Starting phenix.real_space_refine on Mon Mar 11 04:45:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba7_15939/03_2024/8ba7_15939.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba7_15939/03_2024/8ba7_15939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba7_15939/03_2024/8ba7_15939.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba7_15939/03_2024/8ba7_15939.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba7_15939/03_2024/8ba7_15939.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ba7_15939/03_2024/8ba7_15939.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 280 5.16 5 C 33558 2.51 5 N 9310 2.21 5 O 10822 1.98 5 H 55706 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 115": "OD1" <-> "OD2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E ASP 121": "OD1" <-> "OD2" Residue "F PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 196": "OD1" <-> "OD2" Residue "I TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 67": "OE1" <-> "OE2" Residue "M ASP 83": "OD1" <-> "OD2" Residue "M TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 109676 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7834 Classifications: {'peptide': 524} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "B" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7834 Classifications: {'peptide': 524} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "C" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7834 Classifications: {'peptide': 524} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "D" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7834 Classifications: {'peptide': 524} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "E" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7834 Classifications: {'peptide': 524} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "F" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7834 Classifications: {'peptide': 524} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "G" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7834 Classifications: {'peptide': 524} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "H" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7834 Classifications: {'peptide': 524} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "I" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7834 Classifications: {'peptide': 524} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "J" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7834 Classifications: {'peptide': 524} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "K" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7834 Classifications: {'peptide': 524} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "L" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7834 Classifications: {'peptide': 524} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "M" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7834 Classifications: {'peptide': 524} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "N" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 7834 Classifications: {'peptide': 524} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Time building chain proxies: 30.10, per 1000 atoms: 0.27 Number of scatterers: 109676 At special positions: 0 Unit cell: (160.8, 160.8, 162.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 280 16.00 O 10822 8.00 N 9310 7.00 C 33558 6.00 H 55706 1.00 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: 63.42 Conformation dependent library (CDL) restraints added in 7.4 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: 13272 Finding SS restraints... Secondary structure from input PDB file: 310 helices and 84 sheets defined 61.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.82 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 64 through 86 removed outlier: 3.703A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 110 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 169 removed outlier: 3.863A pdb=" N GLY A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.812A pdb=" N LYS A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.572A pdb=" N ARG A 368 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 410 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 433 through 447 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 497 through 516 Processing helix chain 'B' and resid 9 through 28 removed outlier: 3.833A pdb=" N GLY B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 64 through 79 removed outlier: 3.882A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 Processing helix chain 'B' and resid 88 through 109 removed outlier: 3.745A pdb=" N GLU B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 255 through 269 Processing helix chain 'B' and resid 281 through 297 removed outlier: 3.589A pdb=" N LYS B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 358 through 375 removed outlier: 3.930A pdb=" N GLY B 375 " --> pdb=" O LYS B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 410 removed outlier: 3.671A pdb=" N GLU B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 433 through 447 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 461 through 472 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: 4.065A pdb=" N LYS C 15 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 64 through 86 removed outlier: 3.828A pdb=" N LYS C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 110 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 233 through 244 removed outlier: 3.793A pdb=" N ALA C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 269 Processing helix chain 'C' and resid 281 through 297 removed outlier: 3.593A pdb=" N LYS C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) 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 removed outlier: 3.538A pdb=" N ARG C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 410 removed outlier: 4.116A pdb=" N LYS C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 426 Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing helix chain 'C' and resid 433 through 447 removed outlier: 3.653A pdb=" N MET C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 461 through 472 Processing helix chain 'C' and resid 496 through 516 Processing helix chain 'D' and resid 9 through 28 removed outlier: 4.661A pdb=" N LYS D 15 " --> pdb=" O ASP D 11 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 52 through 59 Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.705A pdb=" N LYS D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA D 81 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 110 Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 139 through 152 removed outlier: 3.770A pdb=" N ALA D 143 " --> pdb=" O SER D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 169 Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 281 through 297 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 358 through 374 Processing helix chain 'D' and resid 385 through 410 Processing helix chain 'D' and resid 416 through 426 Processing helix chain 'D' and resid 433 through 448 Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.933A pdb=" N ARG D 452 " --> pdb=" O GLU D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 472 removed outlier: 3.725A pdb=" N VAL D 465 " --> pdb=" O GLU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 516 Processing helix chain 'E' and resid 9 through 28 removed outlier: 4.155A pdb=" N LYS E 15 " --> pdb=" O ASP E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 52 through 60 Processing helix chain 'E' and resid 64 through 86 removed outlier: 3.811A pdb=" N LYS E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA E 81 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 109 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 232 through 244 removed outlier: 4.421A pdb=" N VAL E 236 " --> pdb=" O GLU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 281 through 297 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 358 through 373 Processing helix chain 'E' and resid 385 through 410 Processing helix chain 'E' and resid 416 through 426 removed outlier: 3.765A pdb=" N ILE E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS E 425 " --> pdb=" O ARG E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 497 through 516 Processing helix chain 'F' and resid 9 through 28 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 86 removed outlier: 3.838A pdb=" N LYS F 80 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA F 81 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 109 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 169 removed outlier: 3.578A pdb=" N GLY F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) 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 255 through 269 Processing helix chain 'F' and resid 281 through 297 Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 308 through 312 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 426 Processing helix chain 'F' and resid 433 through 447 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 497 through 516 Processing helix chain 'G' and resid 9 through 29 removed outlier: 4.235A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 60 Processing helix chain 'G' and resid 64 through 86 removed outlier: 3.593A pdb=" N LYS G 80 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 110 removed outlier: 3.894A pdb=" N GLU G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) 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 Processing helix chain 'G' and resid 201 through 205 Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 255 through 269 Processing helix chain 'G' and resid 281 through 297 Processing helix chain 'G' and resid 