Starting phenix.real_space_refine on Fri Feb 23 14:55:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnn_32043/02_2024/7vnn_32043.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnn_32043/02_2024/7vnn_32043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnn_32043/02_2024/7vnn_32043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnn_32043/02_2024/7vnn_32043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnn_32043/02_2024/7vnn_32043.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnn_32043/02_2024/7vnn_32043.pdb" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 21 9.91 5 S 75 5.16 5 C 24325 2.51 5 N 6320 2.21 5 O 8082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 218": "OD1" <-> "OD2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 577": "OE1" <-> "OE2" Residue "A ASP 590": "OD1" <-> "OD2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 453": "OD1" <-> "OD2" Residue "B GLU 499": "OE1" <-> "OE2" Residue "B ASP 572": "OD1" <-> "OD2" Residue "B ASP 582": "OD1" <-> "OD2" Residue "B TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 662": "OE1" <-> "OE2" Residue "B ASP 696": "OD1" <-> "OD2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 799": "OD1" <-> "OD2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 282": "OD1" <-> "OD2" Residue "C ASP 362": "OD1" <-> "OD2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "C ASP 511": "OD1" <-> "OD2" Residue "C GLU 524": "OE1" <-> "OE2" Residue "C TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 771": "OD1" <-> "OD2" Residue "C TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 866": "OD1" <-> "OD2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "D TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 763": "OD1" <-> "OD2" Residue "D ASP 771": "OD1" <-> "OD2" Residue "D TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 251": "OE1" <-> "OE2" Residue "E PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 417": "OD1" <-> "OD2" Residue "E ASP 471": "OD1" <-> "OD2" Residue "E ASP 597": "OD1" <-> "OD2" Residue "E TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 712": "OE1" <-> "OE2" Residue "E GLU 715": "OE1" <-> "OE2" Residue "E PHE 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 817": "OD1" <-> "OD2" Residue "F PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 318": "OD1" <-> "OD2" Residue "G TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 221": "OD1" <-> "OD2" Residue "H GLU 380": "OE1" <-> "OE2" Residue "H TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38823 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 bond proxies already assigned to first conformer: 5058 Chain: "B" Number of atoms: 5103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 bond proxies already assigned to first conformer: 5058 Chain: "C" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 Chain: "D" Number of atoms: 5134 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 641, 5066 Classifications: {'peptide': 641} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 613} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 641, 5066 Classifications: {'peptide': 641} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 613} Chain breaks: 1 bond proxies already assigned to first conformer: 5091 Chain: "E" Number of atoms: 5103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 bond proxies already assigned to first conformer: 5058 Chain: "F" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 Chain: "G" Number of atoms: 5103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 bond proxies already assigned to first conformer: 5058 Chain: "H" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3186 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 71 residue: pdb=" N AGLY A 488 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 488 " occ=0.50 residue: pdb=" N ATHR A 489 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 489 " occ=0.50 residue: pdb=" N ALYS A 490 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 490 " occ=0.50 residue: pdb=" N AASN A 491 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 491 " occ=0.50 residue: pdb=" N ASER A 492 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 492 " occ=0.50 residue: pdb=" N ASER A 493 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 493 " occ=0.50 residue: pdb=" N AGLY A 494 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 494 " occ=0.50 residue: pdb=" N AGLN A 495 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 495 " occ=0.50 residue: pdb=" N AILE A 496 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 496 " occ=0.50 residue: pdb=" N AVAL A 497 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 497 " occ=0.50 residue: pdb=" N THR A 498 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 THR A 498 " occ=0.50 residue: pdb=" N AGLY B 488 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 488 " occ=0.50 ... (remaining 59 not shown) Time building chain proxies: 30.85, per 1000 atoms: 0.79 Number of scatterers: 38823 At special positions: 0 Unit cell: (180.4, 176.88, 201.52, 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) Ca 21 19.99 S 75 16.00 O 8082 8.00 N 6320 7.00 C 24325 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: 16.37 Conformation dependent library (CDL) restraints added in 12.5 seconds 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9232 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 100 sheets defined 18.7% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.16 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.598A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.686A pdb=" N ILE A 429 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 503 through 513 removed outlier: 4.567A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 513 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 581 through 595 removed outlier: 3.784A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 757 through 765 removed outlier: 3.612A pdb=" N HIS A 765 " --> pdb=" O ILE A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 800 Processing helix chain 'A' and resid 829 through 831 No H-bonds generated for 'chain 'A' and resid 829 through 831' Processing helix chain 'A' and resid 843 through 845 No H-bonds generated for 'chain 'A' and resid 843 through 845' Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 248 through 253 removed outlier: 4.306A pdb=" N GLN B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY B 253 " --> pdb=" O PHE B 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 253' Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 291 removed outlier: 4.059A pdb=" N ASP B 291 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.726A pdb=" N ILE B 429 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 Processing helix chain 'B' and resid 503 through 513 removed outlier: 4.750A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 581 through 594 removed outlier: 3.691A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'B' and resid 757 through 765 removed outlier: 3.691A pdb=" N HIS B 765 " --> pdb=" O ILE B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'B' and resid 843 through 845 No H-bonds generated for 'chain 'B' and resid 843 through 845' Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 246 through 253 removed outlier: 3.786A pdb=" N GLU C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 253 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.816A pdb=" N ASP C 291 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.726A pdb=" N ILE C 429 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 503 through 513 removed outlier: 4.611A pdb=" N SER C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLN C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 581 through 593 Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 757 through 765 Processing helix chain 'C' and resid 794 through 800 Processing helix chain 'C' and resid 829 through 831 No H-bonds generated for 'chain 'C' and resid 829 through 831' Processing helix chain 'C' and resid 843 through 845 No H-bonds generated for 'chain 'C' and resid 843 through 845' Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 246 through 253 removed outlier: 3.628A pdb=" N GLU D 251 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.751A pdb=" N ASP D 291 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.745A pdb=" N ILE D 429 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 503 through 513 removed outlier: 4.552A pdb=" N SER D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLN D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE D 513 " --> pdb=" O GLN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 556 Processing helix chain 'D' and resid 581 through 595 removed outlier: 3.825A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'D' and resid 757 through 765 removed outlier: 3.590A pdb=" N HIS D 765 " --> pdb=" O ILE D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 800 Processing helix chain 'D' and resid 829 through 831 No H-bonds generated for 'chain 'D' and resid 829 through 831' Processing helix chain 'D' and resid 843 through 845 No H-bonds generated for 'chain 'D' and resid 843 through 845' Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 253 removed outlier: 3.506A pdb=" N ALA E 250 " --> pdb=" O ASP E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 291 removed outlier: 4.004A pdb=" N ASP E 291 " --> pdb=" O GLU E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.719A pdb=" N ILE E 429 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 503 through 513 removed outlier: 4.540A pdb=" N SER E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLN E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE E 513 " --> pdb=" O GLN E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 581 through 593 removed outlier: 3.834A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'E' and resid 757 through 765 removed outlier: 3.712A pdb=" N HIS E 765 " --> pdb=" O ILE E 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 794 through 800 Processing helix chain 'E' and resid 829 through 831 No H-bonds generated for 'chain 'E' and resid 829 through 831' Processing helix chain 'E' and resid 843 through 845 No H-bonds generated for 'chain 'E' and resid 843 through 845' Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 246 through 253 Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 