Starting phenix.real_space_refine on Thu Dec 7 22:53:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xol_33351/12_2023/7xol_33351.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xol_33351/12_2023/7xol_33351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xol_33351/12_2023/7xol_33351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xol_33351/12_2023/7xol_33351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xol_33351/12_2023/7xol_33351.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xol_33351/12_2023/7xol_33351.pdb" } resolution = 3.26 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 280 5.16 5 C 33558 2.51 5 N 9310 2.21 5 O 10822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 355": "OE1" <-> "OE2" Residue "K TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 53970 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "B" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "C" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "D" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "E" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "F" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "G" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "H" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "I" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "J" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "K" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "L" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "M" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "N" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Time building chain proxies: 20.57, per 1000 atoms: 0.38 Number of scatterers: 53970 At special positions: 0 Unit cell: (156.6, 159.21, 156.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 280 16.00 O 10822 8.00 N 9310 7.00 C 33558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.28 Conformation dependent library (CDL) restraints added in 7.8 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: 258 helices and 84 sheets defined 60.0% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.07 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 4.099A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.536A pdb=" N VAL A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 86 Processing helix chain 'A' and resid 88 through 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 170 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.985A pdb=" N MET A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 256 through 269 Processing helix chain 'A' and resid 282 through 297 Processing helix chain 'A' and resid 338 through 355 Processing helix chain 'A' and resid 358 through 375 removed outlier: 4.043A 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 427 removed outlier: 3.767A pdb=" N ILE A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 458 Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 497 through 516 Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.244A pdb=" N VAL B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.512A pdb=" N VAL B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 86 Processing helix chain 'B' and resid 88 through 110 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 229 through 244 removed outlier: 4.057A pdb=" N MET B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 256 through 269 Processing helix chain 'B' and resid 281 through 297 Processing helix chain 'B' and resid 338 through 355 removed outlier: 3.733A pdb=" N ILE B 342 " --> pdb=" O GLU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 375 removed outlier: 4.302A pdb=" N GLY B 375 " --> pdb=" O LYS B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 410 Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.660A pdb=" N ILE B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 459 Proline residue: B 450 - end of helix 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: 4.315A pdb=" N VAL C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.579A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 86 Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 155 through 170 removed outlier: 3.514A pdb=" N GLY C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 229 through 244 removed outlier: 4.018A pdb=" N MET C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 256 through 269 Processing helix chain 'C' and resid 282 through 297 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 358 through 375 removed outlier: 4.136A pdb=" N GLY C 375 " --> pdb=" O LYS C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 410 Processing helix chain 'C' and resid 416 through 426 removed outlier: 3.773A pdb=" N ILE C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) 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 459 Proline residue: C 450 - end of helix Processing helix chain 'C' and resid 461 through 472 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 497 through 516 Processing helix chain 'D' and resid 9 through 29 removed outlier: 4.283A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 Processing helix chain 'D' and resid 64 through 85 Processing helix chain 'D' and resid 88 through 109 Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 255 through 269 removed outlier: 3.676A pdb=" N LEU D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 297 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 358 through 375 removed outlier: 4.061A pdb=" N GLY D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 410 Processing helix chain 'D' and resid 416 through 427 removed outlier: 4.023A pdb=" N ILE D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 459 Proline residue: D 450 - end of helix Processing helix chain 'D' and resid 461 through 472 removed outlier: 3.553A pdb=" N VAL D 465 " --> pdb=" O GLU D 461 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 472 " --> pdb=" O THR D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 516 Processing helix chain 'E' and resid 9 through 29 removed outlier: 4.268A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 