308 through 312 removed outlier: 3.771A pdb=" N ALA G 312 " --> pdb=" O LEU G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 358 through 375 removed outlier: 3.953A pdb=" N GLY G 375 " --> pdb=" O LYS G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 410 Processing helix chain 'G' and resid 416 through 426 Processing helix chain 'G' and resid 433 through 447 Processing helix chain 'G' and resid 448 through 459 removed outlier: 3.502A pdb=" N ARG G 452 " --> pdb=" O GLU G 448 " (cutoff:3.500A) 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 removed outlier: 3.612A pdb=" N THR G 516 " --> pdb=" O GLY G 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 28 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 52 through 59 Processing helix chain 'H' and resid 64 through 86 removed outlier: 3.514A pdb=" N ALA H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) 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 169 Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 207 through 210 Processing helix chain 'H' and resid 233 through 244 Processing helix chain 'H' and resid 255 through 269 Processing helix chain 'H' and resid 281 through 297 Processing helix chain 'H' and resid 308 through 312 Processing helix chain 'H' and resid 338 through 356 Processing helix chain 'H' and resid 358 through 374 Processing helix chain 'H' and resid 385 through 409 Processing helix chain 'H' and resid 416 through 426 Processing helix chain 'H' and resid 433 through 448 removed outlier: 3.746A pdb=" N GLU H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 448 through 459 Processing helix chain 'H' and resid 461 through 472 removed outlier: 3.870A pdb=" N VAL H 465 " --> pdb=" O GLU H 461 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY H 472 " --> pdb=" O THR H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 516 removed outlier: 3.661A pdb=" N THR H 500 " --> pdb=" O PRO H 496 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 29 removed outlier: 4.172A pdb=" N LYS I 15 " --> pdb=" O ASP I 11 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 60 Processing helix chain 'I' and resid 64 through 86 removed outlier: 3.933A pdb=" N LYS I 80 " --> pdb=" O GLU I 76 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 110 removed outlier: 3.679A pdb=" N GLU I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) 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 169 removed outlier: 3.720A 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 233 through 244 Processing helix chain 'I' and resid 255 through 268 Processing helix chain 'I' and resid 281 through 297 Processing helix chain 'I' and resid 338 through 356 Processing helix chain 'I' and resid 358 through 375 removed outlier: 4.155A pdb=" N ARG I 368 " --> pdb=" O LYS I 364 " (cutoff:3.500A) removed outlier: 3.834A 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: 3.662A pdb=" N LYS I 425 " --> pdb=" O ARG I 421 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU I 426 " --> pdb=" O VAL I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 448 removed outlier: 3.748A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) Processing helix chain 'I' and resid 448 through 459 Processing helix chain 'I' and resid 461 through 472 Processing helix chain 'I' and resid 488 through 492 Processing helix chain 'I' and resid 497 through 516 Processing helix chain 'J' and resid 9 through 29 removed outlier: 4.377A pdb=" N LYS J 15 " --> pdb=" O ASP J 11 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 60 Processing helix chain 'J' and resid 64 through 86 removed outlier: 3.709A pdb=" N LYS J 80 " --> pdb=" O GLU J 76 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA J 81 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 110 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 169 Processing helix chain 'J' and resid 201 through 205 Processing helix chain 'J' and resid 229 through 244 removed outlier: 3.962A pdb=" N MET J 233 " --> pdb=" O ASN J 229 " (cutoff:3.500A) Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 255 through 269 Processing helix chain 'J' and resid 282 through 297 Processing helix chain 'J' and resid 308 through 312 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 409 Processing helix chain 'J' and resid 416 through 426 Processing helix chain 'J' and resid 433 through 447 Processing helix chain 'J' and resid 448 through 459 Processing helix chain 'J' and resid 461 through 472 Processing helix chain 'J' and resid 488 through 492 Processing helix chain 'J' and resid 496 through 516 removed outlier: 3.820A pdb=" N THR J 500 " --> pdb=" O PRO J 496 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR J 516 " --> pdb=" O GLY J 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 29 removed outlier: 3.860A pdb=" N LYS K 15 " --> pdb=" O ASP K 11 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY K 19 " --> pdb=" O LYS K 15 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 60 Processing helix chain 'K' and resid 64 through 86 removed outlier: 3.620A pdb=" N VAL K 74 " --> pdb=" O GLY K 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA K 81 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 109 removed outlier: 3.694A pdb=" N GLU K 102 " --> pdb=" O ALA K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 Processing helix chain 'K' and resid 201 through 205 Processing helix chain 'K' and resid 229 through 232 Processing helix chain 'K' and resid 233 through 244 Processing helix chain 'K' and resid 255 through 268 Processing helix chain 'K' and resid 281 through 297 Processing helix chain 'K' and resid 308 through 312 removed outlier: 3.648A pdb=" N ALA K 312 " --> pdb=" O LEU K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 356 Processing helix chain 'K' and resid 358 through 375 Processing helix chain 'K' and resid 385 through 410 Processing helix chain 'K' and resid 416 through 426 removed outlier: 3.626A pdb=" N ILE K 420 " --> pdb=" O GLY K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 448 removed outlier: 3.688A pdb=" N GLU K 448 " --> pdb=" O LEU K 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 448 through 459 Processing helix chain 'K' and resid 461 through 472 Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 497 through 516 removed outlier: 3.757A pdb=" N THR K 516 " --> pdb=" O GLY K 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 29 removed outlier: 4.060A pdb=" N LYS L 15 " --> pdb=" O ASP L 11 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 60 Processing helix chain 'L' and resid 64 through 86 removed outlier: 3.688A pdb=" N LYS L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA L 81 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN L 82 " --> pdb=" O ALA L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 110 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 244 removed outlier: 3.972A pdb=" N MET L 233 " --> pdb=" O ASN L 229 " (cutoff:3.500A) Proline residue: L 235 - end of helix Processing helix chain 'L' and resid 255 through 269 Processing helix chain 'L' and resid 281 through 297 Processing helix chain 'L' and resid 308 through 312 Processing helix chain 'L' and resid 313 through 317 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 removed outlier: 4.204A pdb=" N GLU L 408 " --> pdb=" O ARG L 404 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU L 409 " --> pdb=" O ALA L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 426 Processing helix chain 'L' and resid 433 through 448 Processing helix chain 'L' and resid 448 through 459 removed outlier: 3.709A pdb=" N ARG L 452 " --> pdb=" O GLU L 448 " (cutoff:3.500A) 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: 4.268A pdb=" N LYS M 15 " --> pdb=" O ASP M 11 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 59 removed outlier: 3.633A pdb=" N GLU M 59 " --> pdb=" O SER M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 86 removed outlier: 3.744A pdb=" N VAL M 74 " --> pdb=" O GLY M 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS M 80 " --> pdb=" O GLU M 76 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA M 81 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN M 82 " --> pdb=" O ALA M 78 " (cutoff:3.500A) 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 255 through 269 Processing helix chain 'M' and resid 281 through 297 Processing helix chain 'M' and resid 308 through 312 Processing helix chain 'M' and resid 338 through 356 Processing helix chain 'M' and resid 358 through 374 Processing helix chain 'M' and resid 385 through 409 Processing helix chain 'M' and resid 416 through 426 Processing helix chain 'M' and resid 433 through 447 Processing helix chain 'M' and resid 448 through 459 Processing helix chain 'M' and resid 463 through 472 Processing helix chain 'M' and resid 488 through 492 Processing helix chain 'M' and resid 497 through 516 removed outlier: 4.042A pdb=" N LEU M 504 " --> pdb=" O THR M 500 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 29 removed outlier: 4.371A pdb=" N VAL N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 60 Processing helix chain 'N' and resid 64 through 86 removed outlier: 3.597A pdb=" N VAL N 74 " --> pdb=" O GLY N 70 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS N 80 " --> pdb=" O GLU N 76 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA N 81 " --> pdb=" O VAL N 77 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN N 82 " --> pdb=" O ALA N 78 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP N 83 " --> pdb=" O SER N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 110 removed outlier: 3.910A pdb=" N GLU N 102 " --> pdb=" O ALA N 98 " (cutoff:3.500A) 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 169 