291 removed outlier: 4.188A pdb=" N ASP F 291 " --> pdb=" O GLU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.820A pdb=" N ILE F 429 " --> pdb=" O GLU F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 503 through 513 removed outlier: 4.592A pdb=" N SER F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN F 509 " --> pdb=" O ASP F 505 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE F 513 " --> pdb=" O GLN F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 581 through 594 removed outlier: 3.849A pdb=" N LYS F 593 " --> pdb=" O LYS F 589 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR F 594 " --> pdb=" O ASP F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 Processing helix chain 'F' and resid 757 through 765 removed outlier: 3.795A pdb=" N HIS F 765 " --> pdb=" O ILE F 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 794 through 801 Processing helix chain 'F' and resid 829 through 831 No H-bonds generated for 'chain 'F' and resid 829 through 831' Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 246 through 250 Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 291 removed outlier: 4.107A pdb=" N ASP G 291 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.648A pdb=" N ILE G 429 " --> pdb=" O GLU G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 471 Processing helix chain 'G' and resid 503 through 513 removed outlier: 4.665A pdb=" N SER G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLN G 509 " --> pdb=" O ASP G 505 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE G 513 " --> pdb=" O GLN G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 556 Processing helix chain 'G' and resid 581 through 595 removed outlier: 3.891A pdb=" N LYS G 593 " --> pdb=" O LYS G 589 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR G 594 " --> pdb=" O ASP G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 Processing helix chain 'G' and resid 757 through 765 removed outlier: 3.573A pdb=" N HIS G 765 " --> pdb=" O ILE G 761 " (cutoff:3.500A) Processing helix chain 'G' and resid 794 through 801 removed outlier: 3.723A pdb=" N ILE G 801 " --> pdb=" O ALA G 797 " (cutoff:3.500A) Processing helix chain 'G' and resid 829 through 831 No H-bonds generated for 'chain 'G' and resid 829 through 831' Processing helix chain 'G' and resid 841 through 845 Processing helix chain 'H' and resid 21 through 30 removed outlier: 3.844A pdb=" N GLN H 29 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS H 30 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 45 removed outlier: 3.692A pdb=" N LYS H 44 " --> pdb=" O GLU H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 removed outlier: 3.913A pdb=" N THR H 55 " --> pdb=" O LYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 67 removed outlier: 3.535A pdb=" N ASN H 67 " --> pdb=" O GLN H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 83 removed outlier: 4.225A pdb=" N ASN H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 101 removed outlier: 3.961A pdb=" N ALA H 101 " --> pdb=" O GLU H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 126 removed outlier: 3.723A pdb=" N ILE H 126 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 229 Processing helix chain 'H' and resid 231 through 235 removed outlier: 3.521A pdb=" N LYS H 234 " --> pdb=" O TRP H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 250 Processing helix chain 'H' and resid 250 through 260 removed outlier: 3.975A pdb=" N ASN H 255 " --> pdb=" O TYR H 251 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN H 256 " --> pdb=" O THR H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 266 Processing helix chain 'H' and resid 268 through 285 removed outlier: 4.246A pdb=" N LYS H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU H 285 " --> pdb=" O ALA H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 312 Processing helix chain 'H' and resid 315 through 327 removed outlier: 3.857A pdb=" N ILE H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 311 removed outlier: 6.886A pdb=" N ASN A 392 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 439 removed outlier: 3.907A pdb=" N ALA A 387 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 360 through 382 removed outlier: 3.689A pdb=" N SER F 370 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN G 371 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN F 329 " --> pdb=" O VAL G 367 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL G 367 " --> pdb=" O ASN F 329 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 361 through 382 current: chain 'E' and resid 313 through 335 removed outlier: 3.564A pdb=" N THR E 332 " --> pdb=" O ASP E 362 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 367 " --> pdb=" O ASN D 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP D 362 " --> pdb=" O THR D 332 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR D 361 " --> pdb=" O ASN C 335 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER C 364 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP C 375 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 361 " --> pdb=" O ASN G 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.765A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR A 404 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN A 432 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.765A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 531 removed outlier: 9.288A pdb=" N ILE A 611 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AB1, first strand: chain 'A' and resid 618 through 620 removed outlier: 3.518A pdb=" N TYR A 618 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU A 733 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS A 676 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN A 735 " --> pdb=" O TYR A 674 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR A 674 " --> pdb=" O ASN A 735 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 618 through 620 removed outlier: 3.518A pdb=" N TYR A 618 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU A 733 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS A 676 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN A 735 " --> pdb=" O TYR A 674 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR A 674 " --> pdb=" O ASN A 735 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 655 through 658 removed outlier: 3.882A pdb=" N ILE A 656 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 723 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 768 through 773 removed outlier: 6.279A pdb=" N PHE A 769 " --> pdb=" O MET A 786 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N MET A 786 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASP A 771 " --> pdb=" O ASN A 784 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 815 through 821 removed outlier: 6.140A pdb=" N VAL A 806 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR A 820 " --> pdb=" O TYR A 804 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR A 804 " --> pdb=" O THR A 820 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS A 803 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 863 " --> pdb=" O LYS A 803 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A 858 " --> pdb=" O SER A 874 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER A 874 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 860 " --> pdb=" O VAL A 872 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 826 through 827 Processing sheet with id=AB7, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB8, first strand: chain 'B' and resid 300 through 311 removed outlier: 6.879A pdb=" N ASN B 392 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 438 through 439 removed outlier: 3.806A pdb=" N ALA B 387 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.914A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR B 404 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN B 432 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.914A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LYS B 405 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 485 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AC4, first strand: chain 'B' and resid 526 through 531 removed outlier: 9.427A pdb=" N ILE B 611 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AC6, first strand: chain 'B' and resid 618 through 620 removed outlier: 5.319A pdb=" N LEU B 733 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS B 676 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN B 735 " --> pdb=" O TYR B 674 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR B 674 " --> pdb=" O ASN B 735 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 705 " --> pdb=" O SER B 675 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 618 through 620 removed outlier: 5.319A pdb=" N LEU B 733 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS B 676 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN B 735 " --> pdb=" O TYR B 674 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR B 674 " --> pdb=" O ASN B 735 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B 713 " --> pdb=" O LYS B 667 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 655 through 658 removed outlier: 3.673A pdb=" N ILE B 656 " --> pdb=" O ILE B 723 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 723 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 768 through 773 removed outlier: 6.452A pdb=" N PHE B 769 " --> pdb=" O MET B 786 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET B 786 " --> pdb=" O PHE B 769 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP B 771 " --> pdb=" O ASN B 784 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 815 through 821 removed outlier: 6.097A pdb=" N VAL B 806 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 820 " --> pdb=" O TYR B 804 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR B 804 " --> pdb=" O THR B 820 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS B 803 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 863 " --> pdb=" O LYS B 803 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B 858 " --> pdb=" O SER B 874 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER B 874 " --> pdb=" O LEU B 858 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE B 860 " --> pdb=" O VAL B 872 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 826 through 827 Processing