Starting phenix.real_space_refine (version: dev) on Fri May 13 16:08:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/05_2022/7wub_32827_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/05_2022/7wub_32827.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/05_2022/7wub_32827_trim_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/05_2022/7wub_32827_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/05_2022/7wub_32827_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/05_2022/7wub_32827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/05_2022/7wub_32827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/05_2022/7wub_32827_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wub_32827/05_2022/7wub_32827_trim_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4597/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: {'PTRANS': 29, 'TRANS': 544, 'PCIS': 2} Chain: "B" Number of atoms: 4494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4494 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 29, 'TRANS': 544, 'PCIS': 2} Chain: "C" Number of atoms: 4490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4490 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 29, 'TRANS': 544, 'PCIS': 2} Chain: "D" Number of atoms: 4487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4487 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 28, 'TRANS': 544, 'PCIS': 2} 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: {'PTRANS': 29, 'TRANS': 544, 'PCIS': 2} Chain: "F" Number of atoms: 4494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4494 Classifications: {'peptide': 576} Link IDs: {'PTRANS': 29, 'TRANS': 544, 'PCIS': 2} Chain: "G" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'PTRANS': 39, 'CIS': 1, 'TRANS': 711, 'PCIS': 3} Chain: "H" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'PTRANS': 39, 'CIS': 1, 'TRANS': 711, 'PCIS': 3} Chain: "I" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'PTRANS': 39, 'CIS': 1, 'TRANS': 711, 'PCIS': 3} Chain: "J" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'PTRANS': 39, 'CIS': 1, 'TRANS': 711, 'PCIS': 3} Chain: "K" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'PTRANS': 39, 'CIS': 1, 'TRANS': 711, 'PCIS': 3} Chain: "L" Number of atoms: 5925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5925 Classifications: {'peptide': 755} Link IDs: {'PTRANS': 39, 'CIS': 1, 'TRANS': 711, 'PCIS': 3} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'Y6Y': 1, 'ADP': 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: {'Y6Y': 1, 'ADP': 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: {'Y6Y': 1, 'ADP': 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: {'Y6Y': 1, 'ADP': 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: {'Y6Y': 1, 'ADP': 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: {'Y6Y': 1, 'ADP': 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: {'Y6Y': 1, 'ADP': 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: {'Y6Y': 1, 'ADP': 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: {'Y6Y': 1, 'ADP': 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: {'Y6Y': 1, 'ADP': 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: {'Y6Y': 1, 'ADP': 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: {'Y6Y': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.43, per 1000 atoms: 0.40 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: 19.94 Conformation dependent library (CDL) restraints added in 6.8 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: 7.44 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: 23.62 Time building geometry restraints manager: 21.90 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=" C20 Y6Y C 802 " pdb=" C21 Y6Y C 802 " ideal model delta sigma weight residual 1.678 1.331 0.347 2.00e-02 2.50e+03 3.01e+02 bond pdb=" C20 Y6Y F 802 " pdb=" C21 Y6Y F 802 " ideal model delta sigma weight residual 1.678 1.331 0.347 2.00e-02 2.50e+03 3.01e+02 bond pdb=" C20 Y6Y E 802 " pdb=" C21 Y6Y E 802 " ideal model delta sigma weight residual 1.678 1.331 0.347 2.00e-02 2.50e+03 3.01e+02 bond pdb=" C20 Y6Y A 802 " pdb=" C21 Y6Y A 802 " ideal model delta sigma weight residual 1.678 1.331 0.347 2.00e-02 2.50e+03 3.00e+02 bond pdb=" C20 Y6Y B 802 " pdb=" C21 Y6Y B 802 " ideal model delta sigma weight residual 1.678 1.332 0.346 2.00e-02 2.50e+03 3.00e+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 - 30.40: 38401 30.40 - 60.80: 1126 60.80 - 91.20: 170 91.20 - 121.60: 12 121.60 - 152.01: 12 Dihedral angle restraints: 39721 sinusoidal: 16757 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 39718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 7006 0.043 - 0.086: 1740 0.086 - 0.129: 764 0.129 - 0.172: 97 0.172 - 0.215: 29 Chirality restraints: 9636 Sorted by residual: chirality pdb=" CA ARG J 741 " pdb=" N ARG J 741 " pdb=" C ARG J 741 " pdb=" CB ARG J 741 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ARG H 741 " pdb=" N ARG H 741 " pdb=" C ARG H 741 " pdb=" CB ARG H 741 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ARG L 741 " pdb=" N ARG L 741 " pdb=" C ARG L 741 " pdb=" CB ARG L 741 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+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 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. 