Processing helix chain 'N' and resid 201 through 205 Processing helix chain 'N' and resid 207 through 211 Processing helix chain 'N' and resid 229 through 232 Processing helix chain 'N' and resid 233 through 244 Processing helix chain 'N' and resid 255 through 268 Processing helix chain 'N' and resid 281 through 297 Processing helix chain 'N' and resid 338 through 356 Processing helix chain 'N' and resid 358 through 374 Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 426 Processing helix chain 'N' and resid 427 through 429 No H-bonds generated for 'chain 'N' and resid 427 through 429' Processing helix chain 'N' and resid 433 through 448 Processing helix chain 'N' and resid 448 through 459 removed outlier: 3.722A pdb=" N ARG N 452 " --> pdb=" O GLU N 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 461 through 472 removed outlier: 3.855A pdb=" N VAL N 465 " --> pdb=" O GLU N 461 " (cutoff:3.500A) Processing helix chain 'N' and resid 488 through 492 Processing helix chain 'N' and resid 496 through 516 removed outlier: 3.752A pdb=" N THR N 500 " --> pdb=" O PRO N 496 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR N 516 " --> pdb=" O GLY N 512 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 3.591A pdb=" N LYS A 7 " --> pdb=" O MET A 520 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN B 37 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS A 519 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 40 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 48 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 8.132A pdb=" N ASN A 37 " --> pdb=" O GLU G 518 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N MET G 520 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL A 39 " --> pdb=" O MET G 520 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N THR G 522 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS G 7 " --> pdb=" O MET G 520 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 179 Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 195 removed outlier: 6.593A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 193 through 195 removed outlier: 6.593A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 251 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 412 Processing sheet with id=AA8, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AA9, first strand: chain 'B' and resid 4 through 8 removed outlier: 3.555A pdb=" N THR B 522 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS B 7 " --> pdb=" O MET B 520 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET B 520 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 517 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL C 39 " --> pdb=" O THR B 517 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N CYS B 519 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 40 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR C 48 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 175 through 179 removed outlier: 6.680A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLU B 178 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 194 through 195 removed outlier: 6.324A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 194 through 195 removed outlier: 6.324A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU B 247 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU B 221 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE B 249 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ALA B 223 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA B 251 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS B 225 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP B 253 " --> pdb=" O LYS B 225 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AB5, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB6, first strand: chain 'C' and resid 4 through 8 removed outlier: 8.090A pdb=" N VAL D 39 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N MET C 520 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 48 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 175 through 179 removed outlier: 3.551A pdb=" N ASP C 188 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 192 through 195 removed outlier: 6.620A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 192 through 195 removed outlier: 6.620A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLU C 252 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N ALA C 223 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL C 254 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N LYS C 225 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C 274 " --> pdb=" O LEU C 247 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.162A pdb=" N ASN E 37 " --> pdb=" O THR D 517 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N CYS D 519 " --> pdb=" O ASN E 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 175 through 179 removed outlier: 7.152A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLU D 178 " --> pdb=" O VAL D 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.556A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.318A 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: 6.556A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLU D 252 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ALA D 223 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL D 254 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N LYS D 225 " --> pdb=" O VAL D 254 " (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 Processing sheet with id=AC8, first strand: chain 'E' and resid 4 through 8 removed outlier: 4.370A pdb=" N THR E 517 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL F 39 " --> pdb=" O THR E 517 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS E 519 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU F 40 " --> pdb=" O THR F 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 175 through 179 removed outlier: 3.659A pdb=" N THR E 176 " --> pdb=" O ALA E 377 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 192 through 195 removed outlier: 6.236A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.000A 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: 6.236A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU E 252 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N ALA E 223 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL E 254 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N LYS E 225 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 3.515A 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 Processing sheet with id=AD5, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.558A pdb=" N ASN G 37 " --> pdb=" O THR F 517 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS F 519 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL G 39 " --> pdb=" O CYS F 519 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 175 through 179 removed outlier: 6.761A pdb=" N THR F 176 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL F 381 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU F 178 " --> pdb=" O VAL F 381 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 192 through 195 removed outlier: 6.583A pdb=" N THR F 330 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE F 325 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE F 332 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL F 323 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP F 334 " --> pdb=" O LYS F 321 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 192 through 195 removed outlier: 6.583A pdb=" N THR F 330 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE F 325 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE F 332 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL F 323 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP F 334 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU F 247 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU F 221 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ILE F 249 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ALA F 223 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA F 251 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS F 225 " --> pdb=" O ALA F 251 " (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 Processing sheet with id=AE2, first strand: chain 'G' and resid 175 through 179 removed outlier: 3.505A pdb=" N GLU G 186 " --> pdb=" O LYS G 380 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.475A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.168A 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: 6.475A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY G 318 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLU G 252 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ALA G 223 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL G 254 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 10.572A pdb=" N LYS G 225 " --> pdb=" O VAL G 254 " (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 478 Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AE8, first strand: chain 'H' and resid 48 through 50 removed outlier: 6.522A pdb=" N ASN H 37 " --> pdb=" O THR N 517 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYS N 519 " --> pdb=" O ASN H 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 175 through 179 removed outlier: 6.440A pdb=" N THR H 176 " --> pdb=" O ILE H 379 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL H 381 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU H 178 " --> pdb=" O VAL H 381 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 192 through 195 removed outlier: 6.439A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLU H 252 " --> pdb=" O LEU H 221 