sheet with id=AD3, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AD4, first strand: chain 'C' and resid 300 through 302 Processing sheet with id=AD5, first strand: chain 'C' and resid 306 through 311 removed outlier: 3.642A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 306 through 311 removed outlier: 3.642A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA C 387 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE C 460 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.845A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR C 404 " --> pdb=" O ASN C 432 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN C 432 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.845A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS C 405 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY C 485 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR C 407 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL C 483 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 525 through 531 Processing sheet with id=AE1, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AE2, first strand: chain 'C' and resid 618 through 620 removed outlier: 4.459A pdb=" N LEU C 736 " --> pdb=" O SER C 672 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER C 672 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE C 738 " --> pdb=" O VAL C 670 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 670 " --> pdb=" O ILE C 738 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU C 740 " --> pdb=" O ARG C 668 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ARG C 668 " --> pdb=" O GLU C 740 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 705 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 618 through 620 removed outlier: 4.459A pdb=" N LEU C 736 " --> pdb=" O SER C 672 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER C 672 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE C 738 " --> pdb=" O VAL C 670 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 670 " --> pdb=" O ILE C 738 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU C 740 " --> pdb=" O ARG C 668 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ARG C 668 " --> pdb=" O GLU C 740 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 655 through 658 removed outlier: 3.526A pdb=" N ILE C 656 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 723 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 770 through 773 removed outlier: 6.597A pdb=" N ASP C 771 " --> pdb=" O ASN C 784 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 815 through 821 removed outlier: 6.353A pdb=" N VAL C 806 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR C 820 " --> pdb=" O TYR C 804 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR C 804 " --> pdb=" O THR C 820 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS C 803 " --> pdb=" O ILE C 863 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 863 " --> pdb=" O LYS C 803 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU C 858 " --> pdb=" O SER C 874 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER C 874 " --> pdb=" O LEU C 858 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE C 860 " --> pdb=" O VAL C 872 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 826 through 827 Processing sheet with id=AE8, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AE9, first strand: chain 'D' and resid 300 through 311 removed outlier: 5.849A pdb=" N VAL D 302 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR D 396 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET D 304 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG D 394 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS D 306 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 438 through 439 removed outlier: 4.110A pdb=" N ALA D 387 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE D 460 " --> pdb=" O ILE D 389 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.788A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR D 404 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN D 432 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.788A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS D 405 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN D 486 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN D 482 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN D 411 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THR D 480 " --> pdb=" O ASN D 411 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL D 413 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU D 478 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AF5, first strand: chain 'D' and resid 525 through 531 Processing sheet with id=AF6, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AF7, first strand: chain 'D' and resid 618 through 620 removed outlier: 4.276A pdb=" N LEU D 736 " --> pdb=" O SER D 672 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER D 672 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE D 738 " --> pdb=" O VAL D 670 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL D 670 " --> pdb=" O ILE D 738 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU D 740 " --> pdb=" O ARG D 668 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ARG D 668 " --> pdb=" O GLU D 740 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 655 through 658 removed outlier: 4.908A pdb=" N GLU D 722 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS D 689 " --> pdb=" O GLU D 722 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 698 " --> pdb=" O ILE D 684 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP D 696 " --> pdb=" O VAL D 686 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 768 through 773 removed outlier: 6.208A pdb=" N PHE D 769 " --> pdb=" O MET D 786 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N MET D 786 " --> pdb=" O PHE D 769 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP D 771 " --> pdb=" O ASN D 784 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 815 through 821 removed outlier: 6.054A pdb=" N VAL D 806 " --> pdb=" O ILE D 818 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR D 820 " --> pdb=" O TYR D 804 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR D 804 " --> pdb=" O THR D 820 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LYS D 803 " --> pdb=" O ILE D 863 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 863 " --> pdb=" O LYS D 803 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU D 858 " --> pdb=" O SER D 874 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER D 874 " --> pdb=" O LEU D 858 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE D 860 " --> pdb=" O VAL D 872 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 826 through 827 Processing sheet with id=AG3, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AG4, first strand: chain 'E' and resid 300 through 311 removed outlier: 5.598A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS E 306 " --> pdb=" O ASN E 392 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 438 through 439 removed outlier: 4.004A pdb=" N ALA E 387 " --> pdb=" O ILE E 462 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 418 through 423 removed outlier: 7.009A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR E 404 " --> pdb=" O ASN E 432 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN E 432 " --> pdb=" O TYR E 404 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 418 through 423 removed outlier: 7.009A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LYS E 405 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN E 486 " --> pdb=" O LYS E 405 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN E 482 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN E 411 " --> pdb=" O THR E 480 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N THR E 480 " --> pdb=" O ASN E 411 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL E 413 " --> pdb=" O LEU E 478 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU E 478 " --> pdb=" O VAL E 413 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AG9, first strand: chain 'E' and resid 524 through 531 removed outlier: 3.795A pdb=" N GLU E 524 " --> pdb=" O THR E 521 " (cutoff:3.500A) removed outlier: 9.472A pdb=" N ILE E 611 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AH2, first strand: chain 'E' and resid 618 through 620 removed outlier: 3.648A pdb=" N TYR E 618 " --> pdb=" O ILE E 738 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU E 736 " --> pdb=" O SER E 672 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER E 672 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE E 738 " --> pdb=" O VAL E 670 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 670 " --> pdb=" O ILE E 738 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU E 740 " --> pdb=" O ARG E 668 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG E 668 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 618 through 620 removed outlier: 3.648A pdb=" N TYR E 618 " --> pdb=" O ILE E 738 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU E 736 " --> pdb=" O SER E 672 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER E 672 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE E 738 " --> pdb=" O VAL E 670 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 670 " --> pdb=" O ILE E 738 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU E 740 " --> pdb=" O ARG E 668 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG E 668 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 655 through 658 removed outlier: 3.739A pdb=" N GLU E 722 " --> pdb=" O LYS E 689 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 698 " --> pdb=" O ILE E 684 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE E 688 " --> pdb=" O LYS E 694 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS E 694 " --> pdb=" O ILE E 688 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 768 through 773 removed outlier: 6.478A pdb=" N PHE E 769 " --> pdb=" O MET E 786 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N MET E 786 " --> pdb=" O PHE E 769 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP E 771 " --> pdb=" O ASN E 784 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 815 through 821 removed outlier: 6.007A pdb=" N VAL E 806 " --> pdb=" O ILE E 818 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR E 820 " --> pdb=" O TYR E 804 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TYR E 804 " --> pdb=" O THR E 820 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS E 803 " --> pdb=" O ILE E 863 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 863 " --> pdb=" O LYS E 803 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU E 858 " --> pdb=" O SER E 874 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER E 874 " --> pdb=" O LEU E 858 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE E 860 " --> pdb=" O VAL E 872 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 826 through 827 Processing sheet with id=AH8, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AH9, first strand: chain 'F' and resid 300 through 311 removed outlier: 6.876A pdb=" N ASN F 392 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 438 through 439 removed outlier: 3.916A pdb=" N ALA F 387 " --> pdb=" O ILE F 462 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.776A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS F 405 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY F 485 " --> pdb=" O LYS F 405 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR F 407 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL F 483 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 489 through 490 removed outlier: 3.555A pdb=" N VAL F 497 " --> pdb=" O THR F 489 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 524 through 531 removed outlier: 3.787A pdb=" N GLU F 524 " --> pdb=" O THR F 521 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU F 577 " --> pdb=" O LYS F 614 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AI6, first strand: chain 'F' and resid 618 through 620 removed outlier: 5.722A pdb=" N LEU F 733 " --> pdb=" O LYS F 676 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LYS F 676 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN F 735 " --> pdb=" O TYR F 674 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR F 674 " --> pdb=" O ASN F 735 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER F 675 " --> pdb=" O THR F 705 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR F 705 " --> pdb=" O SER F 675 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 618 through 620 removed outlier: 5.722A pdb=" N LEU F 733 " --> pdb=" O LYS F 676 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LYS F 676 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN F 735 " --> pdb=" O TYR F 674 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR F 674 " --> pdb=" O ASN F 735 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE F 711 " --> pdb=" O TYR F 669 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 655 through 658 removed outlier: 3.607A pdb=" N GLU F 722 " --> pdb=" O LYS F 689 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS F 694 " --> pdb=" O ILE F 688 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 768 through 773 removed outlier: 6.376A pdb=" N PHE F 769 " --> pdb=" O MET F 786 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET F 786 " --> pdb=" O PHE F 769 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP F 771 " --> pdb=" O ASN F 784 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 815 through 821 removed outlier: 6.405A pdb=" N VAL F 806 " --> pdb=" O ILE F 818 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR F 820 " --> pdb=" O TYR F 804 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR F 804 " --> pdb=" O THR F 820 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS F 803 " --> pdb=" O ILE F 863 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE F 863 " --> pdb=" O LYS F 803 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU F 858 " --> pdb=" O SER F 874 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER F 874 " --> pdb=" O LEU F 858 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE F 860 " --> pdb=" O VAL F 872 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 826 through 827 Processing sheet with id=AJ3, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AJ4, first strand: chain 'G' and resid 300 through 311 removed outlier: 6.825A pdb=" N ASN G 392 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'G' and resid 438 through 439 removed outlier: 3.704A pdb=" N ALA G 387 " --> pdb=" O ILE G 462 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.739A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS G 405 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASN G 486 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN G 482 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN G 411 " --> pdb=" O THR G 480 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N THR G 480 " --> pdb=" O ASN G 411 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL G 413 " --> pdb=" O LEU G 478 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU G 478 " --> pdb=" O VAL G 413 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AJ8, first strand: chain 'G' and resid 525 through 531 Processing sheet with id=AJ9, first strand: chain 'G' and resid 558 through 559 Processing sheet with id=AK1, first strand: chain 'G' and resid 618 through 620 removed outlier: 5.737A pdb=" N LEU G 733 " --> pdb=" O LYS G 676 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS G 676 " --> pdb=" O LEU G 733 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASN G 735 " --> pdb=" O TYR G 674 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR G 674 " --> pdb=" O ASN G 735 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR G 705 " --> pdb=" O SER G 675 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'G' and resid 618 through 620 removed outlier: 5.737A pdb=" N LEU G 733 " --> pdb=" O LYS G 676 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS G 676 " --> pdb=" O LEU G 733 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASN G 735 " --> pdb=" O TYR G 674 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR G 674 " --> pdb=" O ASN G 735 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'G' and resid 655 through 658 removed outlier: 3.847A pdb=" N GLU G 722 " --> pdb=" O LYS G 689 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS G 689 " --> pdb=" O GLU G 722 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS G 687 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP G 696 " --> pdb=" O VAL G 686 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'G' and resid 768 through 773 removed outlier: 3.563A pdb=" N PHE G 769 " --> pdb=" O TYR G 787 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN G 773 " --> pdb=" O ILE G 783 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE G 783 " --> pdb=" O ASN G 773 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'G' and resid 815 through 821 removed outlier: 6.061A pdb=" N VAL G 806 " --> pdb=" O ILE G 818 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N THR G 820 " --> pdb=" O TYR G 804 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR G 804 " --> pdb=" O THR G 820 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS G 803 " --> pdb=" O ILE G 863 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE G 863 " --> pdb=" O LYS G 803 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA G 862 " --> pdb=" O LEU G 871 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU G 871 " --> pdb=" O ALA G 862 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'G' and resid 826 through 827 Processing sheet with id=AK7, first strand: chain 'H' and resid 89 through 94 removed outlier: 3.630A pdb=" N TYR H 93 " --> pdb=" O MET H 156 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET H 156 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL H 207 " --> pdb=" O LYS H 159 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS H 189 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER H 206 " --> pdb=" O ILE H 187 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE H 187 " --> pdb=" O SER H 206 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL H 208 " --> pdb=" O ILE H 185 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE H 185 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR H 183 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'H' and resid 136 through 139 removed outlier: 3.857A pdb=" N LEU H 178 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU H 167 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'H' and resid 291 through 297 removed outlier: 4.147A pdb=" N ILE H 354 " --> pdb=" O SER H 297 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR H 397 " --> pdb=" O LYS H 404 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS H 393 " --> pdb=" O ASP H 408 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR H 410 " --> pdb=" O ILE H 391 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE H 391 " --> pdb=" O THR H 410 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER H 387 " --> pdb=" O TYR H 333 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'H' and resid 337 through 340 removed outlier: 3.804A pdb=" N ILE H 337 " --> pdb=" O LEU H 383 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU H 382 " --> pdb=" O ALA H 367 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA H 367 " --> pdb=" O LEU H 382 " (cutoff:3.500A) 1382 hydrogen bonds defined for protein. 3615 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: 19.13 Time building geometry restraints manager: 17.