Starting phenix.real_space_refine on Sun Mar 10 23:05:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xom_33352/03_2024/7xom_33352.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xom_33352/03_2024/7xom_33352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xom_33352/03_2024/7xom_33352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xom_33352/03_2024/7xom_33352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xom_33352/03_2024/7xom_33352.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xom_33352/03_2024/7xom_33352.pdb" } resolution = 3.2 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= 0.001 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 280 5.16 5 C 33653 2.51 5 N 9342 2.21 5 O 10854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 63": "OE1" <-> "OE2" Residue "A ASP 361": "OD1" <-> "OD2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 473": "OD1" <-> "OD2" Residue "G PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 398": "OD1" <-> "OD2" Residue "G TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 428": "OD1" <-> "OD2" Residue "K ASP 5": "OD1" <-> "OD2" Residue "K PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 121": "OD1" <-> "OD2" Residue "M TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 54129 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "B" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "C" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "D" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "E" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "F" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "G" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "H" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "I" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "J" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "K" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "L" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "M" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "N" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "U" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 159 Classifications: {'peptide': 32} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 31} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 32} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 20.84, per 1000 atoms: 0.39 Number of scatterers: 54129 At special positions: 0 Unit cell: (156.6, 162.69, 154.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 280 16.00 O 10854 8.00 N 9342 7.00 C 33653 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: 15.86 Conformation dependent library (CDL) restraints added in 7.5 seconds 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13334 Finding SS restraints... Secondary structure from input PDB file: 271 helices and 84 sheets defined 60.0% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 4.081A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.586A pdb=" N VAL A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 86 Processing helix chain 'A' and resid 88 through 109 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.765A pdb=" N ILE A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 282 through 297 Processing helix chain 'A' and resid 308 through 312 removed outlier: 3.634A pdb=" N LYS A 311 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 356 removed outlier: 3.826A pdb=" N ILE A 342 " --> pdb=" O GLU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 385 through 410 Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.983A pdb=" N ILE A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 458 Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.504A pdb=" N VAL A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 516 removed outlier: 3.512A pdb=" N THR A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.139A pdb=" N VAL B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.516A pdb=" N VAL B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 86 Processing helix chain 'B' and resid 88 through 109 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.711A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 229 through 244 removed outlier: 4.304A pdb=" N MET B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 282 through 297 removed outlier: 3.640A pdb=" N LYS B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 356 removed outlier: 3.522A pdb=" N ILE B 342 " --> pdb=" O GLU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 374 Processing helix chain 'B' and resid 385 through 410 Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.995A pdb=" N ILE B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 458 Proline residue: B 450 - end of helix Processing helix chain 'B' and resid 461 through 472 removed outlier: 3.582A pdb=" N VAL B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'C' and resid 9 through 29 removed outlier: 4.092A pdb=" N VAL C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.512A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 86 Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 140 through 152 removed outlier: 3.533A pdb=" N ALA C 152 " --> pdb=" O GLY C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 170 removed outlier: 3.530A pdb=" N GLY C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.568A pdb=" N PHE C 204 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 256 through 269 Processing helix chain 'C' and resid 282 through 297 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 358 through 374 Processing helix chain 'C' and resid 385 through 410 Processing helix chain 'C' and resid 416 through 426 removed outlier: 3.885A pdb=" N ILE C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 458 Proline residue: C 450 - end of helix Processing helix chain 'C' and resid 461 through 472 removed outlier: 3.520A pdb=" N GLY C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 497 through 516 Processing helix chain 'D' and resid 9 through 29 removed outlier: 4.175A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 59 Processing helix chain 'D' and resid 64 through 86 Processing helix chain 'D' and resid 88 through 109 Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 removed outlier: 3.599A pdb=" N GLY D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.538A pdb=" N PHE D 204 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 256 through 269 Processing helix chain 'D' and resid 282 through 297 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 358 through 375 removed outlier: 4.399A pdb=" N GLY D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 410 Processing helix chain 'D' and resid 416 through 427 removed outlier: 3.961A pdb=" N ILE D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 458 Proline residue: D 450 - end of helix Processing helix chain 'D' and resid 461 through 472 removed outlier: 3.524A pdb=" N GLY D 472 " --> pdb=" O THR D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 516 Processing helix chain 'E' and resid 9 through 29 removed outlier: 4.233A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 59 removed outlier: 3.624A pdb=" N VAL E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 86 Processing helix chain 'E' and resid 88 through 110 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 256 through 269 Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 358 through 375 removed outlier: 4.294A pdb=" N GLY E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 410 Processing helix chain 'E' and resid 416 through 427 removed outlier: 4.067A pdb=" N ILE E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 458 Proline residue: E 450 - end of helix Processing helix chain 'E' and resid 461 through 472 removed outlier: 3.550A pdb=" N GLY E 472 " --> pdb=" O THR E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 516 Processing helix chain 'F' and resid 9 through 29 removed outlier: 4.170A pdb=" N VAL F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 59 removed outlier: 3.609A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 86 Processing helix chain 'F' and resid 88 through 110 Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 256 through 269 removed outlier: 3.894A pdb=" N ALA F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 297 removed outlier: 3.513A pdb=" N ARG F 285 " --> pdb=" O PHE F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 356 Processing helix chain 'F' and resid 358 through 374 Processing helix chain 'F' and resid 385 through 410 Processing helix chain 'F' and resid 416 through 427 removed outlier: 3.903A pdb=" N ILE F 420 " --> pdb=" O GLY F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 458 Proline residue: F 450 - end of helix Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'F' and resid 497 through 516 Processing helix chain 'G' and resid 9 through 29 removed outlier: 4.109A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 59 removed outlier: 3.550A pdb=" N VAL G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 86 Processing helix chain 'G' and resid 88 through 109 Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 155 through 170 removed outlier: 3.634A pdb=" N GLY G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 205 removed outlier: 3.633A pdb=" N PHE G 204 " --> pdb=" O SER G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 232 removed outlier: 3.525A pdb=" N GLU G 232 " --> pdb=" O ASN G 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 229 through 232' Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 256 through 269 Processing helix chain 'G' and resid 282 through 297 Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 358 through 374 Processing helix chain 'G' and resid 385 through 410 Processing helix chain 'G' and resid 416 through 427 removed outlier: 3.849A pdb=" N ILE G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 458 Proline residue: G 450 - end of helix Processing helix chain 'G' and resid 461 through 472 Processing helix chain 'G' and resid 488 through 492 Processing helix chain 'G' and resid 497 through 516 Processing helix chain 'H' and resid 9 through 29 removed outlier: 4.081A pdb=" N VAL H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 60 removed outlier: 3.534A pdb=" N VAL H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 86 Processing helix chain 'H' and resid 88 through 109 Processing helix chain 'H' and resid 112 through 135 Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 155 through 170 removed outlier: 3.635A pdb=" N GLY H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 229 through 244 removed outlier: 4.397A pdb=" N MET H 233 " --> pdb=" O ASN H 229 " (cutoff:3.500A) Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 256 through 269 Processing helix chain 'H' and resid 282 through 297 Processing helix chain 'H' and resid 338 through 355 removed outlier: 3.584A pdb=" N ILE H 342 " --> pdb=" O GLU H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 375 removed outlier: 4.217A pdb=" N GLY H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 410 Processing helix chain 'H' and resid 416 through 427 removed outlier: 3.799A pdb=" N ILE H 420 " --> pdb=" O GLY H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 458 Proline residue: H 450 - end of helix Processing helix chain 'H' and resid 461 through 472 Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 497 through 516 Processing helix chain 'I' and resid 9 through 29 removed outlier: 4.217A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 60 removed outlier: 3.666A pdb=" N VAL I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 86 Processing helix chain 'I' and resid 88 through 109 Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 removed outlier: 3.616A pdb=" N GLY I 159 " --> pdb=" O ASP I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 229 through 244 removed outlier: 4.488A pdb=" N MET I 233 " --> pdb=" O ASN I 229 " (cutoff:3.500A) Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 256 through 269 removed outlier: 3.805A pdb=" N ALA I 260 " --> pdb=" O GLY I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 297 Processing helix chain 'I' and resid 338 through 355 removed outlier: 3.889A pdb=" N ILE I 342 " --> pdb=" O GLU I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 375 removed outlier: 4.091A pdb=" N GLY I 375 " --> pdb=" O LYS I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 410 Processing helix chain 'I' and resid 416 through 426 removed outlier: 3.768A pdb=" N ILE I 420 " --> pdb=" O GLY I 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 458 Proline residue: I 450 - end of helix Processing helix chain 'I' and resid 461 through 472 Processing helix chain 'I' and resid 497 through 516 Processing helix chain 'J' and resid 9 through 29 removed outlier: 4.141A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 60 removed outlier: 3.578A pdb=" N VAL J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 86 Processing helix chain 'J' and resid 88 through 109 Processing helix chain 'J' and resid 112 through 135 Processing helix chain 'J' and resid 140 through 152 Processing helix chain 'J' and resid 155 through 170 removed outlier: 3.601A pdb=" N GLY J 159 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 205 Processing helix chain 'J' and resid 229 through 232 Processing helix chain 'J' and resid 233 through 244 Processing helix chain 'J' and resid 256 through 269 Processing helix chain 'J' and resid 282 through 297 Processing helix chain 'J' and resid 338 through 356 Processing helix chain 'J' and resid 358 through 374 Processing helix chain 'J' and resid 385 through 410 Processing helix chain 'J' and resid 416 through 427 removed outlier: 3.962A pdb=" N ILE J 420 " --> pdb=" O GLY J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 458 Proline residue: J 450 - end of helix Processing helix chain 'J' and resid 461 through 472 Processing helix chain 'J' and resid 488 through 492 removed outlier: 3.559A pdb=" N GLY J 492 " --> pdb=" O MET J 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 488 through 492' Processing helix chain 'J' and resid 497 through 516 Processing helix chain 'K' and resid 9 through 28 Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 52 through 60 removed outlier: 3.821A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 Processing helix chain 'K' and resid 88 through 110 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 151 Processing helix chain 'K' and resid 155 through 170 removed outlier: 3.571A pdb=" N GLY K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 205 removed outlier: 3.892A pdb=" N ILE K 205 " --> pdb=" O PRO K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 244 removed outlier: 3.527A pdb=" N LEU K 237 " --> pdb=" O MET K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 269 removed outlier: 4.130A pdb=" N LEU K 259 " --> pdb=" O GLU K 255 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA K 260 " --> pdb=" O GLY K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 297 Processing helix chain 'K' and resid 338 through 355 removed outlier: 3.817A pdb=" N ILE K 342 " --> pdb=" O GLU K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 375 removed outlier: 4.264A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 410 removed outlier: 3.630A pdb=" N MET K 389 " --> pdb=" O THR K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 426 Processing helix chain 'K' and resid 433 through 459 Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 461 through 472 removed outlier: 4.318A pdb=" N VAL K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A) Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 497 through 516 Processing helix chain 'L' and resid 9 through 29 removed outlier: 4.121A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 60 removed outlier: 3.596A pdb=" N VAL L 56 " --> pdb=" O ASP L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 86 Processing helix chain 'L' and resid 88 through 109 Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 169 Processing helix chain 'L' and resid 201 through 205 Processing helix chain 'L' and resid 229 through 232 Processing helix chain 'L' and resid 233 through 244 Processing helix chain 'L' and resid 256 through 269 Processing helix chain 'L' and resid 281 through 297 Processing helix chain 'L' and resid 338 through 356 Processing helix chain 'L' and resid 358 through 374 Processing helix chain 'L' and resid 385 through 410 Processing helix chain 'L' and resid 417 through 427 Processing helix chain 'L' and resid 433 through 458 Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 461 through 472 Processing helix chain 'L' and resid 488 through 492 Processing helix chain 'L' and resid 497 through 516 Processing helix chain 'M' and resid 9 through 29 removed outlier: 4.128A pdb=" N VAL M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 59 removed outlier: 3.685A pdb=" N VAL M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 86 Processing helix chain 'M' and resid 88 through 109 Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 155 through 170 Processing helix chain 'M' and resid 201 through 205 Processing helix chain 'M' and resid 229 through 232 Processing helix chain 'M' and resid 233 through 244 Processing helix chain 'M' and resid 256 through 269 Processing helix chain 'M' and resid 282 through 297 Processing helix chain 'M' and resid 338 through 356 removed outlier: 3.907A pdb=" N ILE M 342 " --> pdb=" O GLU M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 374 Processing helix chain 'M' and resid 385 through 410 Processing helix chain 'M' and resid 416 through 427 removed outlier: 3.941A pdb=" N ILE M 420 " --> pdb=" O GLY M 416 " (cutoff:3.500A) Processing helix chain 'M' and resid 433 through 458 Proline residue: M 450 - end of helix Processing helix chain 'M' and resid 461 through 472 removed outlier: 3.525A pdb=" N GLY M 472 " --> pdb=" O THR M 468 " (cutoff:3.500A) Processing helix chain 'M' and resid 497 through 516 Processing helix chain 'N' and resid 9 through 29 removed outlier: 4.030A pdb=" N VAL N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 59 Processing helix chain 'N' and resid 64 through 86 Processing helix chain 'N' and resid 88 through 109 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 140 through 152 Processing helix chain 'N' and resid 155 through 170 removed outlier: 3.655A pdb=" N GLY N 159 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 205 Processing helix chain 'N' and resid 229 through 232 Processing helix chain 'N' and resid 233 through 244 Processing helix chain 'N' and resid 256 through 269 Processing helix chain 'N' and resid 282 through 297 Processing helix chain 'N' and resid 338 through 356 Processing helix chain 'N' and resid 358 through 375 removed outlier: 4.351A pdb=" N GLY N 375 " --> pdb=" O LYS N 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 427 removed outlier: 3.795A pdb=" N ILE N 420 " --> pdb=" O GLY N 416 " (cutoff:3.500A) Processing helix chain 'N' and resid 433 through 458 Proline residue: N 450 - end of helix Processing helix chain 'N' and resid 461 through 472 removed outlier: 3.516A pdb=" N GLY N 472 " --> pdb=" O THR N 468 " (cutoff:3.500A) Processing helix chain 'N' and resid 497 through 516 Processing helix chain 'U' and resid 15 through 29 removed outlier: 4.284A pdb=" N UNK U 22 " --> pdb=" O UNK U 18 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N UNK U 23 " --> pdb=" O UNK U 19 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK U 25 " --> pdb=" O UNK U 21 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.508A pdb=" N ASN G 37 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N CYS A 519 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.369A pdb=" N ASN A 37 " --> pdb=" O THR B 517 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N CYS B 519 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.460A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU A 178 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 195 removed outlier: 6.835A pdb=" N THR A 330 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE A 325 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 332 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 323 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASP A 334 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 193 through 195 removed outlier: 6.835A pdb=" N THR A 330 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE A 325 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE A 332 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 323 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASP A 334 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 411 through 413 removed outlier: 3.512A pdb=" N ASP A 495 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 476 through 479 