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N ALA H 223 " --> pdb=" O GLU H 252 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N VAL H 254 " --> pdb=" O ALA H 223 " (cutoff:3.500A) removed outlier: 11.566A pdb=" N LYS H 225 " --> pdb=" O VAL H 254 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 212 through 216 Processing sheet with id=AF3, first strand: chain 'H' and resid 412 through 413 Processing sheet with id=AF4, first strand: chain 'H' and resid 476 through 478 Processing sheet with id=AF5, first strand: chain 'H' and resid 517 through 520 removed outlier: 7.717A pdb=" N VAL I 39 " --> pdb=" O GLU H 518 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N MET H 520 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 8 removed outlier: 3.621A pdb=" N LYS I 7 " --> pdb=" O MET I 520 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET I 520 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR I 517 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL J 39 " --> pdb=" O THR I 517 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N CYS I 519 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 175 through 179 Processing sheet with id=AF8, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.361A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL I 323 " --> pdb=" O LEU I 215 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.361A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU I 247 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU I 221 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE I 249 " --> pdb=" O LEU I 221 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA I 223 " --> pdb=" O ILE I 249 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA I 251 " --> pdb=" O ALA I 223 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LYS I 225 " --> pdb=" O ALA I 251 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP I 253 " --> pdb=" O LYS I 225 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA I 274 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA I 251 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AG2, first strand: chain 'I' and resid 476 through 479 Processing sheet with id=AG3, first strand: chain 'J' and resid 4 through 6 removed outlier: 6.067A pdb=" N ASN K 37 " --> pdb=" O THR J 517 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N CYS J 519 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL K 39 " --> pdb=" O CYS J 519 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 175 through 179 removed outlier: 6.545A pdb=" N THR J 176 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL J 381 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLU J 178 " --> pdb=" O VAL J 381 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 192 through 195 removed outlier: 6.547A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 192 through 195 removed outlier: 6.547A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLU J 252 " --> pdb=" O LEU J 221 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N ALA J 223 " --> pdb=" O GLU J 252 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL J 254 " --> pdb=" O ALA J 223 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N LYS J 225 " --> pdb=" O VAL J 254 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA J 251 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 412 through 413 Processing sheet with id=AG8, first strand: chain 'J' and resid 476 through 478 Processing sheet with id=AG9, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.706A pdb=" N ASN L 37 " --> pdb=" O THR K 517 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N CYS K 519 " --> pdb=" O ASN L 37 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU L 40 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 175 through 179 removed outlier: 6.815A pdb=" N THR K 176 " --> pdb=" O ILE K 379 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL K 381 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU K 178 " --> pdb=" O VAL K 381 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 192 through 195 removed outlier: 3.576A pdb=" N ARG K 322 " --> pdb=" O ILE K 333 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 192 through 195 removed outlier: 3.576A pdb=" N ARG K 322 " --> pdb=" O ILE K 333 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU K 247 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU K 221 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ILE K 249 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA K 223 " --> pdb=" O ILE K 249 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA K 251 " --> pdb=" O ALA K 223 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS K 225 " --> pdb=" O ALA K 251 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP K 253 " --> pdb=" O LYS K 225 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA K 274 " --> pdb=" O LEU K 247 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AH5, first strand: chain 'K' and resid 476 through 478 Processing sheet with id=AH6, first strand: chain 'L' and resid 4 through 8 removed outlier: 3.974A pdb=" N LYS L 7 " --> pdb=" O MET L 520 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET L 520 " --> pdb=" O LYS L 7 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU L 518 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL M 39 " --> pdb=" O GLU L 518 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET L 520 " --> pdb=" O VAL M 39 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 175 through 179 Processing sheet with id=AH8, first strand: chain 'L' and resid 192 through 195 removed outlier: 6.430A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA L 223 " --> pdb=" O ILE L 249 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA L 251 " --> pdb=" O ALA L 223 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LYS L 225 " --> pdb=" O ALA L 251 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP L 253 " --> pdb=" O LYS L 225 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 213 through 216 removed outlier: 5.889A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA L 251 " --> pdb=" O VAL L 276 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 411 through 412 Processing sheet with id=AI2, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AI3, first strand: chain 'M' and resid 4 through 8 removed outlier: 3.534A pdb=" N LYS M 7 " --> pdb=" O MET M 520 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET M 520 " --> pdb=" O LYS M 7 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASN N 37 " --> pdb=" O THR M 517 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYS M 519 " --> pdb=" O ASN N 37 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL N 39 " --> pdb=" O CYS M 519 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR N 48 " --> pdb=" O LEU N 40 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 175 through 179 removed outlier: 6.731A pdb=" N THR M 176 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL M 381 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLU M 178 " --> pdb=" O VAL M 381 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 192 through 195 removed outlier: 6.778A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLU M 252 " --> pdb=" O LEU M 221 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N ALA M 223 " --> pdb=" O GLU M 252 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N VAL M 254 " --> pdb=" O ALA M 223 " (cutoff:3.500A) removed outlier: 11.633A pdb=" N LYS M 225 " --> pdb=" O VAL M 254 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA M 274 " --> pdb=" O LEU M 247 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 213 through 216 removed outlier: 3.653A pdb=" N VAL M 323 " --> pdb=" O LEU M 215 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AI8, first strand: chain 'M' and resid 476 through 479 Processing sheet with id=AI9, first strand: chain 'N' and resid 175 through 179 removed outlier: 6.589A pdb=" N THR N 176 " --> pdb=" O ILE N 379 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL N 381 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU N 178 " --> pdb=" O VAL N 381 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 192 through 195 removed outlier: 3.609A pdb=" N MET N 193 " --> pdb=" O ILE N 332 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR N 330 " --> pdb=" O ILE N 325 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE N 325 " --> pdb=" O THR N 330 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE N 332 " --> pdb=" O VAL N 323 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL N 323 " --> pdb=" O ILE N 332 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP N 334 " --> pdb=" O LYS N 321 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 192 through 195 removed outlier: 3.609A pdb=" N MET N 193 " --> pdb=" O ILE N 332 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR N 330 " --> pdb=" O ILE N 325 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE N 325 " --> pdb=" O THR N 330 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE N 332 " --> pdb=" O VAL N 323 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL N 323 " --> pdb=" O ILE N 332 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP N 334 " --> pdb=" O LYS N 321 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLU N 252 " --> pdb=" O LEU N 221 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N ALA N 223 " --> pdb=" O GLU N 252 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL N 254 " --> pdb=" O ALA N 223 " (cutoff:3.500A) removed outlier: 11.435A pdb=" N LYS N 225 " --> pdb=" O VAL N 254 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA N 251 " --> pdb=" O VAL N 276 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'N' and resid 476 through 479 3783 hydrogen bonds defined for protein. 