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12742 1.34 - 1.46: 7837 1.46 - 1.58: 18798 1.58 - 1.70: 0 1.70 - 1.81: 143 Bond restraints: 39520 Sorted by residual: bond pdb=" N ASP B 282 " pdb=" CA ASP B 282 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.28e-02 6.10e+03 6.86e+00 bond pdb=" N PHE A 281 " pdb=" CA PHE A 281 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.17e-02 7.31e+03 6.74e+00 bond pdb=" N PHE F 281 " pdb=" CA PHE F 281 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.17e-02 7.31e+03 6.56e+00 bond pdb=" N PHE E 281 " pdb=" CA PHE E 281 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.17e-02 7.31e+03 6.40e+00 bond pdb=" N PHE C 281 " pdb=" CA PHE C 281 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.41e-02 5.03e+03 6.40e+00 ... (remaining 39515 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.57: 895 106.57 - 113.44: 21594 113.44 - 120.31: 13824 120.31 - 127.18: 17019 127.18 - 134.05: 260 Bond angle restraints: 53592 Sorted by residual: angle pdb=" CA PHE A 281 " pdb=" CB PHE A 281 " pdb=" CG PHE A 281 " ideal model delta sigma weight residual 113.80 119.34 -5.54 1.00e+00 1.00e+00 3.07e+01 angle pdb=" CA PHE B 281 " pdb=" CB PHE B 281 " pdb=" CG PHE B 281 " ideal model delta sigma weight residual 113.80 119.24 -5.44 1.00e+00 1.00e+00 2.95e+01 angle pdb=" CA PHE D 281 " pdb=" CB PHE D 281 " pdb=" CG PHE D 281 " ideal model delta sigma weight residual 113.80 119.21 -5.41 1.00e+00 1.00e+00 2.93e+01 angle pdb=" CA PHE E 281 " pdb=" CB PHE E 281 " pdb=" CG PHE E 281 " ideal model delta sigma weight residual 113.80 119.19 -5.39 1.00e+00 1.00e+00 2.90e+01 angle pdb=" CA PHE G 281 " pdb=" CB PHE G 281 " pdb=" CG PHE G 281 " ideal model delta sigma weight residual 113.80 118.69 -4.89 1.00e+00 1.00e+00 2.39e+01 ... (remaining 53587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 21959 17.83 - 35.66: 1700 35.66 - 53.49: 291 53.49 - 71.32: 91 71.32 - 89.15: 39 Dihedral angle restraints: 24080 sinusoidal: 9648 harmonic: 14432 Sorted by residual: dihedral pdb=" CA TYR C 709 " pdb=" C TYR C 709 " pdb=" N GLU C 710 " pdb=" CA GLU C 710 " ideal model delta harmonic sigma weight residual 180.00 -156.44 -23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA THR E 714 " pdb=" C THR E 714 " pdb=" N GLU E 715 " pdb=" CA GLU E 715 " ideal model delta harmonic sigma weight residual -180.00 -158.36 -21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ASN G 775 " pdb=" C ASN G 775 " pdb=" N PRO G 776 " pdb=" CA PRO G 776 " ideal model delta harmonic sigma weight residual -180.00 -158.37 -21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 24077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 4061 0.035 - 0.071: 1239 0.071 - 0.106: 470 0.106 - 0.141: 226 0.141 - 0.177: 7 Chirality restraints: 6003 Sorted by residual: chirality pdb=" CA PHE B 281 " pdb=" N PHE B 281 " pdb=" C PHE B 281 " pdb=" CB PHE B 281 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CA PHE D 281 " pdb=" N PHE D 281 " pdb=" C PHE D 281 " pdb=" CB PHE D 281 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA PHE G 281 " pdb=" N PHE G 281 " pdb=" C PHE G 281 " pdb=" CB PHE G 281 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 6000 not shown) Planarity restraints: 6990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 664 " -0.050 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO G 665 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO G 665 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 665 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 864 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO F 865 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO F 865 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 865 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 117 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C GLU H 117 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU H 117 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS H 118 " -0.009 2.00e-02 2.50e+03 ... (remaining 6987 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1613 2.72 - 3.26: 37092 3.26 - 3.81: 59979 3.81 - 4.35: 79635 4.35 - 4.90: 133864 Nonbonded interactions: 312183 Sorted by model distance: nonbonded pdb=" OG1 THR G 864 " pdb=" OD1 ASP G 866 " model vdw 2.169 2.440 nonbonded pdb=" O PHE E 788 " pdb=" OG1 THR E 837 " model vdw 2.172 2.440 nonbonded pdb=" O ASN E 775 " pdb=" ND2 ASN E 780 " model vdw 2.184 2.520 nonbonded pdb=" OD2 ASP H 212 " pdb=" OG1 THR H 292 " model vdw 2.191 2.440 nonbonded pdb=" NH2 ARG E 394 " pdb=" O LEU E 444 " model vdw 2.212 2.520 ... (remaining 312178 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 217 through 487 or resid 498 through 876 or resid 901 thro \ ugh 903)) selection = (chain 'B' and (resid 217 through 487 or resid 498 through 876 or resid 901 thro \ ugh 903)) selection = (chain 'C' and (resid 217 through 487 or resid 498 through 876 or resid 901 thro \ ugh 903)) selection = (chain 'D' and (resid 217 through 487 or resid 498 through 876 or resid 901 thro \ ugh 903)) selection = (chain 'E' and (resid 217 through 487 or resid 498 through 876 or resid 901 thro \ ugh 903)) selection = (chain 'F' and (resid 217 through 487 or resid 498 through 876 or resid 901 thro \ ugh 903)) selection = (chain 'G' and (resid 217 through 487 or resid 498 through 876 or resid 901 thro \ ugh 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.120 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: 0.030 Extract box with map and model: 18.240 Check model and map are aligned: 0.540 Set scattering table: 0.350 Process input model: 122.480 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.003 0.053 39520 Z= 0.173 Angle : 0.537 9.691 53592 Z= 0.305 Chirality : 0.044 0.177 6003 Planarity : 0.004 0.076 6990 Dihedral : 13.907 89.147 14848 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.37 % Allowed : 0.55 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.12), residues: 4893 helix: -0.03 (0.19), residues: 745 sheet: 0.21 (0.14), residues: 1466 loop : -1.27 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 375 HIS 0.003 0.001 HIS H 157 PHE 0.015 0.001 PHE H 322 TYR 0.016 0.001 TYR A 230 ARG 0.002 0.000 ARG F 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 365 time to evaluate : 4.228 Fit side-chains REVERT: B 627 ASN cc_start: 0.7700 (t0) cc_final: 0.7495 (t160) REVERT: B 786 MET cc_start: 0.8670 (tpp) cc_final: 0.8438 (tpp) REVERT: C 660 MET cc_start: 0.5143 (tpt) cc_final: 0.4758 (tpt) REVERT: C 853 MET cc_start: 0.7768 (mmm) cc_final: 0.7476 (mmm) REVERT: D 773 ASN cc_start: 0.7380 (t160) cc_final: 0.6899 (p0) REVERT: E 698 LEU cc_start: 0.5846 (pt) cc_final: 0.5609 (pt) REVERT: F 376 ASN cc_start: 0.7884 (m110) cc_final: 0.7659 (t0) REVERT: H 49 ILE cc_start: 0.4760 (mt) cc_final: 0.4537 (mt) REVERT: H 120 ASN cc_start: 0.4950 (m-40) cc_final: 0.4537 (m-40) REVERT: H 149 GLU cc_start: 0.4089 (pp20) cc_final: 0.3084 (tp30) REVERT: H 284 ARG cc_start: 0.2217 (ttm-80) cc_final: 0.1260 (tmt-80) outliers start: 12 outliers final: 7 residues processed: 376 average time/residue: 1.4194 time to fit residues: 653.4495 Evaluate side-chains 237 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 230 time to evaluate : 4.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 406 optimal weight: 3.9990 chunk 364 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 377 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 280 optimal weight: 4.9990 chunk 436 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 HIS A 567 ASN B 811 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN ** C 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 ASN ** C 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 773 ASN D 780 ASN ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN F 376 ASN F 811 GLN G 376 ASN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 120 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 39520 Z= 0.468 Angle : 0.733 14.724 53592 Z= 0.395 Chirality : 0.052 0.277 6003 Planarity : 0.005 0.061 6990 Dihedral : 5.685 45.117 5327 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.99 % Allowed : 7.79 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.12), residues: 4893 helix: -0.17 (0.19), residues: 726 sheet: 0.20 (0.13), residues: 1504 loop : -1.54 (0.12), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 503 HIS 0.005 0.002 HIS D 359 PHE 0.025 0.003 PHE C 711 TYR 0.027 0.003 TYR A 230 ARG 0.008 0.001 ARG G 805 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 270 time to evaluate : 4.484 Fit side-chains REVERT: A 560 LYS cc_start: 0.5458 (mttm) cc_final: 0.5246 (mmpt) REVERT: A 696 ASP cc_start: 0.6067 (OUTLIER) cc_final: 0.5651 (t70) REVERT: A 722 GLU cc_start: 0.6708 (mt-10) cc_final: 0.6411 (mm-30) REVERT: B 627 ASN cc_start: 0.7767 (t0) cc_final: 0.7561 (t160) REVERT: B 660 MET cc_start: 0.7424 (tpt) cc_final: 0.7191 (tmm) REVERT: B 786 MET cc_start: 0.8573 (tpp) cc_final: 0.8236 (tpp) REVERT: C 591 SER cc_start: 0.8509 (t) cc_final: 0.8242 (p) REVERT: C 687 LYS cc_start: 0.6932 (mmtm) cc_final: 0.6679 (mmmm) REVERT: C 853 MET cc_start: 0.7958 (mmm) cc_final: 0.7531 (mmm) REVERT: D 644 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6499 (mm-40) REVERT: D 722 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6309 (pm20) REVERT: D 773 ASN cc_start: 0.7457 (t0) cc_final: 0.7071 (p0) REVERT: E 716 LYS cc_start: 0.6834 (tttt) cc_final: 0.6581 (ttmm) REVERT: F 786 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7275 (ttm) REVERT: F 826 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.5831 (mmt90) REVERT: G 583 ASN cc_start: 0.7029 (m-40) cc_final: 0.6647 (t0) REVERT: G 668 ARG cc_start: 0.6872 (tmm-80) cc_final: 0.6314 (pmt170) REVERT: G 689 LYS cc_start: 0.6117 (tmmt) cc_final: 0.5864 (ttpp) REVERT: G 774 PHE cc_start: 0.7403 (t80) cc_final: 0.7190 (t80) REVERT: H 48 GLU cc_start: 0.3942 (OUTLIER) cc_final: 0.3633 (tt0) REVERT: H 57 ASN cc_start: 0.4547 (p0) cc_final: 0.4154 (p0) REVERT: H 89 MET cc_start: 0.3891 (ptm) cc_final: 0.3517 (ptp) REVERT: H 113 GLU cc_start: 0.6584 (pt0) cc_final: 0.6184 (tt0) REVERT: H 120 ASN cc_start: 0.5295 (m110) cc_final: 0.5082 (m-40) REVERT: H 202 LYS cc_start: 0.4693 (ttpt) cc_final: 0.4368 (ttmt) REVERT: H 284 ARG cc_start: 0.2164 (ttm170) cc_final: 0.1113 (ttp-110) REVERT: H 346 MET cc_start: 0.2080 (OUTLIER) cc_final: 0.1117 (mmt) outliers start: 80 outliers final: 40 residues processed: 325 average time/residue: 1.3940 time to fit residues: 561.5960 Evaluate side-chains 279 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 232 time to evaluate : 4.