp) REVERT: J 720 MET cc_start: 0.4175 (ptt) cc_final: 0.3911 (ptt) REVERT: K 62 LYS cc_start: 0.8196 (mttt) cc_final: 0.7766 (mttt) REVERT: K 198 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7211 (tt) REVERT: K 663 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8158 (mtmm) REVERT: L 62 LYS cc_start: 0.7890 (mtpt) cc_final: 0.7243 (mttm) REVERT: L 198 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7601 (tt) REVERT: L 244 TYR cc_start: 0.8349 (p90) cc_final: 0.8103 (p90) REVERT: L 467 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8645 (p) REVERT: L 479 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8359 (mm) REVERT: L 487 ARG cc_start: 0.7353 (mtp85) cc_final: 0.7124 (ttp-110) outliers start: 163 outliers final: 119 residues processed: 759 average time/residue: 1.3117 time to fit residues: 1307.0119 Evaluate side-chains 731 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 599 time to evaluate : 5.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 627 ASP Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 285 ASN Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 467 THR Chi-restraints excluded: chain F residue 627 ASP Chi-restraints excluded: chain F residue 728 VAL Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 307 ASP Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 364 ASP Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 387 ASN Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 403 THR Chi-restraints excluded: chain G residue 427 MET Chi-restraints excluded: chain G residue 448 THR Chi-restraints excluded: chain G residue 474 VAL Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 627 ASP Chi-restraints excluded: chain G residue 629 ILE Chi-restraints excluded: chain G residue 707 ILE Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 364 ASP Chi-restraints excluded: chain H residue 387 ASN Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 448 THR Chi-restraints excluded: chain H residue 468 VAL Chi-restraints excluded: chain H residue 474 VAL Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 627 ASP Chi-restraints excluded: chain H residue 629 ILE Chi-restraints excluded: chain H residue 633 ILE Chi-restraints excluded: chain H residue 663 LYS Chi-restraints excluded: chain H residue 734 ASP Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 198 LEU Chi-restraints excluded: chain I residue 201 VAL Chi-restraints excluded: chain I residue 233 ILE Chi-restraints excluded: chain I residue 364 ASP Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 387 ASN Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 448 THR Chi-restraints excluded: chain I residue 474 VAL Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 627 ASP Chi-restraints excluded: chain I residue 633 ILE Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 672 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain J residue 364 ASP Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 387 ASN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 403 THR Chi-restraints excluded: chain J residue 448 THR Chi-restraints excluded: chain J residue 468 VAL Chi-restraints excluded: chain J residue 474 VAL Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 627 ASP Chi-restraints excluded: chain J residue 629 ILE Chi-restraints excluded: chain J residue 663 LYS Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 198 LEU Chi-restraints excluded: chain K residue 286 LEU Chi-restraints excluded: chain K residue 330 THR Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 468 VAL Chi-restraints excluded: chain K residue 474 VAL Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 629 ILE Chi-restraints excluded: chain K residue 663 LYS Chi-restraints excluded: chain K residue 734 ASP Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 198 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 467 THR Chi-restraints excluded: chain L residue 474 VAL Chi-restraints excluded: chain L residue 479 ILE Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 627 ASP Chi-restraints excluded: chain L residue 633 ILE Chi-restraints excluded: chain L residue 670 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 499 optimal weight: 5.9990 chunk 669 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 chunk 579 optimal weight: 9.9990 chunk 92 optimal weight: 0.3980 chunk 174 optimal weight: 0.8980 chunk 629 optimal weight: 1.9990 chunk 263 optimal weight: 0.7980 chunk 646 optimal weight: 0.0020 chunk 79 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS F 226 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 348 ASN ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 ASN ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.174193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.130287 restraints weight = 73649.467| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.43 r_work: 0.3294 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 64379 Z= 0.185 Angle : 0.618 11.883 87011 Z= 0.297 Chirality : 0.044 0.313 9636 Planarity : 0.004 0.071 11498 Dihedral : 6.153 117.917 9165 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.86 % Favored : 94.01 % Rotamer: Outliers : 2.22 % Allowed : 18.88 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.38 (0.10), residues: 7959 helix: 1.26 (0.09), residues: 3526 sheet: 0.14 (0.16), residues: 1098 loop : -0.77 (0.11), residues: 3335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 454 HIS 0.015 0.001 HIS A 406 PHE 0.014 0.001 PHE B 363 TYR 0.021 0.001 TYR I 244 ARG 0.014 0.000 ARG J 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22515.75 seconds wall clock time: 391 minutes 2.96 seconds (23462.96 seconds total)