10848 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: 48.08 Time building geometry restraints manager: 66.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 55664 1.03 - 1.23: 51 1.23 - 1.42: 20319 1.42 - 1.62: 33516 1.62 - 1.81: 518 Bond restraints: 110068 Sorted by residual: bond pdb=" CB VAL I 510 " pdb=" CG2 VAL I 510 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.24e+00 bond pdb=" CA SER J 217 " pdb=" C SER J 217 " ideal model delta sigma weight residual 1.532 1.524 0.009 6.50e-03 2.37e+04 1.71e+00 bond pdb=" CG LYS H 34 " pdb=" CD LYS H 34 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.43e+00 bond pdb=" CG MET N 114 " pdb=" SD MET N 114 " ideal model delta sigma weight residual 1.803 1.775 0.028 2.50e-02 1.60e+03 1.26e+00 bond pdb=" CB MET J 488 " pdb=" CG MET J 488 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.20e+00 ... (remaining 110063 not shown) Histogram of bond angle deviations from ideal: 59.50 - 74.10: 18 74.10 - 88.70: 81 88.70 - 103.29: 456 103.29 - 117.89: 157324 117.89 - 132.48: 42769 Bond angle restraints: 200648 Sorted by residual: angle pdb=" C VAL B 14 " pdb=" N LYS B 15 " pdb=" H LYS B 15 " ideal model delta sigma weight residual 125.01 69.77 55.24 3.00e+00 1.11e-01 3.39e+02 angle pdb=" CA LYS B 15 " pdb=" N LYS B 15 " pdb=" H LYS B 15 " ideal model delta sigma weight residual 114.71 59.50 55.21 3.00e+00 1.11e-01 3.39e+02 angle pdb=" C THR A 313 " pdb=" CA THR A 313 " pdb=" HA THR A 313 " ideal model delta sigma weight residual 109.00 73.25 35.75 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CB VAL E 236 " pdb=" CA VAL E 236 " pdb=" HA VAL E 236 " ideal model delta sigma weight residual 109.00 73.33 35.67 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C THR C 313 " pdb=" CA THR C 313 " pdb=" HA THR C 313 " ideal model delta sigma weight residual 109.00 73.34 35.66 3.00e+00 1.11e-01 1.41e+02 ... (remaining 200643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 45349 17.97 - 35.95: 3546 35.95 - 53.92: 1212 53.92 - 71.90: 423 71.90 - 89.87: 94 Dihedral angle restraints: 50624 sinusoidal: 29008 harmonic: 21616 Sorted by residual: dihedral pdb=" CA GLY J 88 " pdb=" C GLY J 88 " pdb=" N THR J 89 " pdb=" CA THR J 89 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" N GLU A 354 " pdb=" C GLU A 354 " pdb=" CA GLU A 354 " pdb=" CB GLU A 354 " ideal model delta harmonic sigma weight residual 122.80 133.71 -10.91 0 2.50e+00 1.60e-01 1.90e+01 dihedral pdb=" C GLU A 354 " pdb=" N GLU A 354 " pdb=" CA GLU A 354 " pdb=" CB GLU A 354 " ideal model delta harmonic sigma weight residual -122.60 -133.44 10.84 0 2.50e+00 1.60e-01 1.88e+01 ... (remaining 50621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.289: 8902 0.289 - 0.578: 23 0.578 - 0.868: 0 0.868 - 1.157: 0 1.157 - 1.446: 7 Chirality restraints: 8932 Sorted by residual: chirality pdb=" CB THR E 266 " pdb=" CA THR E 266 " pdb=" OG1 THR E 266 " pdb=" CG2 THR E 266 " both_signs ideal model delta sigma weight residual False 2.55 1.11 1.45 2.00e-01 2.50e+01 5.23e+01 chirality pdb=" CB THR C 357 " pdb=" CA THR C 357 " pdb=" OG1 THR C 357 " pdb=" CG2 THR C 357 " both_signs ideal model delta sigma weight residual False 2.55 1.12 1.43 2.00e-01 2.50e+01 5.11e+01 chirality pdb=" CB THR N 357 " pdb=" CA THR N 357 " pdb=" OG1 THR N 357 " pdb=" CG2 THR N 357 " both_signs ideal model delta sigma weight residual False 2.55 1.12 1.43 2.00e-01 2.50e+01 5.11e+01 ... (remaining 8929 not shown) Planarity restraints: 16744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 387 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C VAL E 387 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL E 387 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU E 388 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 404 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C ARG A 404 " 0.032 2.00e-02 2.50e+03 pdb=" O ARG A 404 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 405 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 96 " 0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C ALA B 96 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA B 96 " 0.011 2.00e-02 2.50e+03 pdb=" N GLN B 97 " 0.010 2.00e-02 2.50e+03 ... (remaining 16741 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 1679 2.03 - 2.67: 173208 2.67 - 3.31: 338274 3.31 - 3.96: 417296 3.96 - 4.60: 652313 Nonbonded interactions: 1582770 Sorted by model distance: nonbonded pdb=" OE1 GLU J 461 " pdb=" H VAL J 464 " model vdw 1.385 1.850 nonbonded pdb=" OE1 GLU F 461 " pdb=" H VAL F 464 " model vdw 1.483 1.850 nonbonded pdb=" O LEU N 17 " pdb="HD21 ASN N 21 " model vdw 1.502 1.850 nonbonded pdb=" H GLN I 432 " pdb=" OE1 GLN I 436 " model vdw 1.503 1.850 nonbonded pdb=" H SER J 217 " pdb=" O LYS J 321 " model vdw 1.506 1.850 ... (remaining 1582765 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 group one per residue 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: 2.050 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: 1.210 Extract box with map and model: 13.510 Check model and map are aligned: 1.060 Set scattering table: 0.650 Process input model: 249.540 Find NCS groups from input model: 3.900 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 275.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 0.049 54362 Z= 0.164 Angle : 0.520 11.660 73402 Z= 0.294 Chirality : 0.059 1.446 8932 Planarity : 0.003 0.042 9618 Dihedral : 13.644 89.872 20496 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.05 % 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: 1.23 (0.10), residues: 7308 helix: 1.83 (0.08), residues: 4214 sheet: -0.49 (0.19), residues: 714 loop : -0.56 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 401 PHE 0.016 0.001 PHE F 66 TYR 0.016 0.001 TYR H 203 ARG 0.004 0.000 ARG I 58 *********************** 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 458 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 458 time to evaluate : 6.140 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 ASP cc_start: 0.8850 (p0) cc_final: 0.8560 (p0) REVERT: B 398 ASP cc_start: 0.9221 (m-30) cc_final: 0.8952 (m-30) REVERT: C 233 MET cc_start: 0.9467 (mmp) cc_final: 0.9027 (mmm) REVERT: D 162 ILE cc_start: 0.9695 (mt) cc_final: 0.9441 (tt) REVERT: D 307 MET cc_start: 0.8602 (tpt) cc_final: 0.8159 (tpp) REVERT: G 330 THR cc_start: 0.6063 (m) cc_final: 0.5795 (m) REVERT: G 495 ASP cc_start: 0.8388 (m-30) cc_final: 0.8106 (m-30) REVERT: H 121 ASP cc_start: 0.8696 (m-30) cc_final: 0.8429 (m-30) REVERT: H 166 MET cc_start: 0.9523 (mmp) cc_final: 0.9321 (mmm) REVERT: H 288 MET cc_start: 0.9733 (mtp) cc_final: 0.9468 (mtp) REVERT: I 193 MET cc_start: 0.9436 (tmm) cc_final: 0.9235 (tmm) REVERT: I 398 ASP cc_start: 0.9173 (m-30) cc_final: 0.8956 (m-30) REVERT: J 131 LEU cc_start: 0.9722 (tp) cc_final: 0.9466 (tp) REVERT: J 193 MET cc_start: 0.8881 (tpp) cc_final: 0.8111 (tpp) REVERT: K 68 ASN cc_start: 0.9072 (t0) cc_final: 0.8465 (t0) REVERT: L 111 MET cc_start: 0.8230 (mmp) cc_final: 0.7604 (mmp) REVERT: M 188 ASP cc_start: 0.9077 (p0) cc_final: 0.8865 (p0) REVERT: M 288 MET cc_start: 0.9536 (mtm) cc_final: 0.9293 (mtp) REVERT: M 506 TYR cc_start: 0.9288 (m-80) cc_final: 0.8907 (m-10) REVERT: N 166 MET cc_start: 0.9055 (ttm) cc_final: 0.8508 (tmm) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 1.0786 time to fit residues: 855.6474 Evaluate side-chains 398 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 6.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 1.9990 chunk 551 optimal weight: 7.9990 chunk 306 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 372 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 570 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 346 optimal weight: 6.9990 chunk 424 optimal weight: 2.9990 chunk 661 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 GLN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 ASN ** E 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 319 GLN L 467 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 54362 Z= 0.240 Angle : 0.538 11.577 73402 Z= 0.310 Chirality : 0.059 1.438 8932 Planarity : 0.003 0.061 9618 Dihedral : 4.123 24.923 7728 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.03 % 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: 0.98 (0.10), residues: 7308 helix: 1.69 (0.08), residues: 4256 sheet: -0.76 (0.18), residues: 714 loop : -0.80 (0.13), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 401 PHE 0.013 0.001 PHE M 281 TYR 0.009 0.001 TYR J 506 ARG 0.005 0.000 ARG D 421 *********************** 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 449 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 449 time to evaluate : 6.151 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: 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: 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: 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: 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: 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: 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: 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: 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 193 MET cc_start: 0.8767 (tpp) cc_final: 0.8432 (tpp) REVERT: B 188 ASP cc_start: 0.8765 (p0) cc_final: 0.8490 (p0) REVERT: B 247 LEU cc_start: 0.9618 (tp) cc_final: 0.9395 (tp) REVERT: B 398 ASP cc_start: 0.9238 (m-30) cc_final: 0.8973 (m-30) REVERT: B 497 THR cc_start: 0.9250 (m) cc_final: 0.9047 (m) REVERT: C 233 MET cc_start: 0.9472 (mmp) cc_final: 0.8994 (mmm) REVERT: C 447 MET cc_start: 0.8636 (mpp) cc_final: 0.8386 (mpp) REVERT: D 162 ILE cc_start: 0.9677 (mt) cc_final: 0.9440 (tt) REVERT: D 307 MET cc_start: 0.8625 (tpt) cc_final: 0.8185 (tpp) REVERT: E 193 MET cc_start: 0.9351 (tmm) cc_final: 0.9083 (tmm) REVERT: G 330 THR cc_start: 0.5977 (m) cc_final: 0.5690 (m) REVERT: G 495 ASP cc_start: 0.8377 (m-30) cc_final: 0.8155 (m-30) REVERT: H 121 ASP cc_start: 0.8768 (m-30) cc_final: 0.8491 (m-30) REVERT: I 389 MET cc_start: 0.8580 (tmm) cc_final: 0.8307 (tmm) REVERT: I 398 ASP cc_start: 0.9181 (m-30) cc_final: 0.8950 (m-30) REVERT: J 16 MET cc_start: 0.7748 (ppp) cc_final: 0.7411 (ppp) REVERT: J 131 LEU cc_start: 0.9742 (tp) cc_final: 0.9508 (tp) REVERT: J 193 MET cc_start: 0.8906 (tpp) cc_final: 0.8224 (tpp) REVERT: L 111 MET cc_start: 0.8219 (mmp) cc_final: 0.7626 (mmp) REVERT: M 188 ASP cc_start: 0.8831 (p0) cc_final: 0.8600 (p0) REVERT: M 288 MET cc_start: 0.9522 (mtm) cc_final: 0.9213 (mtp) REVERT: M 506 TYR cc_start: 0.9317 (m-80) cc_final: 0.8980 (m-10) REVERT: N 25 ASP cc_start: 0.8553 (t0) cc_final: 0.8248 (t0) REVERT: N 166 MET cc_start: 0.9088 (ttm) cc_final: 0.8582 (tmm) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 1.0723 time to fit residues: 835.9875 Evaluate side-chains 396 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 6.