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 491 ASN Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 523 ASN Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain G residue 793 THR Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 410 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 242 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 363 optimal weight: 4.9990 chunk 297 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 437 optimal weight: 0.7980 chunk 472 optimal weight: 2.9990 chunk 389 optimal weight: 4.9990 chunk 433 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 351 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 811 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 ASN C 834 GLN D 780 ASN ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 ASN E 501 ASN F 811 GLN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 39520 Z= 0.237 Angle : 0.569 11.357 53592 Z= 0.309 Chirality : 0.046 0.182 6003 Planarity : 0.004 0.052 6990 Dihedral : 5.185 46.767 5327 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.92 % Allowed : 10.43 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.12), residues: 4893 helix: 0.41 (0.20), residues: 685 sheet: 0.36 (0.14), residues: 1470 loop : -1.47 (0.11), residues: 2738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 375 HIS 0.004 0.001 HIS B 314 PHE 0.028 0.002 PHE C 774 TYR 0.024 0.001 TYR H 397 ARG 0.007 0.000 ARG D 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 250 time to evaluate : 4.701 Fit side-chains REVERT: A 689 LYS cc_start: 0.6288 (tmmt) cc_final: 0.5511 (ttpt) REVERT: A 722 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6310 (mm-30) REVERT: A 853 MET cc_start: 0.8277 (mmm) cc_final: 0.8048 (mmm) REVERT: B 786 MET cc_start: 0.8635 (tpp) cc_final: 0.8256 (tpp) REVERT: C 591 SER cc_start: 0.8393 (t) cc_final: 0.8112 (p) REVERT: C 655 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6259 (mttt) REVERT: C 853 MET cc_start: 0.7819 (mmm) cc_final: 0.7476 (mmm) REVERT: D 722 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6248 (pm20) REVERT: F 786 MET cc_start: 0.7593 (ttm) cc_final: 0.7320 (ttm) REVERT: F 826 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6943 (mtt180) REVERT: G 569 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7892 (tt) REVERT: G 595 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6988 (mm) REVERT: G 668 ARG cc_start: 0.6851 (tmm-80) cc_final: 0.6393 (pmt170) REVERT: G 689 LYS cc_start: 0.6145 (tmmt) cc_final: 0.5892 (ttpp) REVERT: G 774 PHE cc_start: 0.7362 (t80) cc_final: 0.7081 (t80) REVERT: H 20 GLU cc_start: 0.3612 (mm-30) cc_final: 0.1880 (pm20) REVERT: H 48 GLU cc_start: 0.3992 (OUTLIER) cc_final: 0.3729 (tt0) REVERT: H 89 MET cc_start: 0.4105 (ptm) cc_final: 0.3852 (ptp) REVERT: H 120 ASN cc_start: 0.5431 (m110) cc_final: 0.5172 (m-40) REVERT: H 159 LYS cc_start: 0.4382 (tttt) cc_final: 0.2654 (mttt) REVERT: H 202 LYS cc_start: 0.4725 (ttpt) cc_final: 0.4378 (ttpt) REVERT: H 284 ARG cc_start: 0.2268 (ttm170) cc_final: 0.1201 (ttp-110) REVERT: H 346 MET cc_start: 0.2260 (OUTLIER) cc_final: 0.1339 (mmt) outliers start: 75 outliers final: 44 residues processed: 304 average time/residue: 1.3761 time to fit residues: 519.7649 Evaluate side-chains 279 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 228 time to evaluate : 4.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 704 TYR Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 635 VAL Chi-restraints excluded: chain F residue 762 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain G residue 755 ILE Chi-restraints excluded: chain G residue 793 THR Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 225 LYS Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 410 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 432 optimal weight: 2.9990 chunk 328 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 293 optimal weight: 10.0000 chunk 439 optimal weight: 3.9990 chunk 464 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 416 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 811 GLN A 851 ASN ** B 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** C 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 ASN ** D 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN E 463 ASN F 811 GLN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 ASN ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 39520 Z= 0.461 Angle : 0.713 14.774 53592 Z= 0.385 Chirality : 0.051 0.276 6003 Planarity : 0.005 0.058 6990 Dihedral : 5.778 45.311 5327 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 2.90 % Allowed : 11.71 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.12), residues: 4893 helix: -0.08 (0.19), residues: 713 sheet: 0.26 (0.14), residues: 1446 loop : -1.75 (0.11), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 503 HIS 0.005 0.002 HIS D 359 PHE 0.023 0.003 PHE C 711 TYR 0.035 0.002 TYR B 704 ARG 0.007 0.001 ARG B 668 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 241 time to evaluate : 4.748 Fit side-chains REVERT: A 560 LYS cc_start: 0.5818 (mttm) cc_final: 0.5466 (mmpt) REVERT: A 696 ASP cc_start: 0.6039 (OUTLIER) cc_final: 0.5653 (t70) REVERT: A 722 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6457 (mm-30) REVERT: B 325 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.6294 (ttp80) REVERT: B 657 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.6076 (mmtp) REVERT: B 786 MET cc_start: 0.8615 (tpp) cc_final: 0.8336 (tpp) REVERT: C 655 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6360 (mttt) REVERT: C 853 MET cc_start: 0.7959 (mmm) cc_final: 0.7621 (mmm) REVERT: D 644 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6385 (mm-40) REVERT: D 722 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6290 (pm20) REVERT: D 762 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7173 (mpp) REVERT: E 716 LYS cc_start: 0.6967 (tttt) cc_final: 0.6701 (ttmm) REVERT: E 807 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7447 (mt-10) REVERT: F 368 GLN cc_start: 0.7058 (tt0) cc_final: 0.6673 (tt0) REVERT: F 786 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7122 (tpp) REVERT: F 826 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.5810 (mmt90) REVERT: G 595 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6766 (mm) REVERT: G 668 ARG cc_start: 0.6853 (tmm-80) cc_final: 0.6368 (ttt180) REVERT: G 689 LYS cc_start: 0.6141 (tmmt) cc_final: 0.5864 (ttpp) REVERT: G 691 LYS cc_start: 0.5704 (OUTLIER) cc_final: 0.4771 (ptmt) REVERT: G 710 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7206 (mt-10) REVERT: H 89 MET cc_start: 0.4215 (ptm) cc_final: 0.3903 (ptp) REVERT: H 113 GLU cc_start: 0.6632 (pt0) cc_final: 0.6237 (tt0) REVERT: H 120 ASN cc_start: 0.5424 (m110) cc_final: 0.5159 (m-40) REVERT: H 284 ARG cc_start: 0.2141 (ttm170) cc_final: 0.1069 (ttp-110) REVERT: H 346 MET cc_start: 0.2347 (OUTLIER) cc_final: 0.1245 (mmt) outliers start: 116 outliers final: 64 residues processed: 325 average time/residue: 1.3529 time to fit residues: 548.4017 Evaluate side-chains 302 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 225 time to evaluate : 4.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 626 ASN Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 634 ASN Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain D residue 762 MET Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 807 GLU Chi-restraints excluded: chain E residue 817 ASP Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 635 VAL Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 667 LYS Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 762 MET Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain G residue 691 LYS Chi-restraints excluded: chain G residue 755 ILE Chi-restraints excluded: chain G residue 793 THR Chi-restraints excluded: chain G residue 875 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 225 LYS Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 410 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 387 optimal weight: 0.7980 chunk 263 optimal weight: 7.9990 chunk 6 optimal weight: 0.2980 chunk 346 optimal weight: 0.0370 chunk 191 optimal weight: 0.8980 chunk 396 optimal weight: 0.9980 chunk 321 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 237 optimal weight: 0.9980 chunk 417 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN ** C 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 567 ASN D 368 GLN D 648 ASN E 312 ASN E 463 ASN F 811 GLN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 ASN G 640 GLN H 120 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 39520 Z= 0.147 Angle : 0.511 8.783 53592 Z= 0.277 Chirality : 0.044 0.171 6003 Planarity : 0.004 0.048 6990 Dihedral : 4.878 43.812 5327 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.99 % Allowed : 13.33 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.12), residues: 4893 helix: 0.59 (0.20), residues: 687 sheet: 0.54 (0.14), residues: 1490 loop : -1.49 (0.11), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 375 HIS 0.003 0.001 HIS B 314 PHE 0.030 0.001 PHE C 774 TYR 0.023 0.001 TYR H 397 ARG 0.008 0.000 ARG D 325 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 258 time to evaluate : 4.602 Fit side-chains REVERT: A 370 SER cc_start: 0.7059 (p) cc_final: 0.6825 (t) REVERT: A 689 LYS cc_start: 0.6307 (tmmt) cc_final: 0.5134 (mtmt) REVERT: A 696 ASP cc_start: 0.5934 (OUTLIER) cc_final: 0.5478 (t70) REVERT: A 709 TYR cc_start: 0.6130 (m-10) cc_final: 0.5868 (m-80) REVERT: A 722 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6400 (mm-30) REVERT: B 701 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6859 (mt-10) REVERT: B 786 MET cc_start: 0.8675 (tpp) cc_final: 0.8365 (tpp) REVERT: C 591 SER cc_start: 0.8384 (t) cc_final: 0.8123 (p) REVERT: C 655 LYS cc_start: 0.6584 (OUTLIER) cc_final: 0.6214 (mttt) REVERT: C 853 MET cc_start: 0.7740 (mmm) cc_final: 0.7411 (mmm) REVERT: D 793 THR cc_start: 0.8854 (p) cc_final: 0.8481 (t) REVERT: E 772 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7721 (mp) REVERT: F 786 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7322 (ttm) REVERT: F 826 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6893 (mtt180) REVERT: G 668 ARG cc_start: 0.6887 (tmm-80) cc_final: 0.6274 (pmt170) REVERT: G 689 LYS cc_start: 0.6212 (tmmt) cc_final: 0.5962 (ttpp) REVERT: G 710 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7471 (tt0) REVERT: H 20 GLU cc_start: 0.3697 (mm-30) cc_final: 0.2003 (pm20) REVERT: H 120 ASN cc_start: 0.5482 (m-40) cc_final: 0.5092 (m-40) REVERT: H 284 ARG cc_start: 0.2268 (ttm170) cc_final: 0.1176 (ttp-110) REVERT: H 346 MET cc_start: 0.2512 (OUTLIER) cc_final: 0.1562 (mmt) outliers start: 74 outliers final: 34 residues processed: 317 average time/residue: 1.2961 time to fit residues: 516.5398 Evaluate side-chains 271 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 231 time to evaluate : 4.