removed outlier: 3.659A pdb=" N GLU A 484 " --> pdb=" O ASN A 479 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.528A pdb=" N ASN B 37 " --> pdb=" O THR C 517 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N CYS C 519 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 179 Processing sheet with id=AB1, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.175A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU B 247 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 213 through 216 removed outlier: 8.286A pdb=" N ILE B 301 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU B 222 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 411 through 413 removed outlier: 3.654A pdb=" N ASP B 495 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.533A pdb=" N GLU B 484 " --> pdb=" O ASN B 479 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.339A pdb=" N ASN C 37 " --> pdb=" O THR D 517 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N CYS D 519 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 174 through 179 removed outlier: 6.563A pdb=" N VAL C 174 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE C 379 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR C 176 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL C 381 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLU C 178 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 192 through 195 removed outlier: 3.594A pdb=" N ARG C 322 " --> pdb=" O ILE C 333 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 192 through 195 removed outlier: 3.594A pdb=" N ARG C 322 " --> pdb=" O ILE C 333 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC1, first strand: chain 'C' and resid 476 through 479 removed outlier: 3.533A pdb=" N GLU C 484 " --> pdb=" O ASN C 479 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 48 through 50 removed outlier: 6.904A pdb=" N ASN D 37 " --> pdb=" O CYS E 519 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N VAL E 521 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL D 39 " --> pdb=" O VAL E 521 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ASP E 523 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 174 through 179 Processing sheet with id=AC4, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.481A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.481A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 251 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AC7, first strand: chain 'D' and resid 476 through 479 removed outlier: 3.692A pdb=" N GLU D 484 " --> pdb=" O ASN D 479 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 48 through 50 removed outlier: 6.479A pdb=" N ASN E 37 " --> pdb=" O CYS F 519 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N VAL F 521 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL E 39 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N ASP F 523 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 174 through 179 Processing sheet with id=AD1, first strand: chain 'E' and resid 192 through 195 removed outlier: 6.186A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 192 through 195 removed outlier: 6.186A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA E 251 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AD4, first strand: chain 'E' and resid 476 through 479 removed outlier: 3.706A pdb=" N GLU E 484 " --> pdb=" O ASN E 479 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.379A pdb=" N ASN F 37 " --> pdb=" O THR G 517 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N CYS G 519 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS G 7 " --> pdb=" O MET G 520 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 174 through 179 Processing sheet with id=AD7, first strand: chain 'F' and resid 194 through 195 removed outlier: 3.584A pdb=" N ARG F 322 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA F 274 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 251 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 212 through 216 removed outlier: 8.617A pdb=" N ILE F 301 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU F 222 " --> pdb=" O ILE F 301 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AE1, first strand: chain 'F' and resid 476 through 479 removed outlier: 3.599A pdb=" N GLU F 484 " --> pdb=" O ASN F 479 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 174 through 179 removed outlier: 6.580A pdb=" N VAL G 174 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE G 379 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR G 176 " --> pdb=" O ILE G 379 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL G 381 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU G 178 " --> pdb=" O VAL G 381 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.248A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.248A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU G 247 " --> pdb=" O ALA G 274 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N VAL G 276 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE G 249 " --> pdb=" O VAL G 276 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AE6, first strand: chain 'G' and resid 476 through 479 removed outlier: 3.657A pdb=" N GLU G 484 " --> pdb=" O ASN G 479 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.385A pdb=" N ASN N 37 " --> pdb=" O THR H 517 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N CYS H 519 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 48 through 50 removed outlier: 6.873A pdb=" N ASN H 37 " --> pdb=" O CYS I 519 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N VAL I 521 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL H 39 " --> pdb=" O VAL I 521 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ASP I 523 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 174 through 179 removed outlier: 6.474A pdb=" N VAL H 174 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE H 379 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR H 176 " --> pdb=" O ILE H 379 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL H 381 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU H 178 " --> pdb=" O VAL H 381 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 194 through 195 removed outlier: 6.240A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 213 through 216 removed outlier: 8.348A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU H 222 " --> pdb=" O ILE H 301 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AF4, first strand: chain 'H' and resid 476 through 479 removed outlier: 3.524A pdb=" N GLU H 484 " --> pdb=" O ASN H 479 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.570A pdb=" N ASN I 37 " --> pdb=" O THR J 517 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N CYS J 519 " --> pdb=" O ASN I 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 174 through 179 removed outlier: 6.537A pdb=" N VAL I 174 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE I 379 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR I 176 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL I 381 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU I 178 " --> pdb=" O VAL I 381 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 194 through 195 removed outlier: 6.255A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU I 247 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 213 through 216 removed outlier: 8.539A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU I 222 " --> pdb=" O ILE I 301 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AG1, first strand: chain 'I' and resid 476 through 478 Processing sheet with id=AG2, first strand: chain 'J' and resid 48 through 50 removed outlier: 7.130A pdb=" N ASN J 37 " --> pdb=" O CYS K 519 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N VAL K 521 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL J 39 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N ASP K 523 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 174 through 179 Processing sheet with id=AG4, first strand: chain 'J' and resid 193 through 195 removed outlier: 3.713A pdb=" N ARG J 322 " --> pdb=" O ILE J 333 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA J 251 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 213 through 216 removed outlier: 8.710A pdb=" N ILE J 301 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU J 222 " --> pdb=" O ILE J 301 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AG7, first strand: chain 'J' and resid 476 through 479 removed outlier: 3.523A pdb=" N GLU J 484 " --> pdb=" O ASN J 479 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 48 through 50 removed outlier: 7.494A pdb=" N ASN K 37 " --> pdb=" O GLU L 518 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N MET L 520 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL K 39 " --> pdb=" O MET L 520 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N THR L 522 " --> pdb=" O VAL K 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS L 7 " --> pdb=" O MET L 520 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 174 through 179 removed outlier: 6.379A pdb=" N VAL K 174 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE K 379 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR K 176 " --> pdb=" O ILE K 379 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL K 381 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLU K 178 " --> pdb=" O VAL K 381 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 193 through 195 removed outlier: 3.521A pdb=" N VAL K 323 " --> pdb=" O LEU K 215 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 222 through 223 Processing sheet with id=AH3, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AH4, first strand: chain 'K' and resid 476 through 479 Processing sheet with id=AH5, first strand: chain 'L' and resid 48 through 50 removed outlier: 6.608A pdb=" N ASN L 37 " --> pdb=" O CYS M 519 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N VAL M 521 " --> pdb=" O ASN L 37 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL L 39 " --> pdb=" O VAL M 521 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ASP M 523 " --> pdb=" O VAL L 39 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 174 through 179 Processing sheet with id=AH7, first strand: chain 'L' and resid 192 through 195 removed outlier: 6.154A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 192 through 195 removed