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 550 optimal weight: 4.9990 chunk 450 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 662 optimal weight: 6.9990 chunk 715 optimal weight: 3.9990 chunk 589 optimal weight: 4.9990 chunk 656 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 531 optimal weight: 0.9980 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 ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN D 467 ASN E 351 GLN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 467 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 54362 Z= 0.245 Angle : 0.532 11.586 73402 Z= 0.306 Chirality : 0.059 1.432 8932 Planarity : 0.003 0.060 9618 Dihedral : 4.147 24.538 7728 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.02 % Allowed : 1.75 % Favored : 98.23 % Cbeta Deviations : 0.03 % 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: 0.85 (0.10), residues: 7308 helix: 1.63 (0.08), residues: 4256 sheet: -0.88 (0.18), residues: 714 loop : -0.91 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 401 PHE 0.011 0.001 PHE N 44 TYR 0.014 0.001 TYR H 203 ARG 0.005 0.000 ARG J 284 *********************** 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 451 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 450 time to evaluate : 6.213 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: 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: 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: 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: 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: 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: 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: 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: 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: 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 10 ASN cc_start: 0.9196 (m-40) cc_final: 0.8408 (t0) REVERT: B 247 LEU cc_start: 0.9633 (tp) cc_final: 0.9418 (tp) REVERT: C 59 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8151 (tp30) REVERT: C 111 MET cc_start: 0.8784 (mpp) cc_final: 0.8264 (mpp) REVERT: C 233 MET cc_start: 0.9477 (mmp) cc_final: 0.9002 (mmm) REVERT: C 447 MET cc_start: 0.8698 (mpp) cc_final: 0.8334 (mpp) REVERT: D 162 ILE cc_start: 0.9694 (mt) cc_final: 0.9441 (tt) REVERT: D 307 MET cc_start: 0.8566 (tpt) cc_final: 0.8081 (tpp) REVERT: G 330 THR cc_start: 0.6022 (m) cc_final: 0.5764 (m) REVERT: H 25 ASP cc_start: 0.8954 (m-30) cc_final: 0.8737 (m-30) REVERT: H 121 ASP cc_start: 0.8769 (m-30) cc_final: 0.8502 (m-30) REVERT: H 288 MET cc_start: 0.9729 (mtp) cc_final: 0.9463 (mtp) REVERT: I 389 MET cc_start: 0.8623 (tmm) cc_final: 0.8298 (tmm) REVERT: I 398 ASP cc_start: 0.9180 (m-30) cc_final: 0.8954 (m-30) REVERT: J 131 LEU cc_start: 0.9749 (tp) cc_final: 0.9518 (tp) REVERT: J 193 MET cc_start: 0.8924 (tpp) cc_final: 0.8280 (tpp) REVERT: J 281 PHE cc_start: 0.8032 (t80) cc_final: 0.7755 (t80) REVERT: K 68 ASN cc_start: 0.9118 (t0) cc_final: 0.8517 (t0) REVERT: K 288 MET cc_start: 0.9461 (mtp) cc_final: 0.9137 (mpp) REVERT: L 111 MET cc_start: 0.8204 (mmp) cc_final: 0.7609 (mmp) REVERT: M 288 MET cc_start: 0.9519 (mtm) cc_final: 0.9178 (mtp) REVERT: N 25 ASP cc_start: 0.8663 (t0) cc_final: 0.8337 (t0) REVERT: N 166 MET cc_start: 0.9104 (ttm) cc_final: 0.8573 (tmm) outliers start: 1 outliers final: 1 residues processed: 451 average time/residue: 1.0969 time to fit residues: 861.4638 Evaluate side-chains 402 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 401 time to evaluate : 6.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 10.0000 chunk 497 optimal weight: 3.9990 chunk 343 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 316 optimal weight: 3.9990 chunk 444 optimal weight: 3.9990 chunk 664 optimal weight: 4.9990 chunk 703 optimal weight: 10.0000 chunk 347 optimal weight: 6.9990 chunk 629 optimal weight: 2.9990 chunk 189 optimal weight: 0.0670 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN C 457 ASN D 467 ASN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 146 GLN ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 467 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 290 GLN ** N 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 54362 Z= 0.285 Angle : 0.554 11.565 73402 Z= 0.319 Chirality : 0.059 1.432 8932 Planarity : 0.003 0.075 9618 Dihedral : 4.214 23.085 7728 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.02 % Allowed : 2.25 % Favored : 97.74 % Cbeta Deviations : 0.03 % 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: 0.63 (0.10), residues: 7308 helix: 1.45 (0.08), residues: 4256 sheet: -0.97 (0.18), residues: 714 loop : -1.01 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 401 PHE 0.015 0.001 PHE I 195 TYR 0.014 0.001 TYR H 203 ARG 0.007 0.000 ARG G 395 *********************** 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 451 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 450 time to evaluate : 5.523 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 111 MET cc_start: 0.8781 (mpp) cc_final: 0.8329 (mpp) REVERT: C 233 MET cc_start: 0.9467 (mmp) cc_final: 0.8983 (mmm) REVERT: C 447 MET cc_start: 0.8762 (mpp) cc_final: 0.8316 (mpp) REVERT: D 162 ILE cc_start: 0.9703 (mt) cc_final: 0.9454 (tt) REVERT: D 307 MET cc_start: 0.8586 (tpt) cc_final: 0.8102 (tpp) REVERT: D 488 MET cc_start: 0.9225 (mmp) cc_final: 0.8966 (mmm) REVERT: E 193 MET cc_start: 0.9412 (tmm) cc_final: 0.9129 (tmm) REVERT: G 330 THR cc_start: 0.6095 (m) cc_final: 0.5840 (m) REVERT: G 495 ASP cc_start: 0.8470 (m-30) cc_final: 0.8250 (m-30) REVERT: H 111 MET cc_start: 0.9134 (mpp) cc_final: 0.8878 (mpp) REVERT: H 121 ASP cc_start: 0.8769 (m-30) cc_final: 0.8529 (m-30) REVERT: H 166 MET cc_start: 0.9356 (mmm) cc_final: 0.9137 (mmm) REVERT: H 288 MET cc_start: 0.9729 (mtp) cc_final: 0.9455 (mtp) REVERT: H 447 MET cc_start: 0.9104 (mmm) cc_final: 0.8835 (mmm) REVERT: I 389 MET cc_start: 0.8637 (tmm) cc_final: 0.8297 (tmm) REVERT: I 398 ASP cc_start: 0.9210 (m-30) cc_final: 0.8980 (m-30) REVERT: K 68 ASN cc_start: 0.9049 (t0) cc_final: 0.8772 (t0) REVERT: L 16 MET cc_start: 0.8699 (mmt) cc_final: 0.8345 (mmp) REVERT: L 111 MET cc_start: 0.8210 (mmp) cc_final: 0.7606 (mmp) REVERT: M 288 MET cc_start: 0.9518 (mtm) cc_final: 0.9159 (mtp) REVERT: N 25 ASP cc_start: 0.8702 (t0) cc_final: 0.8395 (t0) REVERT: N 166 MET cc_start: 0.9135 (ttm) cc_final: 0.8575 (tmm) outliers start: 1 outliers final: 0 residues processed: 451 average time/residue: 1.0921 time to fit residues: 860.5167 Evaluate side-chains 399 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 6.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 0.9990 chunk 399 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 523 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 chunk 600 optimal weight: 7.9990 chunk 486 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 359 optimal weight: 6.9990 chunk 631 optimal weight: 2.9990 chunk 177 optimal weight: 0.2980 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 ASN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 467 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 54362 Z= 0.209 Angle : 0.519 11.514 73402 Z= 0.295 Chirality : 0.059 1.426 8932 Planarity : 0.003 0.049 9618 Dihedral : 4.151 23.568 7728 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.05 % 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: 0.83 (0.10), residues: 7308 helix: 1.66 (0.08), residues: 4242 sheet: -0.97 (0.18), residues: 714 loop : -0.98 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 401 PHE 0.014 0.001 PHE E 195 TYR 0.017 0.001 TYR H 199 ARG 0.002 0.000 ARG H 421 *********************** 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 461 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 461 time to evaluate : 5.505 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8635 (tpp) cc_final: 0.8357 (tpp) REVERT: A 398 ASP cc_start: 0.9192 (t0) cc_final: 0.8972 (t0) REVERT: C 111 MET cc_start: 0.8747 (mpp) cc_final: 0.8280 (mpp) REVERT: C 233 MET cc_start: 0.9440 (mmp) cc_final: 0.8967 (mmm) REVERT: C 288 MET cc_start: 0.9426 (mtm) cc_final: 0.9010 (mtp) REVERT: C 447 MET cc_start: 0.8757 (mpp) cc_final: 0.8258 (mpp) REVERT: D 162 ILE cc_start: 0.9703 (mt) cc_final: 0.9445 (tt) REVERT: D 307 MET cc_start: 0.8585 (tpt) cc_final: 0.8091 (tpp) REVERT: D 488 MET cc_start: 0.9256 (mmp) cc_final: 0.8971 (mmm) REVERT: E 193 MET cc_start: 0.9425 (tmm) cc_final: 0.9145 (tmm) REVERT: G 330 THR cc_start: 0.6004 (m) cc_final: 0.5745 (m) REVERT: G 495 ASP cc_start: 0.8400 (m-30) cc_final: 0.8174 (m-30) REVERT: H 25 ASP cc_start: 0.8956 (m-30) cc_final: 0.8728 (m-30) REVERT: H 121 ASP cc_start: 0.8740 (m-30) cc_final: 0.8491 (m-30) REVERT: H 166 MET cc_start: 0.9296 (mmm) cc_final: 0.9048 (mmm) REVERT: H 288 MET cc_start: 0.9699 (mtp) cc_final: 0.9403 (mtp) REVERT: H 447 MET cc_start: 0.9066 (mmm) cc_final: 0.8756 (mmm) REVERT: I 389 MET cc_start: 0.8591 (tmm) cc_final: 0.8227 (tmm) REVERT: I 398 ASP cc_start: 0.9186 (m-30) cc_final: 0.8957 (m-30) REVERT: J 114 MET cc_start: 0.8434 (tmm) cc_final: 0.8140 (tmm) REVERT: J 193 MET cc_start: 0.8879 (tpp) cc_final: 0.8277 (tpp) REVERT: K 68 ASN cc_start: 0.9010 (t0) cc_final: 0.8737 (t0) REVERT: K 114 MET cc_start: 0.7567 (tmm) cc_final: 0.7315 (tmm) REVERT: K 233 MET cc_start: 0.9480 (mmp) cc_final: 0.9194 (mmm) REVERT: L 16 MET cc_start: 0.8667 (mmt) cc_final: 0.8341 (mmp) REVERT: L 111 MET cc_start: 0.8193 (mmp) cc_final: 0.7561 (mmp) REVERT: M 288 MET cc_start: 0.9501 (mtm) cc_final: 0.9123 (mtp) REVERT: N 25 ASP cc_start: 0.8570 (t0) cc_final: 0.8248 (t0) REVERT: N 166 MET cc_start: 0.9075 (ttm) cc_final: 0.8539 (tmm) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 1.2217 time to fit residues: 970.7899 Evaluate side-chains 408 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 6.