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: 8.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 52.610 Check model and map are aligned: 0.690 Convert atoms to be neutral: 0.400 Process input model: 123.900 Find NCS groups from input model: 3.890 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 202.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.014 0.347 64379 Z= 0.897 Angle : 1.032 21.581 87011 Z= 0.494 Chirality : 0.047 0.215 9636 Planarity : 0.013 0.445 11498 Dihedral : 14.686 152.006 24831 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 45.69 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.42 % Favored : 94.21 % Rotamer Outliers : 1.96 % 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 *********************** 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 : 5.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 33 residues processed: 1228 average time/residue: 1.4061 time to fit residues: 2209.0367 Evaluate side-chains 707 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 674 time to evaluate : 5.448 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 25 residues processed: 10 average time/residue: 1.4212 time to fit residues: 25.7088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 320 optimal weight: 1.9990 chunk 620 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 377 optimal weight: 0.9990 chunk 462 optimal weight: 3.9990 chunk 719 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 64379 Z= 0.279 Angle : 0.773 17.910 87011 Z= 0.373 Chirality : 0.046 0.182 9636 Planarity : 0.006 0.072 11498 Dihedral : 9.215 150.501 8901 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.24 % Favored : 94.31 % Rotamer Outliers : 3.63 % 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: 0.54 (0.10), residues: 7959 helix: 1.56 (0.09), residues: 3482 sheet: -0.21 (0.17), residues: 978 loop : -0.66 (0.11), residues: 3499 *********************** 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 1029 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 784 time to evaluate : 5.981 Fit side-chains outliers start: 245 outliers final: 91 residues processed: 917 average time/residue: 1.2629 time to fit residues: 1525.0156 Evaluate side-chains 761 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 670 time to evaluate : 5.514 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 62 residues processed: 36 average time/residue: 0.7014 time to fit residues: 46.6926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 399 optimal weight: 8.9990 chunk 223 optimal weight: 3.9990 chunk 598 optimal weight: 4.9990 chunk 489 optimal weight: 4.9990 chunk 198 optimal weight: 0.0050 chunk 720 optimal weight: 10.0000 chunk 778 optimal weight: 0.8980 chunk 641 optimal weight: 5.9990 chunk 714 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 chunk 578 optimal weight: 3.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- 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 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 602 ASN H 24 ASN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 760 GLN ** I 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 ASN ** J 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 602 ASN 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 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 458 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.099 64379 Z= 0.395 Angle : 0.732 13.965 87011 Z= 0.356 Chirality : 0.047 0.170 9636 Planarity : 0.005 0.074 11498 Dihedral : 8.835 138.075 8901 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.19 % Favored : 93.43 % Rotamer Outliers : 3.78 % 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: 0.16 (0.09), residues: 7959 helix: 1.13 (0.09), residues: 3528 sheet: -0.18 (0.17), residues: 990 loop : -0.84 (0.11), residues: 3441 *********************** 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 940 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 685 time to evaluate : 5.461 Fit side-chains outliers start: 255 outliers final: 121 residues processed: 854 average time/residue: 1.2873 time to fit residues: 1455.0990 Evaluate