outlier: 6.154A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA L 251 " --> pdb=" O VAL L 276 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AI1, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AI2, first strand: chain 'M' and resid 48 through 50 removed outlier: 6.822A pdb=" N ASN M 37 " --> pdb=" O CYS N 519 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N VAL N 521 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL M 39 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ASP N 523 " --> pdb=" O VAL M 39 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 174 through 179 removed outlier: 6.727A pdb=" N VAL M 174 " --> pdb=" O ALA M 377 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE M 379 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR M 176 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL M 381 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU M 178 " --> pdb=" O VAL M 381 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 192 through 195 removed outlier: 6.149A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 192 through 195 removed outlier: 6.149A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AI7, first strand: chain 'M' and resid 476 through 479 removed outlier: 3.602A pdb=" N GLU M 484 " --> pdb=" O ASN M 479 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 174 through 179 removed outlier: 6.595A pdb=" N VAL N 174 " --> pdb=" O ALA N 377 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE N 379 " --> pdb=" O VAL N 174 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR N 176 " --> pdb=" O ILE N 379 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL N 381 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU N 178 " --> pdb=" O VAL N 381 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'N' and resid 193 through 195 removed outlier: 6.362A pdb=" N GLY N 335 " --> pdb=" O ALA N 320 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA N 320 " --> pdb=" O GLY N 335 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 193 through 195 removed outlier: 6.362A pdb=" N GLY N 335 " --> pdb=" O ALA N 320 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA N 320 " --> pdb=" O GLY N 335 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU N 247 " --> pdb=" O ALA N 274 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N VAL N 276 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE N 249 " --> pdb=" O VAL N 276 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AJ3, first strand: chain 'N' and resid 476 through 479 3780 hydrogen bonds defined for protein. 10914 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.32 Time building geometry restraints manager: 17.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13324 1.33 - 1.45: 8169 1.45 - 1.58: 32509 1.58 - 1.70: 0 1.70 - 1.82: 518 Bond restraints: 54520 Sorted by residual: bond pdb=" CG LYS K 160 " pdb=" CD LYS K 160 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" CG GLN L 366 " pdb=" CD GLN L 366 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.40e+00 bond pdb=" CG GLU B 354 " pdb=" CD GLU B 354 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.38e+00 bond pdb=" CD GLN L 366 " pdb=" OE1 GLN L 366 " ideal model delta sigma weight residual 1.231 1.209 0.022 1.90e-02 2.77e+03 1.33e+00 bond pdb=" CG GLN L 351 " pdb=" CD GLN L 351 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.31e+00 ... (remaining 54515 not shown) Histogram of bond angle deviations from ideal: 96.88 - 103.77: 638 103.77 - 110.67: 15903 110.67 - 117.56: 25459 117.56 - 124.45: 31332 124.45 - 131.35: 289 Bond angle restraints: 73621 Sorted by residual: angle pdb=" N GLN L 366 " pdb=" CA GLN L 366 " pdb=" CB GLN L 366 " ideal model delta sigma weight residual 110.30 117.27 -6.97 1.54e+00 4.22e-01 2.05e+01 angle pdb=" C ILE K 353 " pdb=" N GLU K 354 " pdb=" CA GLU K 354 " ideal model delta sigma weight residual 121.94 113.07 8.87 2.00e+00 2.50e-01 1.97e+01 angle pdb=" CA MET L 69 " pdb=" CB MET L 69 " pdb=" CG MET L 69 " ideal model delta sigma weight residual 114.10 122.26 -8.16 2.00e+00 2.50e-01 1.67e+01 angle pdb=" N GLN L 351 " pdb=" CA GLN L 351 " pdb=" CB GLN L 351 " ideal model delta sigma weight residual 110.28 116.38 -6.10 1.55e+00 4.16e-01 1.55e+01 angle pdb=" N GLU B 164 " pdb=" CA GLU B 164 " pdb=" CB GLU B 164 " ideal model delta sigma weight residual 110.39 116.88 -6.49 1.66e+00 3.63e-01 1.53e+01 ... (remaining 73616 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 30631 17.07 - 34.14: 2587 34.14 - 51.21: 512 51.21 - 68.28: 102 68.28 - 85.35: 29 Dihedral angle restraints: 33861 sinusoidal: 13076 harmonic: 20785 Sorted by residual: dihedral pdb=" CA ASP K 41 " pdb=" C ASP K 41 " pdb=" N LYS K 42 " pdb=" CA LYS K 42 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE J 60 " pdb=" C ILE J 60 " pdb=" N GLU J 61 " pdb=" CA GLU J 61 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA MET M 233 " pdb=" C MET M 233 " pdb=" N LEU M 234 " pdb=" CA LEU M 234 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 33858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 6647 0.039 - 0.078: 1641 0.078 - 0.117: 597 0.117 - 0.156: 77 0.156 - 0.195: 1 Chirality restraints: 8963 Sorted by residual: chirality pdb=" CA GLU K 354 " pdb=" N GLU K 354 " pdb=" C GLU K 354 " pdb=" CB GLU K 354 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CA GLU B 354 " pdb=" N GLU B 354 " pdb=" C GLU B 354 " pdb=" CB GLU B 354 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA GLU A 367 " pdb=" N GLU A 367 " pdb=" C GLU A 367 " pdb=" CB GLU A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 8960 not shown) Planarity restraints: 9649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 217 " -0.031 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO K 218 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO K 218 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO K 218 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 363 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C GLU A 363 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU A 363 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS A 364 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 461 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.55e+00 pdb=" N PRO B 462 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 462 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 462 " 0.018 5.00e-02 4.00e+02 ... (remaining 9646 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1796 2.72 - 3.27: 57348 3.27 - 3.81: 94932 3.81 - 4.36: 109649 4.36 - 4.90: 189880 Nonbonded interactions: 453605 Sorted by model distance: nonbonded pdb=" O VAL K 147 " pdb=" OG SER K 151 " model vdw 2.175 2.440 nonbonded pdb=" OH TYR C 478 " pdb=" OE1 GLU C 483 " model vdw 2.190 2.440 nonbonded pdb=" O GLU L 339 " pdb=" NE2 GLN L 343 " model vdw 2.194 2.520 nonbonded pdb=" OH TYR J 478 " pdb=" OE1 GLU J 483 " model vdw 2.195 2.440 nonbonded pdb=" OH TYR L 478 " pdb=" OE1 GLU L 483 " model vdw 2.200 2.440 ... (remaining 453600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 7.350 Check model and map are aligned: 0.590 Set scattering table: 0.370 Process input model: 111.100 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.300 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.002 0.043 54520 Z= 0.139 Angle : 0.491 8.875 73621 Z= 0.267 Chirality : 0.039 0.195 8963 Planarity : 0.003 0.046 9649 Dihedral : 13.298 85.353 20527 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.92 % Favored : 99.07 % Rotamer: Outliers : 0.02 % Allowed : 0.19 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.16 (0.10), residues: 7308 helix: 2.46 (0.08), residues: 4100 sheet: 1.09 (0.17), residues: 918 loop : -0.34 (0.12), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 401 PHE 0.013 0.001 PHE E 204 TYR 0.009 0.001 TYR K 199 ARG 0.005 0.000 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 546 time to evaluate : 4.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.7645 (ptt) cc_final: 0.7059 (ppp) REVERT: A 398 ASP cc_start: 0.8925 (m-30) cc_final: 0.8723 (m-30) REVERT: C 203 TYR cc_start: 0.7530 (t80) cc_final: 0.7223 (t80) REVERT: C 204 PHE cc_start: 0.7341 (m-80) cc_final: 0.7089 (m-80) REVERT: C 307 MET cc_start: 0.8016 (mpp) cc_final: 0.7815 (mpp) REVERT: C 342 ILE cc_start: 0.8659 (mm) cc_final: 0.8448 (mm) REVERT: C 389 MET cc_start: 0.8729 (tmm) cc_final: 0.8480 (tmm) REVERT: D 61 GLU cc_start: 0.7825 (tt0) cc_final: 0.7564 (pt0) REVERT: D 140 ASP cc_start: 0.8043 (p0) cc_final: 0.7449 (p0) REVERT: D 389 MET cc_start: 0.8489 (tmm) cc_final: 0.8151 (tmm) REVERT: D 488 MET cc_start: 0.8683 (mmm) cc_final: 0.8331 (mmm) REVERT: E 153 ASN cc_start: 0.8634 (m110) cc_final: 0.8412 (m-40) REVERT: E 389 MET cc_start: 0.8167 (tmm) cc_final: 0.7805 (tmm) REVERT: F 160 LYS cc_start: 0.9243 (ptmm) cc_final: 0.8966 (ptpp) REVERT: G 59 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7646 (mm-30) REVERT: G 83 ASP cc_start: 0.7791 (m-30) cc_final: 0.7565 (m-30) REVERT: G 193 MET cc_start: 0.8778 (ptm) cc_final: 0.8562 (ptm) REVERT: G 204 PHE cc_start: 0.7147 (m-80) cc_final: 0.6929 (m-80) REVERT: H 348 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8581 (tm-30) REVERT: J 288 MET cc_start: 0.8309 (mpp) cc_final: 0.7383 (mpp) REVERT: J 389 MET cc_start: 0.8487 (tpt) cc_final: 0.8192 (tpt) REVERT: K 267 MET cc_start: 0.6030 (mmp) cc_final: 0.5640 (mmm) REVERT: L 233 MET cc_start: 0.8829 (pmm) cc_final: 0.8378 (pmm) REVERT: L 360 TYR cc_start: 0.6551 (t80) cc_final: 0.6324 (t80) REVERT: L 389 MET cc_start: 0.8651 (tmm) cc_final: 0.8247 (tmm) REVERT: L 488 MET cc_start: 0.9039 (mmt) cc_final: 0.8701 (mmt) REVERT: M 111 MET cc_start: 0.8156 (mmt) cc_final: 0.7882 (mmm) REVERT: M 199 TYR cc_start: 0.8080 (p90) cc_final: 0.7803 (p90) REVERT: M 389 MET cc_start: 0.8535 (tmm) cc_final: 0.8079 (tmm) REVERT: N 193 MET cc_start: 0.7744 (ptm) cc_final: 0.7480 (ptm) REVERT: N 288 MET cc_start: 0.7636 (mpp) cc_final: 0.7314 (mpp) REVERT: N 488 MET cc_start: 0.9111 (mmm) cc_final: 0.8887 (tpp) outliers start: 1 outliers final: 0 residues processed: 547 average time/residue: 0.4995 time to fit residues: 464.1557 Evaluate side-chains 405 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 4.