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 3.9990 chunk 633 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 413 optimal weight: 0.0010 chunk 173 optimal weight: 7.9990 chunk 704 optimal weight: 2.9990 chunk 584 optimal weight: 2.9990 chunk 326 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 369 optimal weight: 0.6980 overall best weight: 1.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 ASN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 467 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 54362 Z= 0.199 Angle : 0.513 11.566 73402 Z= 0.291 Chirality : 0.059 1.433 8932 Planarity : 0.003 0.047 9618 Dihedral : 4.108 23.595 7728 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.05 % 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: 0.95 (0.10), residues: 7308 helix: 1.73 (0.08), residues: 4242 sheet: -0.69 (0.21), residues: 574 loop : -0.97 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 401 PHE 0.019 0.001 PHE C 195 TYR 0.015 0.001 TYR H 199 ARG 0.003 0.000 ARG N 197 *********************** 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 457 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 6.150 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: 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: 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: 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: 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: 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: 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: 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: 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: 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 193 MET cc_start: 0.8613 (tpp) cc_final: 0.8333 (tpp) REVERT: A 398 ASP cc_start: 0.9189 (t0) cc_final: 0.8971 (t0) REVERT: C 111 MET cc_start: 0.8771 (mpp) cc_final: 0.8291 (mpp) REVERT: C 233 MET cc_start: 0.9469 (mmp) cc_final: 0.8983 (mmm) REVERT: C 288 MET cc_start: 0.9403 (mtm) cc_final: 0.8948 (mtp) REVERT: C 447 MET cc_start: 0.8761 (mpp) cc_final: 0.8243 (mpp) REVERT: D 162 ILE cc_start: 0.9695 (mt) cc_final: 0.9463 (tt) REVERT: D 307 MET cc_start: 0.8590 (tpt) cc_final: 0.8101 (tpp) REVERT: D 488 MET cc_start: 0.9237 (mmp) cc_final: 0.8955 (mmm) REVERT: F 281 PHE cc_start: 0.7457 (p90) cc_final: 0.7013 (p90) REVERT: G 330 THR cc_start: 0.5984 (m) cc_final: 0.5717 (m) REVERT: G 495 ASP cc_start: 0.8396 (m-30) cc_final: 0.8177 (m-30) REVERT: H 121 ASP cc_start: 0.8725 (m-30) cc_final: 0.8479 (m-30) REVERT: H 166 MET cc_start: 0.9292 (mmm) cc_final: 0.9033 (mmm) REVERT: H 288 MET cc_start: 0.9700 (mtp) cc_final: 0.9401 (mtp) REVERT: H 447 MET cc_start: 0.9067 (mmm) cc_final: 0.8754 (mmm) REVERT: I 389 MET cc_start: 0.8583 (tmm) cc_final: 0.8206 (tmm) REVERT: I 398 ASP cc_start: 0.9182 (m-30) cc_final: 0.8957 (m-30) REVERT: J 193 MET cc_start: 0.8846 (tpp) cc_final: 0.8226 (tpp) REVERT: K 68 ASN cc_start: 0.8957 (t0) cc_final: 0.8744 (t0) REVERT: K 514 MET cc_start: 0.8565 (ttp) cc_final: 0.8355 (ttp) REVERT: L 16 MET cc_start: 0.8673 (mmt) cc_final: 0.8395 (mmp) REVERT: L 111 MET cc_start: 0.8180 (mmp) cc_final: 0.7571 (mmp) REVERT: M 288 MET cc_start: 0.9492 (mtm) cc_final: 0.9102 (mtp) REVERT: N 25 ASP cc_start: 0.8597 (t0) cc_final: 0.8284 (t0) REVERT: N 100 ILE cc_start: 0.9558 (mt) cc_final: 0.9291 (tt) REVERT: N 166 MET cc_start: 0.9077 (ttm) cc_final: 0.8538 (tmm) REVERT: N 398 ASP cc_start: 0.8557 (m-30) cc_final: 0.7977 (m-30) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 1.1635 time to fit residues: 916.9964 Evaluate side-chains 410 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 6.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 401 optimal weight: 8.9990 chunk 514 optimal weight: 0.8980 chunk 398 optimal weight: 4.9990 chunk 592 optimal weight: 0.9990 chunk 393 optimal weight: 2.9990 chunk 701 optimal weight: 8.9990 chunk 439 optimal weight: 0.7980 chunk 427 optimal weight: 1.9990 chunk 323 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 ASN F 290 GLN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 467 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 467 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54362 Z= 0.182 Angle : 0.504 11.497 73402 Z= 0.285 Chirality : 0.059 1.425 8932 Planarity : 0.003 0.051 9618 Dihedral : 4.069 23.202 7728 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.03 % 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: 1.05 (0.10), residues: 7308 helix: 1.81 (0.08), residues: 4256 sheet: -0.68 (0.21), residues: 574 loop : -0.91 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 401 PHE 0.010 0.001 PHE E 195 TYR 0.018 0.001 TYR H 199 ARG 0.003 0.000 ARG B 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 463 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 6.138 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8585 (tpp) cc_final: 0.8309 (tpp) REVERT: A 398 ASP cc_start: 0.9186 (t0) cc_final: 0.8964 (t0) REVERT: C 111 MET cc_start: 0.8749 (mpp) cc_final: 0.8255 (mpp) REVERT: C 233 MET cc_start: 0.9464 (mmp) cc_final: 0.8972 (mmm) REVERT: C 288 MET cc_start: 0.9406 (mtm) cc_final: 0.8971 (mtp) REVERT: C 447 MET cc_start: 0.8776 (mpp) cc_final: 0.8226 (mpp) REVERT: D 162 ILE cc_start: 0.9696 (mt) cc_final: 0.9463 (tt) REVERT: D 307 MET cc_start: 0.8592 (tpt) cc_final: 0.8100 (tpp) REVERT: D 391 GLU cc_start: 0.9087 (mp0) cc_final: 0.8871 (mp0) REVERT: D 488 MET cc_start: 0.9230 (mmp) cc_final: 0.8937 (mmm) REVERT: E 193 MET cc_start: 0.9423 (tmm) cc_final: 0.9152 (tmm) REVERT: F 281 PHE cc_start: 0.7402 (p90) cc_final: 0.6966 (p90) REVERT: G 330 THR cc_start: 0.5941 (m) cc_final: 0.5665 (m) REVERT: G 495 ASP cc_start: 0.8391 (m-30) cc_final: 0.8182 (m-30) REVERT: H 121 ASP cc_start: 0.8718 (m-30) cc_final: 0.8474 (m-30) REVERT: H 166 MET cc_start: 0.9278 (mmm) cc_final: 0.9018 (mmm) REVERT: H 288 MET cc_start: 0.9704 (mtp) cc_final: 0.9403 (mtp) REVERT: H 447 MET cc_start: 0.9072 (mmm) cc_final: 0.8749 (mmm) REVERT: I 389 MET cc_start: 0.8576 (tmm) cc_final: 0.8190 (tmm) REVERT: I 398 ASP cc_start: 0.9177 (m-30) cc_final: 0.8953 (m-30) REVERT: I 520 MET cc_start: 0.8639 (mtp) cc_final: 0.8414 (mtp) REVERT: J 193 MET cc_start: 0.8825 (tpp) cc_final: 0.8234 (tpp) REVERT: J 288 MET cc_start: 0.9319 (mpp) cc_final: 0.9101 (mmt) REVERT: K 68 ASN cc_start: 0.8963 (t0) cc_final: 0.8758 (t0) REVERT: L 111 MET cc_start: 0.8156 (mmp) cc_final: 0.7560 (mmp) REVERT: L 250 ILE cc_start: 0.9096 (mm) cc_final: 0.8857 (mm) REVERT: M 288 MET cc_start: 0.9476 (mtm) cc_final: 0.9084 (mtp) REVERT: N 25 ASP cc_start: 0.8783 (t0) cc_final: 0.8458 (t0) REVERT: N 100 ILE cc_start: 0.9545 (mt) cc_final: 0.9283 (tt) REVERT: N 166 MET cc_start: 0.9119 (ttm) cc_final: 0.8575 (tmm) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 1.1278 time to fit residues: 905.8921 Evaluate side-chains 413 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 6.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 0.9980 chunk 280 optimal weight: 0.4980 chunk 419 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 446 optimal weight: 0.9980 chunk 478 optimal weight: 2.9990 chunk 346 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 551 optimal weight: 8.