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 402 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 156 optimal weight: 0.7980 chunk 418 optimal weight: 0.0870 chunk 91 optimal weight: 0.9980 chunk 272 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 465 optimal weight: 9.9990 chunk 386 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 38 optimal weight: 0.0670 chunk 153 optimal weight: 5.9990 chunk 244 optimal weight: 0.7980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN ** C 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 ASN D 834 GLN ** E 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 610 ASN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 ASN G 640 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 39520 Z= 0.133 Angle : 0.491 8.469 53592 Z= 0.264 Chirality : 0.043 0.155 6003 Planarity : 0.004 0.046 6990 Dihedral : 4.565 44.719 5327 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.89 % Allowed : 13.81 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.12), residues: 4893 helix: 0.85 (0.20), residues: 687 sheet: 0.76 (0.14), residues: 1461 loop : -1.36 (0.12), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 375 HIS 0.004 0.001 HIS H 385 PHE 0.032 0.001 PHE G 774 TYR 0.026 0.001 TYR H 397 ARG 0.004 0.000 ARG H 295 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 259 time to evaluate : 4.418 Fit side-chains REVERT: A 370 SER cc_start: 0.7140 (p) cc_final: 0.6894 (t) REVERT: A 668 ARG cc_start: 0.7372 (tmm-80) cc_final: 0.7147 (tmm-80) REVERT: A 689 LYS cc_start: 0.6194 (tmmt) cc_final: 0.5483 (ttpt) REVERT: A 722 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6482 (mm-30) REVERT: B 668 ARG cc_start: 0.6982 (tmm-80) cc_final: 0.6713 (tmm-80) REVERT: B 687 LYS cc_start: 0.6180 (tttt) cc_final: 0.5662 (ptmt) REVERT: B 701 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6896 (mt-10) REVERT: B 786 MET cc_start: 0.8678 (tpp) cc_final: 0.8369 (tpp) REVERT: C 319 GLN cc_start: 0.7678 (pt0) cc_final: 0.7424 (tt0) REVERT: C 591 SER cc_start: 0.8355 (t) cc_final: 0.8109 (p) REVERT: C 655 LYS cc_start: 0.6559 (OUTLIER) cc_final: 0.6182 (mttt) REVERT: C 705 THR cc_start: 0.5295 (OUTLIER) cc_final: 0.5066 (t) REVERT: C 853 MET cc_start: 0.7727 (mmm) cc_final: 0.7423 (mmm) REVERT: D 648 ASN cc_start: 0.5924 (t0) cc_final: 0.5719 (t0) REVERT: D 793 THR cc_start: 0.8783 (p) cc_final: 0.8323 (t) REVERT: E 772 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7790 (mp) REVERT: E 853 MET cc_start: 0.7120 (mmm) cc_final: 0.6827 (mmp) REVERT: F 660 MET cc_start: 0.6996 (tpp) cc_final: 0.6177 (tmm) REVERT: F 786 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7355 (ttm) REVERT: G 668 ARG cc_start: 0.6806 (tmm-80) cc_final: 0.6329 (pmt170) REVERT: G 689 LYS cc_start: 0.6179 (tmmt) cc_final: 0.5924 (ttpp) REVERT: G 710 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7454 (tm-30) REVERT: H 20 GLU cc_start: 0.3795 (mm-30) cc_final: 0.2120 (pm20) REVERT: H 120 ASN cc_start: 0.5397 (m-40) cc_final: 0.4974 (m-40) REVERT: H 284 ARG cc_start: 0.2301 (ttm170) cc_final: 0.1237 (ttp-110) REVERT: H 346 MET cc_start: 0.2617 (OUTLIER) cc_final: 0.1559 (mmt) outliers start: 70 outliers final: 40 residues processed: 313 average time/residue: 1.3265 time to fit residues: 523.6865 Evaluate side-chains 282 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 237 time to evaluate : 4.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 685 ILE Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 635 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 290 ASN Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 402 ILE Chi-restraints excluded: chain H residue 410 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 448 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 265 optimal weight: 9.9990 chunk 339 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 391 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 463 optimal weight: 1.9990 chunk 290 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN C 392 ASN ** C 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 ASN ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 610 ASN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 ASN G 640 GLN H 127 GLN ** H 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39520 Z= 0.217 Angle : 0.546 10.000 53592 Z= 0.294 Chirality : 0.045 0.210 6003 Planarity : 0.004 0.045 6990 Dihedral : 4.887 46.491 5327 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.26 % Allowed : 14.18 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.12), residues: 4893 helix: 1.05 (0.21), residues: 650 sheet: 0.60 (0.14), residues: 1451 loop : -1.33 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 503 HIS 0.009 0.001 HIS H 157 PHE 0.020 0.002 PHE C 774 TYR 0.021 0.001 TYR H 397 ARG 0.003 0.000 ARG B 668 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 248 time to evaluate : 4.706 Fit side-chains REVERT: A 370 SER cc_start: 0.7167 (p) cc_final: 0.6845 (t) REVERT: A 689 LYS cc_start: 0.6335 (tmmt) cc_final: 0.5419 (ttpt) REVERT: A 722 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6489 (mm-30) REVERT: B 325 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6338 (ttp80) REVERT: B 701 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6908 (mt-10) REVERT: B 786 MET cc_start: 0.8657 (tpp) cc_final: 0.8305 (tpp) REVERT: C 319 GLN cc_start: 0.7706 (pt0) cc_final: 0.7451 (tt0) REVERT: C 568 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6748 (t0) REVERT: C 586 ASN cc_start: 0.7952 (m-40) cc_final: 0.7667 (m110) REVERT: C 591 SER cc_start: 0.8354 (t) cc_final: 0.8108 (p) REVERT: C 655 LYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6253 (mttt) REVERT: C 705 THR cc_start: 0.5361 (OUTLIER) cc_final: 0.5107 (t) REVERT: C 853 MET cc_start: 0.7810 (mmm) cc_final: 0.7503 (mmm) REVERT: D 793 THR cc_start: 0.8797 (p) cc_final: 0.8414 (t) REVERT: E 772 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7787 (mp) REVERT: F 368 GLN cc_start: 0.6952 (tt0) cc_final: 0.6559 (tt0) REVERT: F 786 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7200 (tpp) REVERT: F 826 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6975 (mtt180) REVERT: G 668 ARG cc_start: 0.6846 (tmm-80) cc_final: 0.6304 (pmt170) REVERT: G 689 LYS cc_start: 0.6269 (tmmt) cc_final: 0.6055 (ttpp) REVERT: G 691 LYS cc_start: 0.5713 (OUTLIER) cc_final: 0.4792 (ttmt) REVERT: G 710 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7482 (tm-30) REVERT: H 20 GLU cc_start: 0.3821 (mm-30) cc_final: 0.2105 (pm20) REVERT: H 120 ASN cc_start: 0.5444 (m-40) cc_final: 0.4875 (m110) REVERT: H 284 ARG cc_start: 0.2363 (ttm170) cc_final: 0.1244 (ttp-110) REVERT: H 346 MET cc_start: 0.2490 (OUTLIER) cc_final: 0.1326 (mmt) outliers start: 85 outliers final: 52 residues processed: 307 average time/residue: 1.3575 time to fit residues: 524.7279 Evaluate side-chains 296 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 235 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 634 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 685 ILE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 635 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain G residue 691 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 290 ASN Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 402 ILE Chi-restraints excluded: chain H residue 410 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 286 optimal weight: 2.9990 chunk 185 optimal weight: 0.5980 chunk 276 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 315 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 364 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 ASN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** G 640 GLN H 127 GLN H 157 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 39520 Z= 0.192 Angle : 0.531 9.288 53592 Z= 0.285 Chirality : 0.044 0.206 6003 Planarity : 0.004 0.047 6990 Dihedral : 4.827 45.863 5327 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.37 % Allowed : 14.52 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.12), residues: 4893 helix: 1.07 (0.21), residues: 650 sheet: 0.63 (0.14), residues: 1451 loop : -1.32 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 503 HIS 0.009 0.001 HIS H 157 PHE 0.019 0.001 PHE C 774 TYR 0.023 0.001 TYR H 397 ARG 0.002 0.000 ARG F 528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 237 time to evaluate : 4.773 Fit side-chains REVERT: A 370 SER cc_start: 0.7152 (p) cc_final: 0.6853 (t) REVERT: A 689 LYS cc_start: 0.6298 (tmmt) cc_final: 0.5546 (ttpt) REVERT: A 696 ASP cc_start: 0.5938 (OUTLIER) cc_final: 0.5519 (t70) REVERT: A 722 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6478 (mm-30) REVERT: B 325 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6331 (ttp80) REVERT: B 701 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6869 (mt-10) REVERT: B 786 MET cc_start: 0.8669 (tpp) cc_final: 0.8310 (tpp) REVERT: C 319 GLN cc_start: 0.7680 (pt0) cc_final: 0.7463 (tt0) REVERT: C 568 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6782 (t0) REVERT: C 591 SER cc_start: 0.8352 (t) cc_final: 0.8107 (p) REVERT: C 655 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.6213 (mttt) REVERT: C 705 THR cc_start: 0.5475 (OUTLIER) cc_final: 0.5173 (t) REVERT: C 853 MET cc_start: 0.7805 (mmm) cc_final: 0.7500 (mmm) REVERT: D 793 THR cc_start: 0.8787 (p) cc_final: 0.8399 (t) REVERT: E 772 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7839 (mp) REVERT: F 368 GLN cc_start: 0.6939 (tt0) cc_final: 0.6545 (tt0) REVERT: F 660 MET cc_start: 0.7119 (tpp) cc_final: 0.6237 (tmm) REVERT: F 786 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7190 (tpp) REVERT: F 826 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6953 (mtt180) REVERT: G 668 ARG cc_start: 0.6847 (tmm-80) cc_final: 0.6305 (pmt170) REVERT: G 689 LYS cc_start: 0.6206 (tmmt) cc_final: 0.5980 (ttpp) REVERT: G 691 LYS cc_start: 0.5711 (OUTLIER) cc_final: 0.4788 (ttmt) REVERT: G 710 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7433 (tm-30) REVERT: G 774 PHE cc_start: 0.7143 (t80) cc_final: 0.6624 (t80) REVERT: H 20 GLU cc_start: 0.3748 (mm-30) cc_final: 0.2026 (pm20) REVERT: H 120 ASN cc_start: 0.5447 (m-40) cc_final: 0.4970 (m-40) REVERT: H 284 ARG cc_start: 0.2395 (ttm170) cc_final: 0.1266 (ttp-110) REVERT: H 316 LEU cc_start: 0.3562 (OUTLIER) cc_final: 0.3124 (mt) REVERT: H 346 MET cc_start: 0.2534 (OUTLIER) cc_final: 0.1481 (mmt) outliers start: 90 outliers final: 57 residues processed: 303 average time/residue: 1.3061 time to fit residues: 496.7559 Evaluate side-chains 302 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 234 time to evaluate : 4.