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 617 optimal weight: 1.9990 chunk 554 optimal weight: 7.9990 chunk 307 optimal weight: 9.9990 chunk 189 optimal weight: 10.0000 chunk 373 optimal weight: 0.9980 chunk 296 optimal weight: 8.9990 chunk 572 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 348 optimal weight: 6.9990 chunk 426 optimal weight: 4.9990 chunk 663 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 319 GLN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 153 ASN ** F 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 505 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 366 GLN ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 479 ASN ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 54520 Z= 0.273 Angle : 0.524 11.383 73621 Z= 0.283 Chirality : 0.041 0.178 8963 Planarity : 0.003 0.031 9649 Dihedral : 3.778 20.195 7759 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.26 % Favored : 98.73 % Rotamer: Outliers : 0.74 % Allowed : 6.47 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.10), residues: 7308 helix: 2.50 (0.08), residues: 4130 sheet: 0.98 (0.16), residues: 983 loop : -0.44 (0.12), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 401 PHE 0.015 0.001 PHE K 195 TYR 0.013 0.001 TYR D 360 ARG 0.004 0.000 ARG A 368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 427 time to evaluate : 4.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.7709 (ptt) cc_final: 0.7053 (ppp) REVERT: B 389 MET cc_start: 0.8499 (tmm) cc_final: 0.8032 (tmm) REVERT: C 204 PHE cc_start: 0.7306 (m-80) cc_final: 0.6930 (m-80) REVERT: C 233 MET cc_start: 0.7823 (pmm) cc_final: 0.7092 (ppp) REVERT: C 307 MET cc_start: 0.7987 (mpp) cc_final: 0.7744 (mpp) REVERT: C 389 MET cc_start: 0.8802 (tmm) cc_final: 0.8516 (tmm) REVERT: D 389 MET cc_start: 0.8475 (tmm) cc_final: 0.8106 (tmm) REVERT: D 488 MET cc_start: 0.8690 (mmm) cc_final: 0.8248 (mmm) REVERT: E 153 ASN cc_start: 0.8706 (m110) cc_final: 0.8468 (m-40) REVERT: E 354 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8610 (mm-30) REVERT: E 389 MET cc_start: 0.8194 (tmm) cc_final: 0.7678 (tmm) REVERT: F 160 LYS cc_start: 0.9255 (ptmm) cc_final: 0.8966 (ptpp) REVERT: G 59 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7745 (mm-30) REVERT: G 83 ASP cc_start: 0.7825 (m-30) cc_final: 0.7618 (m-30) REVERT: G 389 MET cc_start: 0.8233 (tpp) cc_final: 0.8015 (tpp) REVERT: G 398 ASP cc_start: 0.8578 (t0) cc_final: 0.8367 (t70) REVERT: I 164 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8607 (pm20) REVERT: I 488 MET cc_start: 0.9239 (tpt) cc_final: 0.8924 (mmt) REVERT: K 267 MET cc_start: 0.6098 (mmp) cc_final: 0.5656 (mmm) REVERT: L 233 MET cc_start: 0.8816 (pmm) cc_final: 0.8204 (pmm) REVERT: M 389 MET cc_start: 0.8607 (tmm) cc_final: 0.8072 (tmm) REVERT: N 193 MET cc_start: 0.7919 (ptm) cc_final: 0.7578 (ptm) REVERT: N 288 MET cc_start: 0.7640 (mpp) cc_final: 0.7201 (mpp) outliers start: 42 outliers final: 17 residues processed: 454 average time/residue: 0.4867 time to fit residues: 382.7202 Evaluate side-chains 404 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 385 time to evaluate : 4.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 229 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 473 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 368 optimal weight: 9.9990 chunk 206 optimal weight: 0.8980 chunk 552 optimal weight: 10.0000 chunk 452 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 665 optimal weight: 0.9990 chunk 718 optimal weight: 9.9990 chunk 592 optimal weight: 0.0980 chunk 659 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 533 optimal weight: 0.0980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN D 343 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 479 ASN J 112 ASN ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 54520 Z= 0.172 Angle : 0.477 9.409 73621 Z= 0.257 Chirality : 0.040 0.174 8963 Planarity : 0.003 0.029 9649 Dihedral : 3.727 17.319 7759 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.74 % Favored : 99.25 % Rotamer: Outliers : 0.92 % Allowed : 8.86 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.22 (0.10), residues: 7308 helix: 2.57 (0.08), residues: 4130 sheet: 0.90 (0.16), residues: 979 loop : -0.43 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 401 PHE 0.021 0.001 PHE F 204 TYR 0.011 0.001 TYR A 203 ARG 0.004 0.000 ARG L 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 411 time to evaluate : 4.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.7708 (ptt) cc_final: 0.7096 (ppp) REVERT: A 362 ARG cc_start: 0.8817 (mmt-90) cc_final: 0.8103 (mmt-90) REVERT: B 199 TYR cc_start: 0.8107 (p90) cc_final: 0.7790 (p90) REVERT: B 221 LEU cc_start: 0.8876 (mt) cc_final: 0.8649 (mm) REVERT: B 343 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8248 (mm-40) REVERT: B 389 MET cc_start: 0.8483 (tmm) cc_final: 0.7994 (tmm) REVERT: C 204 PHE cc_start: 0.7144 (m-80) cc_final: 0.6816 (m-80) REVERT: C 233 MET cc_start: 0.7687 (pmm) cc_final: 0.7123 (ppp) REVERT: C 307 MET cc_start: 0.8017 (mpp) cc_final: 0.7760 (mpp) REVERT: C 389 MET cc_start: 0.8844 (tmm) cc_final: 0.8499 (tmm) REVERT: D 307 MET cc_start: 0.7135 (ppp) cc_final: 0.6846 (ppp) REVERT: D 389 MET cc_start: 0.8482 (tmm) cc_final: 0.8075 (tmm) REVERT: D 397 GLU cc_start: 0.8232 (pp20) cc_final: 0.7951 (pp20) REVERT: D 488 MET cc_start: 0.8661 (mmm) cc_final: 0.8123 (mmm) REVERT: E 153 ASN cc_start: 0.8695 (m110) cc_final: 0.8454 (m-40) REVERT: E 354 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8572 (mm-30) REVERT: E 389 MET cc_start: 0.8230 (tmm) cc_final: 0.7724 (tmm) REVERT: F 160 LYS cc_start: 0.9238 (ptmm) cc_final: 0.8949 (ptpp) REVERT: F 204 PHE cc_start: 0.8006 (m-80) cc_final: 0.7669 (m-80) REVERT: F 389 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.6341 (tpt) REVERT: G 59 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7663 (mm-30) REVERT: G 83 ASP cc_start: 0.7849 (m-30) cc_final: 0.7626 (m-30) REVERT: G 389 MET cc_start: 0.8280 (tpp) cc_final: 0.7729 (tpp) REVERT: G 398 ASP cc_start: 0.8566 (t0) cc_final: 0.8329 (t70) REVERT: H 389 MET cc_start: 0.9050 (tmm) cc_final: 0.8735 (tmm) REVERT: I 164 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8597 (pm20) REVERT: I 488 MET cc_start: 0.9287 (tpt) cc_final: 0.8899 (tpp) REVERT: K 267 MET cc_start: 0.6157 (mmp) cc_final: 0.5704 (mmt) REVERT: K 307 MET cc_start: 0.6747 (ppp) cc_final: 0.6243 (ppp) REVERT: L 231 ARG cc_start: 0.7497 (mtm180) cc_final: 0.7014 (mtt180) REVERT: L 233 MET cc_start: 0.8750 (pmm) cc_final: 0.8139 (pmm) REVERT: L 351 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8727 (mm-40) REVERT: M 199 TYR cc_start: 0.8338 (p90) cc_final: 0.7499 (p90) REVERT: M 389 MET cc_start: 0.8657 (tmm) cc_final: 0.8062 (tmm) REVERT: N 193 MET cc_start: 0.7896 (ptm) cc_final: 0.7529 (ptm) REVERT: N 288 MET cc_start: 0.7730 (mpp) cc_final: 0.7297 (mpp) REVERT: N 349 ILE cc_start: 0.9093 (mm) cc_final: 0.8875 (mt) outliers start: 52 outliers final: 28 residues processed: 444 average time/residue: 0.4862 time to fit residues: 375.5815 Evaluate side-chains 419 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 387 time to evaluate : 4.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 355 GLU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain L residue 351 GLN Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 354 GLU Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 473 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 657 optimal weight: 20.0000 chunk 499 optimal weight: 40.0000 chunk 345 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 317 optimal weight: 3.9990 chunk 446 optimal weight: 6.9990 chunk 667 optimal weight: 7.9990 chunk 706 optimal weight: 4.9990 chunk 348 optimal weight: 7.9990 chunk 632 optimal weight: 3.9990 chunk 190 optimal weight: 30.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 479 ASN ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 505 GLN ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 366 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 54520 Z= 0.272 Angle : 0.494 10.266 73621 Z= 0.267 Chirality : 0.040 0.165 8963 Planarity : 0.003 0.030 9649 Dihedral : 3.758 18.063 7759 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.20 % Favored : 98.78 % Rotamer: Outliers : 1.06 % Allowed : 10.08 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.10), residues: 7308 helix: 2.55 (0.08), residues: 4130 sheet: 0.52 (0.15), residues: 1139 loop : -0.36 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 401 PHE 0.020 0.001 PHE G 204 TYR 0.016 0.001 TYR C 203 ARG 0.005 0.000 ARG L 350 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 394 time to evaluate : 4.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.7650 (ptt) cc_final: 0.7018 (ppp) REVERT: A 321 LYS cc_start: 0.9321 (tmtt) cc_final: 0.9024 (tmtt) REVERT: B 16 MET cc_start: 0.8149 (mmm) cc_final: 0.7594 (mtp) REVERT: B 199 TYR cc_start: 0.8108 (p90) cc_final: 0.7818 (p90) REVERT: B 343 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8258 (mm-40) REVERT: B 389 MET cc_start: 0.8475 (tmm) cc_final: 0.7922 (tmm) REVERT: C 204 PHE cc_start: 0.7296 (m-80) cc_final: 0.6917 (m-80) REVERT: C 233 MET cc_start: 0.7651 (pmm) cc_final: 0.7227 (ppp) REVERT: C 307 MET cc_start: 0.8056 (mpp) cc_final: 0.7767 (mpp) REVERT: C 389 MET cc_start: 0.8878 (tmm) cc_final: 0.8527 (tmm) REVERT: D 59 GLU cc_start: 0.8026 (mp0) cc_final: 0.7657 (mp0) REVERT: D 307 MET cc_start: 0.7109 (ppp) cc_final: 0.6783 (ppp) REVERT: D 389 MET cc_start: 0.8501 (tmm) cc_final: 0.8081 (tmm) REVERT: D 397 GLU cc_start: 0.8238 (pp20) cc_final: 0.7949 (pp20) REVERT: E 153 ASN cc_start: 0.8713 (m110) cc_final: 0.8483 (m-40) REVERT: E 354 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8594 (mm-30) REVERT: E 389 MET cc_start: 0.8197 (tmm) cc_final: 0.7581 (tmm) REVERT: F 160 LYS cc_start: 0.9250 (ptmm) cc_final: 0.8958 (ptpp) REVERT: F 204 PHE cc_start: 0.7849 (m-80) cc_final: 0.7609 (m-80) REVERT: F 389 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6335 (tpt) REVERT: G 59 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7763 (mm-30) REVERT: G 83 ASP cc_start: 0.7854 (m-30) cc_final: 0.7572 (m-30) REVERT: G 111 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7725 (mtt) REVERT: G 389 MET cc_start: 0.8271 (tpp) cc_final: 0.7750 (tpp) REVERT: G 398 ASP cc_start: 0.8529 (t0) cc_final: 0.8215 (t70) REVERT: H 196 ASP cc_start: 0.8579 (m-30) cc_final: 0.8196 (p0) REVERT: I 488 MET cc_start: 0.9345 (tpt) cc_final: 0.8958 (tpp) REVERT: J 288 MET cc_start: 0.8547 (mpp) cc_final: 0.8241 (mpp) REVERT: K 237 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8382 (mt) REVERT: K 267 MET cc_start: 0.5968 (mmp) cc_final: 0.5541 (mmm) REVERT: K 307 MET cc_start: 0.6545 (ppp) cc_final: 0.6148 (ppp) REVERT: L 231 ARG cc_start: 0.7468 (mtm180) cc_final: 0.7039 (mtt180) REVERT: L 233 MET cc_start: 0.8641 (pmm) cc_final: 0.8068 (pmm) REVERT: M 389 MET cc_start: 0.8686 (tmm) cc_final: 0.8088 (tmm) REVERT: N 193 MET cc_start: 0.7901 (ptm) cc_final: 0.7531 (ptm) REVERT: N 288 MET cc_start: 0.7790 (mpp) cc_final: 0.7370 (mpp) REVERT: N 349 ILE cc_start: 0.9078 (mm) cc_final: 0.8784 (mt) REVERT: N 389 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8235 (tmm) outliers start: 60 outliers final: 32 residues processed: 431 average time/residue: 0.4787 time to fit residues: 358.7057 Evaluate side-chains 422 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 385 time to evaluate : 4.