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 ASN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 467 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 467 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 54362 Z= 0.163 Angle : 0.500 11.589 73402 Z= 0.280 Chirality : 0.059 1.439 8932 Planarity : 0.003 0.049 9618 Dihedral : 4.012 22.778 7728 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.03 % 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: 1.12 (0.10), residues: 7308 helix: 1.90 (0.08), residues: 4256 sheet: -0.97 (0.18), residues: 714 loop : -0.85 (0.13), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 401 PHE 0.012 0.001 PHE C 195 TYR 0.019 0.001 TYR H 199 ARG 0.004 0.000 ARG I 445 *********************** 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 461 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 461 time to evaluate : 6.183 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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 73 MET cc_start: 0.9042 (ttm) cc_final: 0.8730 (ttp) REVERT: A 193 MET cc_start: 0.8551 (tpp) cc_final: 0.8277 (tpp) REVERT: A 398 ASP cc_start: 0.9184 (t0) cc_final: 0.8958 (t0) REVERT: C 111 MET cc_start: 0.8738 (mpp) cc_final: 0.8233 (mpp) REVERT: C 233 MET cc_start: 0.9455 (mmp) cc_final: 0.8958 (mmm) REVERT: C 288 MET cc_start: 0.9406 (mtm) cc_final: 0.8962 (mtp) REVERT: D 162 ILE cc_start: 0.9698 (mt) cc_final: 0.9461 (tt) REVERT: D 307 MET cc_start: 0.8590 (tpt) cc_final: 0.8100 (tpp) REVERT: D 488 MET cc_start: 0.9217 (mmp) cc_final: 0.8896 (mmm) REVERT: E 193 MET cc_start: 0.9420 (tmm) cc_final: 0.9007 (tmm) REVERT: F 281 PHE cc_start: 0.7419 (p90) cc_final: 0.6990 (p90) REVERT: G 330 THR cc_start: 0.5915 (m) cc_final: 0.5634 (m) REVERT: G 495 ASP cc_start: 0.8395 (m-30) cc_final: 0.8183 (m-30) REVERT: H 121 ASP cc_start: 0.8710 (m-30) cc_final: 0.8462 (m-30) REVERT: H 166 MET cc_start: 0.9262 (mmm) cc_final: 0.9003 (mmm) REVERT: H 288 MET cc_start: 0.9709 (mtp) cc_final: 0.9403 (mtp) REVERT: H 447 MET cc_start: 0.9069 (mmm) cc_final: 0.8747 (mmm) REVERT: I 389 MET cc_start: 0.8570 (tmm) cc_final: 0.8173 (tmm) REVERT: I 398 ASP cc_start: 0.9174 (m-30) cc_final: 0.8948 (m-30) REVERT: I 520 MET cc_start: 0.8634 (mtp) cc_final: 0.8412 (mtp) REVERT: J 193 MET cc_start: 0.8806 (tpp) cc_final: 0.8210 (tpp) REVERT: K 68 ASN cc_start: 0.8949 (t0) cc_final: 0.8325 (t0) REVERT: K 514 MET cc_start: 0.8618 (ttp) cc_final: 0.8402 (ttp) REVERT: L 111 MET cc_start: 0.8130 (mmp) cc_final: 0.7543 (mmp) REVERT: L 250 ILE cc_start: 0.9099 (mm) cc_final: 0.8874 (mm) REVERT: M 288 MET cc_start: 0.9469 (mtm) cc_final: 0.9065 (mtp) REVERT: N 25 ASP cc_start: 0.8814 (t0) cc_final: 0.8440 (t0) REVERT: N 166 MET cc_start: 0.9152 (ttm) cc_final: 0.8567 (tmm) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 1.1100 time to fit residues: 881.9664 Evaluate side-chains 408 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 6.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 2.9990 chunk 672 optimal weight: 5.9990 chunk 613 optimal weight: 0.6980 chunk 653 optimal weight: 7.9990 chunk 393 optimal weight: 5.9990 chunk 284 optimal weight: 9.9990 chunk 513 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 590 optimal weight: 4.9990 chunk 618 optimal weight: 1.9990 chunk 651 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 ASN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 467 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 467 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 54362 Z= 0.211 Angle : 0.519 11.523 73402 Z= 0.294 Chirality : 0.059 1.427 8932 Planarity : 0.003 0.110 9618 Dihedral : 4.041 23.364 7728 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.03 % 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: 1.07 (0.10), residues: 7308 helix: 1.81 (0.08), residues: 4256 sheet: -0.66 (0.21), residues: 574 loop : -0.89 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 401 PHE 0.028 0.001 PHE M 281 TYR 0.019 0.001 TYR H 199 ARG 0.015 0.000 ARG I 285 *********************** 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 457 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 6.327 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8553 (tpp) cc_final: 0.8282 (tpp) REVERT: A 398 ASP cc_start: 0.9190 (t0) cc_final: 0.8971 (t0) REVERT: B 398 ASP cc_start: 0.9202 (m-30) cc_final: 0.8950 (m-30) REVERT: C 111 MET cc_start: 0.8740 (mpp) cc_final: 0.8207 (mpp) REVERT: C 233 MET cc_start: 0.9455 (mmp) cc_final: 0.8964 (mmm) REVERT: C 288 MET cc_start: 0.9419 (mtm) cc_final: 0.8990 (mtp) REVERT: D 162 ILE cc_start: 0.9701 (mt) cc_final: 0.9469 (tt) REVERT: D 307 MET cc_start: 0.8596 (tpt) cc_final: 0.8108 (tpp) REVERT: D 488 MET cc_start: 0.9243 (mmp) cc_final: 0.8917 (mmm) REVERT: E 193 MET cc_start: 0.9426 (tmm) cc_final: 0.9016 (tmm) REVERT: F 281 PHE cc_start: 0.7516 (p90) cc_final: 0.7090 (p90) REVERT: G 330 THR cc_start: 0.5999 (m) cc_final: 0.5727 (m) REVERT: H 121 ASP cc_start: 0.8728 (m-30) cc_final: 0.8488 (m-30) REVERT: H 166 MET cc_start: 0.9263 (mmm) cc_final: 0.9009 (mmp) REVERT: H 288 MET cc_start: 0.9715 (mtp) cc_final: 0.9409 (mtp) REVERT: H 447 MET cc_start: 0.9084 (mmm) cc_final: 0.8767 (mmm) REVERT: I 193 MET cc_start: 0.9483 (tmm) cc_final: 0.9278 (tmm) REVERT: I 389 MET cc_start: 0.8598 (tmm) cc_final: 0.8207 (tmm) REVERT: I 398 ASP cc_start: 0.9178 (m-30) cc_final: 0.8958 (m-30) REVERT: I 520 MET cc_start: 0.8682 (mtp) cc_final: 0.8464 (mtp) REVERT: J 193 MET cc_start: 0.8808 (tpp) cc_final: 0.8217 (tpp) REVERT: K 114 MET cc_start: 0.7862 (tmm) cc_final: 0.7649 (tmm) REVERT: L 111 MET cc_start: 0.8198 (mmp) cc_final: 0.7501 (mmp) REVERT: L 250 ILE cc_start: 0.9098 (mm) cc_final: 0.8755 (mm) REVERT: M 288 MET cc_start: 0.9459 (mtm) cc_final: 0.9041 (mtp) REVERT: N 25 ASP cc_start: 0.8814 (t0) cc_final: 0.8490 (t0) REVERT: N 166 MET cc_start: 0.9177 (ttm) cc_final: 0.8556 (tmm) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 1.1177 time to fit residues: 877.7856 Evaluate side-chains 411 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 6.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 3.9990 chunk 691 optimal weight: 0.8980 chunk 422 optimal weight: 0.9990 chunk 328 optimal weight: 3.9990 chunk 480 optimal weight: 2.9990 chunk 725 optimal weight: 1.9990 chunk 667 optimal weight: 2.9990 chunk 577 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 446 optimal weight: 3.9990 chunk 354 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 ASN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 467 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 467 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54362 Z= 0.174 Angle : 0.509 11.579 73402 Z= 0.286 Chirality : 0.059 1.438 8932 Planarity : 0.003 0.141 9618 Dihedral : 4.018 22.728 7728 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.03 % 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: 1.17 (0.10), residues: 7308 helix: 1.89 (0.08), residues: 4256 sheet: -0.65 (0.21), residues: 574 loop : -0.84 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 401 PHE 0.035 0.001 PHE F 66 TYR 0.019 0.001 TYR H 199 ARG 0.010 0.000 ARG I 285 ********************** 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 457 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 6.274 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8559 (tpp) cc_final: 0.8283 (tpp) REVERT: A 398 ASP cc_start: 0.9193 (t0) cc_final: 0.8968 (t0) REVERT: B 398 ASP cc_start: 0.9190 (m-30) cc_final: 0.8936 (m-30) REVERT: C 111 MET cc_start: 0.8723 (mpp) cc_final: 0.8181 (mpp) REVERT: C 233 MET cc_start: 0.9448 (mmp) cc_final: 0.8952 (mmm) REVERT: C 288 MET cc_start: 0.9411 (mtm) cc_final: 0.8981 (mtp) REVERT: C 447 MET cc_start: 0.8566 (mpp) cc_final: 0.8111 (mpp) REVERT: D 162 ILE cc_start: 0.9702 (mt) cc_final: 0.9468 (tt) REVERT: D 307 MET cc_start: 0.8596 (tpt) cc_final: 0.8105 (tpp) REVERT: D 488 MET cc_start: 0.9215 (mmp) cc_final: 0.8836 (mmm) REVERT: E 193 MET cc_start: 0.9430 (tmm) cc_final: 0.9018 (tmm) REVERT: F 281 PHE cc_start: 0.7471 (p90) cc_final: 0.7045 (p90) REVERT: G 330 THR cc_start: 0.5956 (m) cc_final: 0.5694 (m) REVERT: G 495 ASP cc_start: 0.8491 (m-30) cc_final: 0.8200 (m-30) REVERT: H 121 ASP cc_start: 0.8707 (m-30) cc_final: 0.8460 (m-30) REVERT: H 166 MET cc_start: 0.9244 (mmm) cc_final: 0.8982 (mmp) REVERT: H 288 MET cc_start: 0.9717 (mtp) cc_final: 0.9404 (mtp) REVERT: H 447 MET cc_start: 0.9075 (mmm) cc_final: 0.8755 (mmm) REVERT: I 389 MET cc_start: 0.8578 (tmm) cc_final: 0.8181 (tmm) REVERT: I 398 ASP cc_start: 0.9172 (m-30) cc_final: 0.8946 (m-30) REVERT: I 520 MET cc_start: 0.8674 (mtp) cc_final: 0.8452 (mtp) REVERT: J 193 MET cc_start: 0.8801 (tpp) cc_final: 0.8199 (tpp) REVERT: K 68 ASN cc_start: 0.8936 (t0) cc_final: 0.8312 (t0) REVERT: K 114 MET cc_start: 0.7829 (tmm) cc_final: 0.7624 (tmm) REVERT: K 514 MET cc_start: 0.8616 (ttp) cc_final: 0.8408 (ttp) REVERT: L 16 MET cc_start: 0.8620 (mmp) cc_final: 0.8393 (mmp) REVERT: L 111 MET cc_start: 0.8136 (mmp) cc_final: 0.7552 (mmp) REVERT: L 250 ILE cc_start: 0.9055 (mm) cc_final: 0.8768 (mm) REVERT: M 288 MET cc_start: 0.9474 (mtm) cc_final: 0.9052 (mtp) REVERT: N 25 ASP cc_start: 0.8795 (t0) cc_final: 0.8464 (t0) REVERT: N 166 MET cc_start: 0.9174 (ttm) cc_final: 0.8548 (tmm) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 1.1654 time to fit residues: 919.5368 Evaluate side-chains 415 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 6.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 1.9990 chunk 615 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 532 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 578 optimal weight: 0.9980 chunk 242 optimal weight: 6.9990 chunk 593 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 ASN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 467 ASN ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 467 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.066839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.046837 restraints weight = 700088.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.049225 restraints weight = 317734.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.050736 restraints weight = 183632.127| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 54362 Z= 0.172 Angle : 0.505 11.470 73402 Z= 0.283 Chirality : 0.059 1.422 8932 Planarity : 0.003 0.129 9618 Dihedral : 3.992 22.809 7728 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.03 % 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: 1.22 (0.10), residues: 7308 helix: 1.93 (0.08), residues: 4256 sheet: -0.65 (0.21), residues: 574 loop : -0.82 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS K 401 PHE 0.020 0.001 PHE F 66 TYR 0.018 0.001 TYR H 199 ARG 0.008 0.000 ARG I 285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15923.58 seconds wall clock time: 277 minutes 40.74 seconds (16660.74 seconds total)