side-chains 733 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 612 time to evaluate : 5.511 Switching outliers to nearest non-outliers outliers start: 121 outliers final: 89 residues processed: 32 average time/residue: 0.6149 time to fit residues: 40.4782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 711 optimal weight: 6.9990 chunk 541 optimal weight: 0.2980 chunk 373 optimal weight: 5.9990 chunk 79 optimal weight: 0.0770 chunk 343 optimal weight: 8.9990 chunk 483 optimal weight: 0.6980 chunk 723 optimal weight: 0.9990 chunk 765 optimal weight: 1.9990 chunk 377 optimal weight: 0.7980 chunk 685 optimal weight: 3.9990 chunk 206 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 458 GLN ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 458 GLN I 760 GLN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 458 GLN ** L 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 760 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.109 64379 Z= 0.192 Angle : 0.648 13.703 87011 Z= 0.312 Chirality : 0.043 0.166 9636 Planarity : 0.005 0.070 11498 Dihedral : 8.402 134.687 8901 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.52 % Favored : 94.11 % Rotamer Outliers : 3.53 % 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: 0.24 (0.09), residues: 7959 helix: 1.23 (0.09), residues: 3487 sheet: -0.02 (0.17), residues: 982 loop : -0.87 (0.10), residues: 3490 *********************** 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 916 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 678 time to evaluate : 5.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 238 outliers final: 112 residues processed: 847 average time/residue: 1.2626 time to fit residues: 1424.8009 Evaluate side-chains 720 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 608 time to evaluate : 5.482 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 97 residues processed: 15 average time/residue: 0.5515 time to fit residues: 22.7359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 637 optimal weight: 10.0000 chunk 434 optimal weight: 8.9990 chunk 11 optimal weight: 0.1980 chunk 570 optimal weight: 3.9990 chunk 315 optimal weight: 0.9990 chunk 653 optimal weight: 1.9990 chunk 529 optimal weight: 0.0170 chunk 0 optimal weight: 10.0000 chunk 390 optimal weight: 3.9990 chunk 687 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 overall best weight: 1.4424 ------------------------------------------------------------------------------- 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 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS F 401 ASN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 ASN ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 317 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 348 ASN ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 348 ASN ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 348 ASN L 406 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.118 64379 Z= 0.303 Angle : 0.668 13.974 87011 Z= 0.323 Chirality : 0.045 0.188 9636 Planarity : 0.005 0.072 11498 Dihedral : 8.141 124.144 8901 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.97 % Favored : 93.69 % Rotamer Outliers : 4.37 % 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: 0.13 (0.09), residues: 7959 helix: 1.08 (0.09), residues: 3541 sheet: -0.08 (0.17), residues: 1002 loop : -0.87 (0.11), residues: 3416 *********************** 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 948 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 653 time to evaluate : 5.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 295 outliers final: 152 residues processed: 869 average time/residue: 1.2493 time to fit residues: 1440.0748 Evaluate side-chains 760 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 608 time to evaluate : 5.453 Switching outliers to nearest non-outliers outliers start: 152 outliers final: 124 residues processed: 30 average time/residue: 0.5838 time to fit residues: 37.0802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 257 optimal weight: 0.0970 chunk 689 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 449 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 766 optimal weight: 0.3980 chunk 636 optimal weight: 8.9990 chunk 354 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 253 optimal weight: 5.9990 chunk 402 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS F 401 ASN ** 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 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.202 64379 Z= 0.281 Angle : 0.658 17.955 87011 Z= 0.318 Chirality : 0.045 0.308 9636 Planarity : 0.005 0.071 11498 Dihedral : 7.944 117.493 8901 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.62 % Favored : 94.08 % Rotamer Outliers : 4.00 % 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: 0.07 (0.09), residues: 7959 helix: 1.01 (0.09), residues: 3544 sheet: -0.06 (0.17), residues: 1002 loop : -0.91 (0.10), residues: 3413 *********************** 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 905 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 635 time to evaluate : 5.