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain L residue 333 ILE Chi-restraints excluded: chain L residue 366 GLN Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 389 MET Chi-restraints excluded: chain N residue 473 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 588 optimal weight: 8.9990 chunk 401 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 526 optimal weight: 1.9990 chunk 291 optimal weight: 0.4980 chunk 602 optimal weight: 0.1980 chunk 488 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 360 optimal weight: 6.9990 chunk 634 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 479 ASN ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 54520 Z= 0.185 Angle : 0.474 8.958 73621 Z= 0.255 Chirality : 0.040 0.164 8963 Planarity : 0.002 0.029 9649 Dihedral : 3.724 16.886 7759 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.83 % Favored : 99.15 % Rotamer: Outliers : 1.17 % Allowed : 11.17 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.20 (0.10), residues: 7308 helix: 2.58 (0.08), residues: 4130 sheet: 0.51 (0.15), residues: 1136 loop : -0.34 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 401 PHE 0.013 0.001 PHE K 195 TYR 0.018 0.001 TYR C 203 ARG 0.004 0.000 ARG A 368 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 404 time to evaluate : 4.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.7705 (ptt) cc_final: 0.7201 (tmm) REVERT: A 321 LYS cc_start: 0.9324 (tmtt) cc_final: 0.9018 (tmtt) REVERT: B 16 MET cc_start: 0.8195 (mmm) cc_final: 0.7725 (mtp) REVERT: B 199 TYR cc_start: 0.8033 (p90) cc_final: 0.7713 (p90) REVERT: B 221 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8678 (mm) REVERT: B 343 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8330 (mm-40) REVERT: B 389 MET cc_start: 0.8493 (tmm) cc_final: 0.7981 (tmm) REVERT: C 204 PHE cc_start: 0.7284 (m-80) cc_final: 0.6875 (m-80) REVERT: C 233 MET cc_start: 0.7625 (pmm) cc_final: 0.7221 (ppp) REVERT: C 307 MET cc_start: 0.8102 (mpp) cc_final: 0.7796 (mpp) REVERT: C 389 MET cc_start: 0.8879 (tmm) cc_final: 0.8546 (tmm) REVERT: D 59 GLU cc_start: 0.8043 (mp0) cc_final: 0.7595 (mp0) REVERT: D 164 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8412 (pm20) REVERT: D 307 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6742 (ppp) REVERT: D 389 MET cc_start: 0.8495 (tmm) cc_final: 0.8055 (tmm) REVERT: D 397 GLU cc_start: 0.8230 (pp20) cc_final: 0.7949 (pp20) REVERT: E 153 ASN cc_start: 0.8695 (m110) cc_final: 0.8464 (m-40) REVERT: E 354 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8598 (mm-30) REVERT: E 389 MET cc_start: 0.8215 (tmm) cc_final: 0.7607 (tmm) REVERT: F 160 LYS cc_start: 0.9246 (ptmm) cc_final: 0.8949 (ptpp) REVERT: F 204 PHE cc_start: 0.7882 (m-80) cc_final: 0.7395 (m-10) REVERT: F 389 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6401 (tpt) REVERT: G 59 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7653 (mm-30) REVERT: G 83 ASP cc_start: 0.7838 (m-30) cc_final: 0.7558 (m-30) REVERT: G 111 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7704 (mtt) REVERT: G 389 MET cc_start: 0.8325 (tpp) cc_final: 0.7748 (tpp) REVERT: G 398 ASP cc_start: 0.8517 (t0) cc_final: 0.8183 (t70) REVERT: H 196 ASP cc_start: 0.8564 (m-30) cc_final: 0.8190 (p0) REVERT: H 389 MET cc_start: 0.9129 (tmm) cc_final: 0.8873 (tmm) REVERT: I 164 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8603 (pm20) REVERT: I 488 MET cc_start: 0.9348 (tpt) cc_final: 0.8989 (mmt) REVERT: J 288 MET cc_start: 0.8542 (mpp) cc_final: 0.8170 (mpp) REVERT: K 193 MET cc_start: 0.6348 (ppp) cc_final: 0.5651 (ppp) REVERT: K 267 MET cc_start: 0.6010 (mmp) cc_final: 0.5609 (mmm) REVERT: L 231 ARG cc_start: 0.7443 (mtm180) cc_final: 0.7003 (mtt180) REVERT: L 233 MET cc_start: 0.8627 (pmm) cc_final: 0.7968 (pmm) REVERT: L 350 ARG cc_start: 0.8887 (mmt90) cc_final: 0.8585 (mmt90) REVERT: L 351 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8205 (pt0) REVERT: M 111 MET cc_start: 0.8312 (mmt) cc_final: 0.7933 (mmm) REVERT: M 199 TYR cc_start: 0.8374 (p90) cc_final: 0.7430 (p90) REVERT: M 389 MET cc_start: 0.8694 (tmm) cc_final: 0.8081 (tmm) REVERT: N 193 MET cc_start: 0.7901 (ptm) cc_final: 0.7529 (ptm) REVERT: N 288 MET cc_start: 0.7810 (mpp) cc_final: 0.7395 (mpp) outliers start: 66 outliers final: 33 residues processed: 448 average time/residue: 0.4902 time to fit residues: 380.7268 Evaluate side-chains 428 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 388 time to evaluate : 4.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain F residue 389 MET Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 432 GLN Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 355 GLU Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain L residue 333 ILE Chi-restraints excluded: chain L residue 366 GLN Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 473 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 237 optimal weight: 5.9990 chunk 636 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 414 optimal weight: 6.9990 chunk 174 optimal weight: 30.0000 chunk 707 optimal weight: 7.9990 chunk 587 optimal weight: 10.0000 chunk 327 optimal weight: 30.0000 chunk 58 optimal weight: 7.9990 chunk 233 optimal weight: 30.0000 chunk 371 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 366 GLN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 479 ASN J 112 ASN J 351 GLN ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 366 GLN N 505 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 54520 Z= 0.358 Angle : 0.537 9.848 73621 Z= 0.286 Chirality : 0.042 0.172 8963 Planarity : 0.003 0.031 9649 Dihedral : 3.832 17.390 7759 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.45 % Favored : 98.54 % Rotamer: Outliers : 1.40 % Allowed : 12.02 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.09 (0.10), residues: 7308 helix: 2.51 (0.08), residues: 4104 sheet: 0.43 (0.15), residues: 1141 loop : -0.38 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 401 PHE 0.020 0.001 PHE A 204 TYR 0.019 0.001 TYR C 203 ARG 0.005 0.000 ARG L 350 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 395 time to evaluate : 4.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.9307 (tmtt) cc_final: 0.9018 (tmtt) REVERT: A 362 ARG cc_start: 0.8699 (mmt-90) cc_final: 0.8444 (mmt-90) REVERT: B 16 MET cc_start: 0.8332 (mmm) cc_final: 0.7974 (mtp) REVERT: B 199 TYR cc_start: 0.8094 (p90) cc_final: 0.7818 (p90) REVERT: B 221 LEU cc_start: 0.8947 (mt) cc_final: 0.8727 (mm) REVERT: B 343 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8314 (mm-40) REVERT: B 389 MET cc_start: 0.8486 (tmm) cc_final: 0.7964 (tmm) REVERT: B 520 MET cc_start: 0.8254 (mmm) cc_final: 0.7910 (mtt) REVERT: C 204 PHE cc_start: 0.7413 (m-80) cc_final: 0.6925 (m-80) REVERT: C 237 LEU cc_start: 0.7216 (tt) cc_final: 0.6840 (pp) REVERT: C 307 MET cc_start: 0.8097 (mpp) cc_final: 0.7759 (mpp) REVERT: C 389 MET cc_start: 0.8867 (tmm) cc_final: 0.8539 (tmm) REVERT: D 307 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6823 (ppp) REVERT: D 389 MET cc_start: 0.8529 (tmm) cc_final: 0.8095 (tmm) REVERT: D 397 GLU cc_start: 0.8242 (pp20) cc_final: 0.7960 (pp20) REVERT: D 488 MET cc_start: 0.8498 (tpp) cc_final: 0.7773 (mmm) REVERT: E 153 ASN cc_start: 0.8720 (m110) cc_final: 0.8505 (m-40) REVERT: E 199 TYR cc_start: 0.7754 (p90) cc_final: 0.7478 (p90) REVERT: E 354 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8603 (mm-30) REVERT: E 385 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.7980 (p) REVERT: E 389 MET cc_start: 0.8233 (tmm) cc_final: 0.7502 (tmm) REVERT: F 160 LYS cc_start: 0.9259 (ptmm) cc_final: 0.8965 (ptpp) REVERT: F 204 PHE cc_start: 0.7890 (m-80) cc_final: 0.7543 (m-10) REVERT: G 83 ASP cc_start: 0.7870 (m-30) cc_final: 0.7602 (m-30) REVERT: G 111 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7740 (mtt) REVERT: G 389 MET cc_start: 0.8273 (tpp) cc_final: 0.7725 (tpp) REVERT: H 196 ASP cc_start: 0.8581 (m-30) cc_final: 0.8185 (p0) REVERT: H 362 ARG cc_start: 0.8662 (ptp90) cc_final: 0.8410 (ptp90) REVERT: I 164 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8577 (pm20) REVERT: I 488 MET cc_start: 0.9375 (tpt) cc_final: 0.9065 (mmt) REVERT: J 288 MET cc_start: 0.8575 (mpp) cc_final: 0.8140 (mpp) REVERT: K 267 MET cc_start: 0.6071 (mmp) cc_final: 0.5648 (mmm) REVERT: K 488 MET cc_start: 0.8551 (mmm) cc_final: 0.8302 (mmm) REVERT: L 231 ARG cc_start: 0.7496 (mtm180) cc_final: 0.7038 (mtt180) REVERT: L 233 MET cc_start: 0.8612 (pmm) cc_final: 0.8142 (pmm) REVERT: M 111 MET cc_start: 0.8379 (mmt) cc_final: 0.7990 (mmm) REVERT: M 389 MET cc_start: 0.8671 (tmm) cc_final: 0.8062 (tmm) REVERT: N 193 MET cc_start: 0.7959 (ptm) cc_final: 0.7627 (ptm) REVERT: N 288 MET cc_start: 0.7849 (mpp) cc_final: 0.7397 (mpp) REVERT: N 389 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8221 (tmm) outliers start: 79 outliers final: 48 residues processed: 450 average time/residue: 0.4891 time to fit residues: 382.3419 Evaluate side-chains 438 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 384 time to evaluate : 4.