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 634 ASN Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 685 ILE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 635 VAL Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain G residue 691 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 290 ASN Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 402 ILE Chi-restraints excluded: chain H residue 410 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 421 optimal weight: 0.2980 chunk 444 optimal weight: 0.9980 chunk 405 optimal weight: 4.9990 chunk 432 optimal weight: 3.9990 chunk 260 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 339 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 390 optimal weight: 7.9990 chunk 408 optimal weight: 1.9990 chunk 430 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 ASN D 648 ASN E 610 ASN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** G 640 GLN H 127 GLN H 157 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 39520 Z= 0.140 Angle : 0.491 9.301 53592 Z= 0.264 Chirality : 0.043 0.187 6003 Planarity : 0.004 0.048 6990 Dihedral : 4.543 45.591 5327 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.19 % Allowed : 14.84 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.12), residues: 4893 helix: 1.23 (0.21), residues: 651 sheet: 0.80 (0.14), residues: 1485 loop : -1.26 (0.12), residues: 2757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 375 HIS 0.008 0.001 HIS H 157 PHE 0.018 0.001 PHE C 774 TYR 0.024 0.001 TYR H 397 ARG 0.003 0.000 ARG H 295 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 253 time to evaluate : 4.565 Fit side-chains REVERT: A 370 SER cc_start: 0.7178 (p) cc_final: 0.6916 (t) REVERT: A 689 LYS cc_start: 0.6221 (tmmt) cc_final: 0.5513 (ttpt) REVERT: A 696 ASP cc_start: 0.5957 (OUTLIER) cc_final: 0.5466 (t70) REVERT: A 722 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6502 (mm-30) REVERT: B 325 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6346 (ttp80) REVERT: B 687 LYS cc_start: 0.6174 (tttt) cc_final: 0.5667 (ptmt) REVERT: B 701 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6837 (mt-10) REVERT: B 786 MET cc_start: 0.8674 (tpp) cc_final: 0.8423 (tpp) REVERT: C 305 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6233 (mm-30) REVERT: C 568 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6753 (t0) REVERT: C 591 SER cc_start: 0.8282 (t) cc_final: 0.8053 (p) REVERT: C 655 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.6205 (mttt) REVERT: C 705 THR cc_start: 0.5406 (OUTLIER) cc_final: 0.5157 (t) REVERT: C 853 MET cc_start: 0.7702 (mmm) cc_final: 0.7436 (mmm) REVERT: D 417 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: D 793 THR cc_start: 0.8777 (p) cc_final: 0.8317 (t) REVERT: E 772 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7836 (mp) REVERT: F 368 GLN cc_start: 0.6926 (tt0) cc_final: 0.6510 (tt0) REVERT: F 660 MET cc_start: 0.7185 (tpp) cc_final: 0.6213 (tmm) REVERT: F 786 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7134 (tpp) REVERT: F 826 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.6874 (mtt180) REVERT: G 668 ARG cc_start: 0.6809 (tmm-80) cc_final: 0.6327 (pmt170) REVERT: G 691 LYS cc_start: 0.5735 (OUTLIER) cc_final: 0.4771 (ttmt) REVERT: G 710 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7433 (tm-30) REVERT: G 774 PHE cc_start: 0.7099 (t80) cc_final: 0.6528 (t80) REVERT: H 20 GLU cc_start: 0.3834 (mm-30) cc_final: 0.2150 (pm20) REVERT: H 120 ASN cc_start: 0.5328 (m-40) cc_final: 0.4892 (m-40) REVERT: H 149 GLU cc_start: 0.4035 (pp20) cc_final: 0.2890 (tp30) REVERT: H 166 MET cc_start: 0.2335 (OUTLIER) cc_final: 0.1602 (tpt) REVERT: H 202 LYS cc_start: 0.4825 (ttpt) cc_final: 0.4625 (ttpp) REVERT: H 284 ARG cc_start: 0.2374 (ttm170) cc_final: 0.1284 (ttp-110) REVERT: H 316 LEU cc_start: 0.3470 (OUTLIER) cc_final: 0.3045 (mt) outliers start: 82 outliers final: 52 residues processed: 313 average time/residue: 1.3603 time to fit residues: 536.1240 Evaluate side-chains 305 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 240 time to evaluate : 4.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 634 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 685 ILE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 635 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 523 ASN Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain G residue 691 LYS Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 290 ASN Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 402 ILE Chi-restraints excluded: chain H residue 410 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 283 optimal weight: 0.0370 chunk 456 optimal weight: 6.9990 chunk 278 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 317 optimal weight: 0.1980 chunk 479 optimal weight: 3.9990 chunk 441 optimal weight: 4.9990 chunk 381 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 chunk 294 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 ASN E 610 ASN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** G 640 GLN H 127 GLN H 157 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 39520 Z= 0.162 Angle : 0.509 9.709 53592 Z= 0.273 Chirality : 0.044 0.189 6003 Planarity : 0.004 0.047 6990 Dihedral : 4.592 46.495 5327 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.10 % Allowed : 15.23 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 4893 helix: 1.23 (0.21), residues: 651 sheet: 0.73 (0.14), residues: 1468 loop : -1.26 (0.12), residues: 2774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 503 HIS 0.009 0.001 HIS H 157 PHE 0.018 0.001 PHE C 774 TYR 0.023 0.001 TYR H 397 ARG 0.009 0.000 ARG G 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 238 time to evaluate : 4.745 Fit side-chains REVERT: A 370 SER cc_start: 0.7164 (p) cc_final: 0.6890 (t) REVERT: A 689 LYS cc_start: 0.6220 (tmmt) cc_final: 0.5512 (ttpt) REVERT: A 696 ASP cc_start: 0.5921 (OUTLIER) cc_final: 0.5421 (t70) REVERT: A 722 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6476 (mm-30) REVERT: B 325 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.6337 (ttp80) REVERT: B 687 LYS cc_start: 0.6193 (tttt) cc_final: 0.5676 (ptmt) REVERT: B 701 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6841 (mt-10) REVERT: B 709 TYR cc_start: 0.6859 (m-80) cc_final: 0.6544 (m-80) REVERT: B 786 MET cc_start: 0.8660 (tpp) cc_final: 0.8316 (tpp) REVERT: C 305 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6164 (mm-30) REVERT: C 568 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6765 (t0) REVERT: C 591 SER cc_start: 0.8237 (t) cc_final: 0.8023 (p) REVERT: C 655 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.6223 (mttt) REVERT: C 705 THR cc_start: 0.5504 (OUTLIER) cc_final: 0.5277 (t) REVERT: C 853 MET cc_start: 0.7758 (mmm) cc_final: 0.7449 (mmm) REVERT: D 793 THR cc_start: 0.8787 (p) cc_final: 0.8326 (t) REVERT: E 251 GLU cc_start: 0.7308 (mm-30) cc_final: 0.7096 (mm-30) REVERT: E 463 ASN cc_start: 0.6723 (OUTLIER) cc_final: 0.6437 (t0) REVERT: E 772 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7824 (mp) REVERT: F 368 GLN cc_start: 0.6946 (tt0) cc_final: 0.6522 (tt0) REVERT: F 660 MET cc_start: 0.7228 (tpp) cc_final: 0.6253 (tmm) REVERT: F 714 THR cc_start: 0.7036 (OUTLIER) cc_final: 0.6501 (p) REVERT: F 786 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7218 (tpp) REVERT: F 826 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6907 (mtt180) REVERT: G 668 ARG cc_start: 0.6816 (tmm-80) cc_final: 0.6320 (pmt170) REVERT: G 691 LYS cc_start: 0.5684 (OUTLIER) cc_final: 0.4697 (ttmt) REVERT: G 710 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7436 (tm-30) REVERT: G 774 PHE cc_start: 0.7084 (t80) cc_final: 0.6549 (t80) REVERT: H 20 GLU cc_start: 0.3751 (mm-30) cc_final: 0.2124 (pm20) REVERT: H 120 ASN cc_start: 0.5280 (m-40) cc_final: 0.4823 (m-40) REVERT: H 149 GLU cc_start: 0.4041 (pp20) cc_final: 0.2890 (tp30) REVERT: H 284 ARG cc_start: 0.2369 (ttm170) cc_final: 0.1249 (ttp-110) REVERT: H 316 LEU cc_start: 0.3434 (OUTLIER) cc_final: 0.3049 (mt) outliers start: 78 outliers final: 55 residues processed: 299 average time/residue: 1.3268 time to fit residues: 500.2351 Evaluate side-chains 300 residues out of total 4300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 232 time to evaluate : 4.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 634 ASN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 637 THR Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 731 THR Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 773 ASN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 463 ASN Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 685 ILE Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 465 ASP Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 635 VAL Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain G residue 691 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 290 ASN Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 316 LEU Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 402 ILE Chi-restraints excluded: chain H residue 410 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 303 optimal weight: 3.9990 chunk 406 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 351 optimal weight: 0.0270 chunk 56 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 382 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 392 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 0.0770 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 ASN F 392 ASN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** G 640 GLN ** H 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.152705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.117971 restraints weight = 184753.872| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.45 r_work: 0.3456 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 39520 Z= 0.227 Angle : 0.556 10.109 53592 Z= 0.299 Chirality : 0.045 0.217 6003 Planarity : 0.004 0.047 6990 Dihedral : 4.901 46.552 5327 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.31 % Allowed : 15.07 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.12), residues: 4893 helix: 1.08 (0.21), residues: 650 sheet: 0.62 (0.14), residues: 1474 loop : -1.31 (0.12), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 503 HIS 0.012 0.001 HIS H 157 PHE 0.018 0.002 PHE C 774 TYR 0.023 0.001 TYR H 397 ARG 0.009 0.000 ARG G 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11516.51 seconds wall clock time: 208 minutes 50.73 seconds (12530.73 seconds total)