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 270 outliers final: 153 residues processed: 853 average time/residue: 1.2552 time to fit residues: 1424.9045 Evaluate side-chains 749 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 596 time to evaluate : 5.586 Switching outliers to nearest non-outliers outliers start: 153 outliers final: 133 residues processed: 20 average time/residue: 0.7055 time to fit residues: 29.8809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 738 optimal weight: 3.9990 chunk 86 optimal weight: 0.1980 chunk 436 optimal weight: 1.9990 chunk 559 optimal weight: 0.9980 chunk 433 optimal weight: 10.0000 chunk 645 optimal weight: 0.6980 chunk 427 optimal weight: 0.8980 chunk 763 optimal weight: 0.9980 chunk 477 optimal weight: 1.9990 chunk 465 optimal weight: 0.8980 chunk 352 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** A 538 ASN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN ** H 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 HIS I 24 ASN ** 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 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 406 HIS ** K 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.147 64379 Z= 0.208 Angle : 0.626 13.825 87011 Z= 0.301 Chirality : 0.044 0.256 9636 Planarity : 0.005 0.146 11498 Dihedral : 7.665 113.222 8901 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.94 % Favored : 93.77 % Rotamer Outliers : 3.46 % 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: 0.18 (0.09), residues: 7959 helix: 1.16 (0.09), residues: 3505 sheet: 0.03 (0.17), residues: 984 loop : -0.90 (0.10), residues: 3470 *********************** 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 884 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 651 time to evaluate : 5.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 233 outliers final: 144 residues processed: 830 average time/residue: 1.2814 time to fit residues: 1422.7040 Evaluate side-chains 747 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 603 time to evaluate : 5.600 Switching outliers to nearest non-outliers outliers start: 144 outliers final: 125 residues processed: 19 average time/residue: 0.5766 time to fit residues: 26.7426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 472 optimal weight: 0.8980 chunk 304 optimal weight: 0.4980 chunk 455 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 485 optimal weight: 0.9990 chunk 520 optimal weight: 1.9990 chunk 377 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 600 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 64379 Z= 0.224 Angle : 0.630 14.220 87011 Z= 0.302 Chirality : 0.044 0.226 9636 Planarity : 0.005 0.104 11498 Dihedral : 7.504 103.521 8901 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.84 % Favored : 93.93 % Rotamer Outliers : 3.11 % 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: 0.18 (0.09), residues: 7959 helix: 1.18 (0.09), residues: 3495 sheet: 0.02 (0.16), residues: 1098 loop : -0.93 (0.11), residues: 3366 *********************** 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 842 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 632 time to evaluate : 5.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 210 outliers final: 148 residues processed: 798 average time/residue: 1.2758 time to fit residues: 1357.7420 Evaluate side-chains 743 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 595 time to evaluate : 5.550 Switching outliers to nearest non-outliers outliers start: 148 outliers final: 134 residues processed: 14 average time/residue: 0.5252 time to fit residues: 20.9123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 694 optimal weight: 1.9990 chunk 731 optimal weight: 3.9990 chunk 667 optimal weight: 0.2980 chunk 711 optimal weight: 6.9990 chunk 428 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 chunk 558 optimal weight: 0.9980 chunk 218 optimal weight: 0.7980 chunk 642 optimal weight: 6.9990 chunk 672 optimal weight: 2.9990 chunk 708 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 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** D 538 ASN F 226 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN G 406 HIS H 24 ASN ** H 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 ASN I 348 ASN ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 ASN ** K 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 64379 Z= 0.269 Angle : 0.646 14.393 87011 Z= 0.309 Chirality : 0.045 0.228 9636 Planarity : 0.005 0.094 11498 Dihedral : 7.450 105.331 8901 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.12 % Favored : 93.68 % Rotamer Outliers : 3.11 % 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: 0.13 (0.09), residues: 7959 helix: 1.04 (0.09), residues: 3545 sheet: -0.06 (0.16), residues: 1104 loop : -0.86 (0.11), residues: 3310 *********************** 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 823 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 613 time to evaluate : 5.