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 351 GLN Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 355 GLU Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain L residue 272 LYS Chi-restraints excluded: chain L residue 333 ILE Chi-restraints excluded: chain L residue 366 GLN Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 288 MET Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 389 MET Chi-restraints excluded: chain N residue 473 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 681 optimal weight: 6.9990 chunk 79 optimal weight: 30.0000 chunk 402 optimal weight: 10.0000 chunk 516 optimal weight: 8.9990 chunk 400 optimal weight: 8.9990 chunk 595 optimal weight: 20.0000 chunk 394 optimal weight: 5.9990 chunk 704 optimal weight: 5.9990 chunk 440 optimal weight: 20.0000 chunk 429 optimal weight: 8.9990 chunk 325 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 HIS C 432 GLN D 194 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 ASN ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 479 ASN ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 366 GLN N 366 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 54520 Z= 0.384 Angle : 0.562 13.814 73621 Z= 0.299 Chirality : 0.042 0.172 8963 Planarity : 0.003 0.029 9649 Dihedral : 3.914 18.442 7759 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.41 % Favored : 98.58 % Rotamer: Outliers : 1.40 % Allowed : 12.80 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.96 (0.10), residues: 7308 helix: 2.43 (0.08), residues: 4102 sheet: 0.27 (0.15), residues: 1219 loop : -0.43 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 401 PHE 0.013 0.001 PHE G 195 TYR 0.015 0.001 TYR K 506 ARG 0.005 0.000 ARG J 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 390 time to evaluate : 4.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.9292 (tmtt) cc_final: 0.8989 (tmtt) REVERT: A 398 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8223 (p0) REVERT: B 16 MET cc_start: 0.8393 (mmm) cc_final: 0.8055 (mtp) REVERT: B 199 TYR cc_start: 0.8125 (p90) cc_final: 0.7881 (p90) REVERT: B 221 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8688 (mm) REVERT: B 389 MET cc_start: 0.8488 (tmm) cc_final: 0.7963 (tmm) REVERT: C 204 PHE cc_start: 0.7599 (m-80) cc_final: 0.7101 (m-80) REVERT: C 233 MET cc_start: 0.7619 (pmm) cc_final: 0.6674 (ppp) REVERT: C 237 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6847 (pp) REVERT: C 307 MET cc_start: 0.8084 (mpp) cc_final: 0.7727 (mpp) REVERT: C 389 MET cc_start: 0.8858 (tmm) cc_final: 0.8530 (tmm) REVERT: D 59 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: D 307 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6950 (ppp) REVERT: D 385 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8035 (p) REVERT: D 389 MET cc_start: 0.8517 (tmm) cc_final: 0.8095 (tmm) REVERT: D 397 GLU cc_start: 0.8259 (pp20) cc_final: 0.7969 (pp20) REVERT: D 488 MET cc_start: 0.8522 (tpp) cc_final: 0.7918 (mmm) REVERT: E 153 ASN cc_start: 0.8737 (m110) cc_final: 0.8522 (m-40) REVERT: E 354 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8596 (mm-30) REVERT: E 385 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.8006 (p) REVERT: E 389 MET cc_start: 0.8267 (tmm) cc_final: 0.7541 (tmm) REVERT: F 160 LYS cc_start: 0.9247 (ptmm) cc_final: 0.8947 (ptpp) REVERT: F 204 PHE cc_start: 0.8047 (m-80) cc_final: 0.7476 (m-10) REVERT: G 83 ASP cc_start: 0.7958 (m-30) cc_final: 0.7687 (m-30) REVERT: G 111 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7746 (mtt) REVERT: G 389 MET cc_start: 0.8275 (tpp) cc_final: 0.8009 (tpp) REVERT: H 196 ASP cc_start: 0.8613 (m-30) cc_final: 0.8177 (p0) REVERT: H 362 ARG cc_start: 0.8683 (ptp90) cc_final: 0.8408 (ptp90) REVERT: I 164 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8592 (pm20) REVERT: I 488 MET cc_start: 0.9375 (tpt) cc_final: 0.9051 (mmt) REVERT: J 288 MET cc_start: 0.8576 (mpp) cc_final: 0.8097 (mpp) REVERT: K 267 MET cc_start: 0.6094 (mmp) cc_final: 0.5670 (mmm) REVERT: K 488 MET cc_start: 0.8562 (mmm) cc_final: 0.8299 (mmm) REVERT: L 231 ARG cc_start: 0.7352 (mtm180) cc_final: 0.6979 (mtt180) REVERT: L 233 MET cc_start: 0.8609 (pmm) cc_final: 0.8136 (pmm) REVERT: M 111 MET cc_start: 0.8387 (mmt) cc_final: 0.7998 (mmm) REVERT: M 199 TYR cc_start: 0.8592 (p90) cc_final: 0.7497 (p90) REVERT: M 389 MET cc_start: 0.8696 (tmm) cc_final: 0.8080 (tmm) REVERT: M 398 ASP cc_start: 0.8297 (p0) cc_final: 0.8061 (p0) REVERT: N 193 MET cc_start: 0.7983 (ptm) cc_final: 0.7652 (ptm) REVERT: N 288 MET cc_start: 0.7850 (mpp) cc_final: 0.7387 (mpp) REVERT: N 389 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8226 (tmm) outliers start: 79 outliers final: 49 residues processed: 442 average time/residue: 0.4893 time to fit residues: 375.8844 Evaluate side-chains 439 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 379 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain J residue 37 ASN Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 355 GLU Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain L residue 272 LYS Chi-restraints excluded: chain L residue 333 ILE Chi-restraints excluded: chain L residue 366 GLN Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 288 MET Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 389 MET Chi-restraints excluded: chain N residue 473 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 435 optimal weight: 6.9990 chunk 281 optimal weight: 8.9990 chunk 420 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 447 optimal weight: 20.0000 chunk 480 optimal weight: 1.9990 chunk 348 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 553 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN D 194 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 479 ASN ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 366 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 54520 Z= 0.335 Angle : 0.547 13.653 73621 Z= 0.290 Chirality : 0.041 0.173 8963 Planarity : 0.003 0.030 9649 Dihedral : 3.925 18.922 7759 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.44 % Favored : 98.55 % Rotamer: Outliers : 1.29 % Allowed : 13.45 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.93 (0.10), residues: 7308 helix: 2.38 (0.08), residues: 4128 sheet: 0.27 (0.15), residues: 1219 loop : -0.44 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.015 0.001 PHE B 204 TYR 0.014 0.001 TYR K 506 ARG 0.011 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 387 time to evaluate : 4.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.9290 (tmtt) cc_final: 0.8986 (tmtt) REVERT: A 362 ARG cc_start: 0.8687 (mmt-90) cc_final: 0.8426 (mmt-90) REVERT: A 398 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8217 (p0) REVERT: B 199 TYR cc_start: 0.8120 (p90) cc_final: 0.7906 (p90) REVERT: B 343 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8089 (mm110) REVERT: C 204 PHE cc_start: 0.7669 (m-80) cc_final: 0.7129 (m-80) REVERT: C 233 MET cc_start: 0.7703 (pmm) cc_final: 0.6814 (ppp) REVERT: C 237 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6849 (pp) REVERT: C 307 MET cc_start: 0.8096 (mpp) cc_final: 0.7740 (mpp) REVERT: C 389 MET cc_start: 0.8854 (tmm) cc_final: 0.8531 (tmm) REVERT: D 59 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: D 307 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6968 (ppp) REVERT: D 372 LEU cc_start: 0.9041 (tt) cc_final: 0.8763 (mp) REVERT: D 385 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8030 (p) REVERT: D 389 MET cc_start: 0.8519 (tmm) cc_final: 0.8117 (tmm) REVERT: D 397 GLU cc_start: 0.8253 (pp20) cc_final: 0.7964 (pp20) REVERT: E 153 ASN cc_start: 0.8747 (m110) cc_final: 0.8529 (m-40) REVERT: E 354 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8600 (mm-30) REVERT: E 385 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.8008 (p) REVERT: E 389 MET cc_start: 0.8313 (tmm) cc_final: 0.7596 (tmm) REVERT: F 160 LYS cc_start: 0.9254 (ptmm) cc_final: 0.8951 (ptpp) REVERT: F 204 PHE cc_start: 0.7963 (m-80) cc_final: 0.7584 (m-10) REVERT: G 83 ASP cc_start: 0.7805 (m-30) cc_final: 0.7520 (m-30) REVERT: G 111 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7743 (mtt) REVERT: G 389 MET cc_start: 0.8277 (tpp) cc_final: 0.7684 (tpp) REVERT: H 196 ASP cc_start: 0.8594 (m-30) cc_final: 0.8140 (p0) REVERT: H 362 ARG cc_start: 0.8708 (ptp90) cc_final: 0.8437 (ptp90) REVERT: I 164 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8580 (pm20) REVERT: I 488 MET cc_start: 0.9373 (tpt) cc_final: 0.9065 (mmt) REVERT: J 288 MET cc_start: 0.8594 (mpp) cc_final: 0.8101 (mpp) REVERT: K 72 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8307 (mp10) REVERT: K 267 MET cc_start: 0.6099 (mmp) cc_final: 0.5715 (mmm) REVERT: K 351 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: K 488 MET cc_start: 0.8539 (mmm) cc_final: 0.8243 (mmm) REVERT: L 231 ARG cc_start: 0.7351 (mtm180) cc_final: 0.6970 (mtt180) REVERT: L 233 MET cc_start: 0.8553 (pmm) cc_final: 0.8069 (pmm) REVERT: M 199 TYR cc_start: 0.8609 (p90) cc_final: 0.7478 (p90) REVERT: M 389 MET cc_start: 0.8715 (tmm) cc_final: 0.8115 (tmm) REVERT: M 398 ASP cc_start: 0.8271 (p0) cc_final: 0.8030 (p0) REVERT: N 193 MET cc_start: 0.7983 (ptm) cc_final: 0.7653 (ptm) REVERT: N 288 MET cc_start: 0.7849 (mpp) cc_final: 0.7402 (mpp) REVERT: N 389 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8228 (tmm) outliers start: 73 outliers final: 51 residues processed: 435 average time/residue: 0.4844 time to fit residues: 366.6119 Evaluate side-chains 445 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 382 time to evaluate : 4.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 193 MET Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 37 ASN Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 351 GLN Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain L residue 272 LYS Chi-restraints excluded: chain L residue 333 ILE Chi-restraints excluded: chain L residue 366 GLN Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 288 MET Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 389 MET Chi-restraints excluded: chain N residue 473 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 640 optimal weight: 10.0000 chunk 674 optimal weight: 0.9990 chunk 615 optimal weight: 0.4980 chunk 656 optimal weight: 20.0000 chunk 395 optimal weight: 10.0000 chunk 286 optimal weight: 7.9990 chunk 515 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 chunk 593 optimal weight: 0.9990 chunk 620 optimal weight: 6.9990 chunk 654 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN D 194 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 184 GLN J 112 ASN ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 290 GLN L 366 GLN N 505 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 54520 Z= 0.178 Angle : 0.504 13.287 73621 Z= 0.267 Chirality : 0.040 0.189 8963 Planarity : 0.003 0.030 9649 Dihedral : 3.819 19.533 7759 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.94 % Favored : 99.04 % Rotamer: Outliers : 0.99 % Allowed : 14.00 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.10), residues: 7308 helix: 2.50 (0.08), residues: 4141 sheet: 0.34 (0.16), residues: 1064 loop : -0.45 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 401 PHE 0.012 0.001 PHE K 195 TYR 0.013 0.001 TYR E 199 ARG 0.002 0.000 ARG A 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 404 time to evaluate : 4.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.7794 (ptt) cc_final: 0.7125 (ppp) REVERT: A 321 LYS cc_start: 0.9309 (tmtt) cc_final: 0.9006 (tmtt) REVERT: A 362 ARG cc_start: 0.8746 (mmt-90) cc_final: 0.8526 (mmt-90) REVERT: B 389 MET cc_start: 0.8461 (tmm) cc_final: 0.7837 (tmm) REVERT: C 204 PHE cc_start: 0.7590 (m-80) cc_final: 0.7065 (m-80) REVERT: C 233 MET cc_start: 0.7817 (pmm) cc_final: 0.7262 (ppp) REVERT: C 307 MET cc_start: 0.8144 (mpp) cc_final: 0.7826 (mpp) REVERT: C 389 MET cc_start: 0.8869 (tmm) cc_final: 0.8576 (tmm) REVERT: D 59 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: D 307 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7018 (ppp) REVERT: D 372 LEU cc_start: 0.9041 (tt) cc_final: 0.8740 (mp) REVERT: D 389 MET cc_start: 0.8528 (tmm) cc_final: 0.8117 (tmm) REVERT: D 397 GLU cc_start: 0.8225 (pp20) cc_final: 0.7965 (pp20) REVERT: E 153 ASN cc_start: 0.8714 (m110) cc_final: 0.8488 (m-40) REVERT: E 354 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8573 (mm-30) REVERT: E 385 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.7997 (p) REVERT: E 389 MET cc_start: 0.8360 (tmm) cc_final: 0.7696 (tmm) REVERT: F 160 LYS cc_start: 0.9246 (ptmm) cc_final: 0.8934 (ptpp) REVERT: F 204 PHE cc_start: 0.7993 (m-80) cc_final: 0.7446 (m-10) REVERT: G 83 ASP cc_start: 0.7782 (m-30) cc_final: 0.7529 (m-30) REVERT: G 111 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7714 (mtt) REVERT: G 389 MET cc_start: 0.8359 (tpp) cc_final: 0.7714 (tpp) REVERT: H 196 ASP cc_start: 0.8561 (m-30) cc_final: 0.8172 (p0) REVERT: H 362 ARG cc_start: 0.8726 (ptp90) cc_final: 0.8460 (ptp90) REVERT: H 389 MET cc_start: 0.8932 (tmt) cc_final: 0.8598 (tmm) REVERT: I 164 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8557 (pm20) REVERT: I 488 MET cc_start: 0.9359 (tpt) cc_final: 0.9046 (mmt) REVERT: J 288 MET cc_start: 0.8615 (mpp) cc_final: 0.8121 (mpp) REVERT: K 193 MET cc_start: 0.6415 (ppp) cc_final: 0.5854 (ppp) REVERT: K 267 MET cc_start: 0.6058 (mmp) cc_final: 0.5741 (mmm) REVERT: K 488 MET cc_start: 0.8535 (mmm) cc_final: 0.8312 (mmm) REVERT: L 231 ARG cc_start: 0.7441 (mtm180) cc_final: 0.7012 (mtt180) REVERT: L 233 MET cc_start: 0.8591 (pmm) cc_final: 0.8115 (pmm) REVERT: M 111 MET cc_start: 0.8303 (mmt) cc_final: 0.7918 (mmm) REVERT: M 199 TYR cc_start: 0.8507 (p90) cc_final: 0.7487 (p90) REVERT: M 389 MET cc_start: 0.8728 (tmm) cc_final: 0.8125 (tmm) REVERT: M 398 ASP cc_start: 0.8186 (p0) cc_final: 0.7948 (p0) REVERT: N 69 MET cc_start: 0.8086 (mtt) cc_final: 0.7711 (mtp) REVERT: N 193 MET cc_start: 0.7938 (ptm) cc_final: 0.7620 (ptm) REVERT: N 288 MET cc_start: 0.7836 (mpp) cc_final: 0.7401 (mpp) REVERT: N 389 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8233 (tmm) outliers start: 56 outliers final: 40 residues processed: 446 average time/residue: 0.4857 time to fit residues: 374.8269 Evaluate side-chains 433 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 386 time to evaluate : 4.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain J residue 37 ASN Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 288 MET Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 387 VAL Chi-restraints excluded: chain N residue 389 MET Chi-restraints excluded: chain N residue 473 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 431 optimal weight: 3.9990 chunk 694 optimal weight: 9.9990 chunk 423 optimal weight: 1.9990 chunk 329 optimal weight: 6.9990 chunk 482 optimal weight: 9.9990 chunk 728 optimal weight: 40.0000 chunk 670 optimal weight: 1.9990 chunk 579 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 447 optimal weight: 0.4980 chunk 355 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN D 194 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 479 ASN ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 54520 Z= 0.170 Angle : 0.502 13.275 73621 Z= 0.267 Chirality : 0.040 0.189 8963 Planarity : 0.003 0.030 9649 Dihedral : 3.759 17.148 7759 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.00 % Favored : 98.99 % Rotamer: Outliers : 0.95 % Allowed : 14.34 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.05 (0.10), residues: 7308 helix: 2.52 (0.08), residues: 4141 sheet: 0.14 (0.16), residues: 1083 loop : -0.36 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS M 401 PHE 0.019 0.001 PHE G 204 TYR 0.027 0.001 TYR C 203 ARG 0.008 0.000 ARG C 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 402 time to evaluate : 4.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 MET cc_start: 0.7773 (ptt) cc_final: 0.7117 (ppp) REVERT: A 321 LYS cc_start: 0.9313 (tmtt) cc_final: 0.9004 (tmtt) REVERT: A 362 ARG cc_start: 0.8758 (mmt-90) cc_final: 0.8538 (mmt-90) REVERT: A 398 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8199 (p0) REVERT: B 389 MET cc_start: 0.8407 (tmm) cc_final: 0.7764 (tmm) REVERT: C 204 PHE cc_start: 0.7591 (m-80) cc_final: 0.7123 (m-80) REVERT: C 233 MET cc_start: 0.7787 (pmm) cc_final: 0.6969 (ppp) REVERT: C 237 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6836 (pp) REVERT: C 307 MET cc_start: 0.8077 (mpp) cc_final: 0.7746 (mpp) REVERT: C 389 MET cc_start: 0.8879 (tmm) cc_final: 0.8592 (tmm) REVERT: D 59 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: D 307 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6983 (ppp) REVERT: D 372 LEU cc_start: 0.9055 (tt) cc_final: 0.8737 (mp) REVERT: D 385 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8016 (p) REVERT: D 389 MET cc_start: 0.8520 (tmm) cc_final: 0.8083 (tmm) REVERT: D 397 GLU cc_start: 0.8219 (pp20) cc_final: 0.7967 (pp20) REVERT: E 153 ASN cc_start: 0.8694 (m110) cc_final: 0.8466 (m-40) REVERT: E 354 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8558 (mm-30) REVERT: E 385 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.8050 (p) REVERT: E 389 MET cc_start: 0.8355 (tmm) cc_final: 0.7672 (tmm) REVERT: F 160 LYS cc_start: 0.9252 (ptmm) cc_final: 0.8893 (ptpp) REVERT: F 204 PHE cc_start: 0.7842 (m-80) cc_final: 0.7517 (m-10) REVERT: G 83 ASP cc_start: 0.7745 (m-30) cc_final: 0.7478 (m-30) REVERT: G 111 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7717 (mtt) REVERT: G 389 MET cc_start: 0.8370 (tpp) cc_final: 0.7721 (tpp) REVERT: H 196 ASP cc_start: 0.8554 (m-30) cc_final: 0.8165 (p0) REVERT: H 233 MET cc_start: 0.7827 (pmm) cc_final: 0.7188 (pmm) REVERT: H 362 ARG cc_start: 0.8727 (ptp90) cc_final: 0.8462 (ptp90) REVERT: I 164 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8577 (pm20) REVERT: I 488 MET cc_start: 0.9351 (tpt) cc_final: 0.9021 (mmt) REVERT: J 288 MET cc_start: 0.8623 (mpp) cc_final: 0.8124 (mpp) REVERT: K 193 MET cc_start: 0.6452 (ppp) cc_final: 0.5898 (ppp) REVERT: K 267 MET cc_start: 0.6045 (mmp) cc_final: 0.5742 (mmm) REVERT: K 488 MET cc_start: 0.8501 (mmm) cc_final: 0.8294 (mmm) REVERT: L 231 ARG cc_start: 0.7450 (mtm180) cc_final: 0.7100 (mtt180) REVERT: L 233 MET cc_start: 0.8589 (pmm) cc_final: 0.8122 (pmm) REVERT: M 111 MET cc_start: 0.8289 (mmt) cc_final: 0.7908 (mmm) REVERT: M 199 TYR cc_start: 0.8511 (p90) cc_final: 0.7501 (p90) REVERT: M 389 MET cc_start: 0.8734 (tmm) cc_final: 0.8126 (tmm) REVERT: M 398 ASP cc_start: 0.8153 (p0) cc_final: 0.7901 (p0) REVERT: N 69 MET cc_start: 0.8066 (mtt) cc_final: 0.7727 (mtp) REVERT: N 193 MET cc_start: 0.7943 (ptm) cc_final: 0.7612 (ptm) REVERT: N 288 MET cc_start: 0.7886 (mpp) cc_final: 0.7435 (mpp) REVERT: N 389 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8229 (tmm) outliers start: 54 outliers final: 39 residues processed: 443 average time/residue: 0.4816 time to fit residues: 370.8788 Evaluate side-chains 444 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 395 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 352 GLN Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 59 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain H residue 234 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 249 ILE Chi-restraints excluded: chain I residue 381 VAL Chi-restraints excluded: chain J residue 37 ASN Chi-restraints excluded: chain J residue 378 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 401 HIS Chi-restraints excluded: chain K residue 411 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain M residue 169 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 240 VAL Chi-restraints excluded: chain M residue 317 LEU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 385 THR Chi-restraints excluded: chain N residue 387 VAL Chi-restraints excluded: chain N residue 389 MET Chi-restraints excluded: chain N residue 473 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 460 optimal weight: 0.3980 chunk 617 optimal weight: 1.9990 chunk 177 optimal weight: 0.3980 chunk 534 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 580 optimal weight: 3.9990 chunk 243 optimal weight: 9.9990 chunk 596 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN D 194 GLN ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN ** E 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 479 ASN ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.098832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067968 restraints weight = 139140.193| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.91 r_work: 0.2943 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 54520 Z= 0.200 Angle : 0.513 13.044 73621 Z= 0.270 Chirality : 0.040 0.181 8963 Planarity : 0.003 0.031 9649 Dihedral : 3.753 17.196 7759 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.12 % Favored : 98.86 % Rotamer: Outliers : 1.04 % Allowed : 14.37 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.10), residues: 7308 helix: 2.51 (0.08), residues: 4141 sheet: 0.15 (0.16), residues: 1099 loop : -0.36 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 401 PHE 0.021 0.001 PHE G 204 TYR 0.043 0.001 TYR C 203 ARG 0.003 0.000 ARG A 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8815.00 seconds wall clock time: 158 minutes 14.49 seconds (9494.49 seconds total)