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 210 outliers final: 153 residues processed: 785 average time/residue: 1.2576 time to fit residues: 1324.7933 Evaluate side-chains 739 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 586 time to evaluate : 5.492 Switching outliers to nearest non-outliers outliers start: 153 outliers final: 139 residues processed: 14 average time/residue: 0.6007 time to fit residues: 22.1348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 467 optimal weight: 0.9990 chunk 752 optimal weight: 0.7980 chunk 459 optimal weight: 4.9990 chunk 356 optimal weight: 3.9990 chunk 522 optimal weight: 2.9990 chunk 789 optimal weight: 5.9990 chunk 726 optimal weight: 6.9990 chunk 628 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 485 optimal weight: 0.4980 chunk 385 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 HIS ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 64379 Z= 0.207 Angle : 0.632 14.491 87011 Z= 0.300 Chirality : 0.044 0.213 9636 Planarity : 0.005 0.103 11498 Dihedral : 7.212 114.915 8901 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.84 % Favored : 94.03 % Rotamer Outliers : 2.57 % 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: 0.21 (0.10), residues: 7959 helix: 1.08 (0.09), residues: 3553 sheet: 0.10 (0.16), residues: 1110 loop : -0.84 (0.11), residues: 3296 ********************** 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 795 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 622 time to evaluate : 5.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 173 outliers final: 151 residues processed: 775 average time/residue: 1.2890 time to fit residues: 1344.6068 Evaluate side-chains 742 residues out of total 6743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 591 time to evaluate : 5.486 Switching outliers to nearest non-outliers outliers start: 151 outliers final: 141 residues processed: 10 average time/residue: 0.6845 time to fit residues: 18.9674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 792 random chunks: chunk 499 optimal weight: 0.6980 chunk 669 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 579 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 174 optimal weight: 0.9990 chunk 629 optimal weight: 0.9980 chunk 263 optimal weight: 0.7980 chunk 646 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** A 538 ASN ** 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** F 226 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 ASN ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.172231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.128175 restraints weight = 73538.660| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.44 r_work: 0.3508 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work: 0.3474 rms_B_bonded: 2.25 restraints_weight: 0.1250 r_work: 0.3457 rms_B_bonded: 2.32 restraints_weight: 0.0625 r_work: 0.3439 rms_B_bonded: 2.43 restraints_weight: 0.0312 r_work: 0.3420 rms_B_bonded: 2.58 restraints_weight: 0.0156 r_work: 0.3400 rms_B_bonded: 2.75 restraints_weight: 0.0078 r_work: 0.3379 rms_B_bonded: 2.96 restraints_weight: 0.0039 r_work: 0.3356 rms_B_bonded: 3.21 restraints_weight: 0.0020 r_work: 0.3331 rms_B_bonded: 3.51 restraints_weight: 0.0010 r_work: 0.3304 rms_B_bonded: 3.85 restraints_weight: 0.0005 r_work: 0.3275 rms_B_bonded: 4.24 restraints_weight: 0.0002 r_work: 0.3242 rms_B_bonded: 4.69 restraints_weight: 0.0001 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 64379 Z= 0.225 Angle : 0.636 14.371 87011 Z= 0.302 Chirality : 0.044 0.218 9636 Planarity : 0.005 0.097 11498 Dihedral : 7.137 116.410 8901 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.14 % Favored : 93.73 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.22 (0.10), residues: 7959 helix: 1.09 (0.09), residues: 3552 sheet: 0.06 (0.16), residues: 1116 loop : -0.80 (0.11), residues: 3291 =============================================================================== Job complete usr+sys time: 20379.83 seconds wall clock time: 354 minutes 18.17 seconds (21258.17 seconds total)