60 removed outlier: 3.511A pdb=" N VAL E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 86 Processing helix chain 'E' and resid 88 through 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 229 through 244 removed outlier: 3.860A pdb=" N MET E 233 " --> pdb=" O ASN E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 256 through 269 Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 338 through 355 Processing helix chain 'E' and resid 358 through 375 removed outlier: 4.006A pdb=" N GLY E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 410 Processing helix chain 'E' and resid 416 through 427 removed outlier: 3.958A pdb=" N ILE E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 459 Proline residue: E 450 - end of helix Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'E' and resid 497 through 516 Processing helix chain 'F' and resid 9 through 29 removed outlier: 4.218A pdb=" N VAL F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.591A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 86 Processing helix chain 'F' and resid 88 through 110 Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 229 through 244 removed outlier: 4.215A pdb=" N MET F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 255 through 269 removed outlier: 3.529A pdb=" N LEU F 259 " --> pdb=" O GLU F 255 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 297 Processing helix chain 'F' and resid 338 through 355 Processing helix chain 'F' and resid 358 through 375 removed outlier: 3.909A pdb=" N GLY F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 410 Processing helix chain 'F' and resid 416 through 427 removed outlier: 4.023A pdb=" N ILE F 420 " --> pdb=" O GLY F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 459 Proline residue: F 450 - end of helix Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'F' and resid 497 through 516 Processing helix chain 'G' and resid 9 through 29 removed outlier: 4.169A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 60 removed outlier: 3.579A pdb=" N VAL G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 86 Processing helix chain 'G' and resid 88 through 110 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 244 removed outlier: 4.020A pdb=" N MET G 233 " --> pdb=" O ASN G 229 " (cutoff:3.500A) Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 256 through 269 Processing helix chain 'G' and resid 282 through 297 Processing helix chain 'G' and resid 338 through 355 Processing helix chain 'G' and resid 358 through 375 removed outlier: 3.827A 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 427 removed outlier: 3.625A pdb=" N ILE G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 459 Proline residue: G 450 - end of helix Processing helix chain 'G' and resid 461 through 472 removed outlier: 3.507A pdb=" N GLY G 472 " --> pdb=" O THR G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 516 Processing helix chain 'H' and resid 9 through 29 removed outlier: 4.192A pdb=" N VAL H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 60 removed outlier: 3.546A pdb=" N VAL H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 86 Processing helix chain 'H' and resid 88 through 110 Processing helix chain 'H' and resid 112 through 135 Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 155 through 170 Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 229 through 244 removed outlier: 4.313A pdb=" N MET H 233 " --> pdb=" O ASN H 229 " (cutoff:3.500A) Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 256 through 269 Processing helix chain 'H' and resid 282 through 297 Processing helix chain 'H' and resid 338 through 355 removed outlier: 3.504A pdb=" N ILE H 342 " --> pdb=" O GLU H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 375 removed outlier: 3.909A pdb=" N GLY H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 410 Processing helix chain 'H' and resid 416 through 427 removed outlier: 3.738A pdb=" N ILE H 420 " --> pdb=" O GLY H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 459 Proline residue: H 450 - end of helix Processing helix chain 'H' and resid 461 through 472 Processing helix chain 'H' and resid 497 through 516 Processing helix chain 'I' and resid 9 through 29 removed outlier: 4.245A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 60 removed outlier: 3.553A pdb=" N VAL I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 86 Processing helix chain 'I' and resid 88 through 109 Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 229 through 244 removed outlier: 4.155A pdb=" N MET I 233 " --> pdb=" O ASN I 229 " (cutoff:3.500A) Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 255 through 269 removed outlier: 3.633A pdb=" N LEU I 259 " --> pdb=" O GLU I 255 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA I 260 " --> pdb=" O GLY I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 297 removed outlier: 3.511A pdb=" N ARG I 285 " --> pdb=" O PHE I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 356 Processing helix chain 'I' and resid 358 through 375 removed outlier: 3.893A 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: 3.717A pdb=" N ILE I 420 " --> pdb=" O GLY I 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 427 through 429 No H-bonds generated for 'chain 'I' and resid 427 through 429' Processing helix chain 'I' and resid 433 through 459 Proline residue: I 450 - end of helix Processing helix chain 'I' and resid 461 through 472 Processing helix chain 'I' and resid 497 through 516 Processing helix chain 'J' and resid 9 through 29 removed outlier: 4.295A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 60 removed outlier: 3.568A pdb=" N VAL J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 86 Processing helix chain 'J' and resid 88 through 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 170 Processing helix chain 'J' and resid 201 through 205 Processing helix chain 'J' and resid 229 through 244 removed outlier: 4.371A 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 256 through 269 Processing helix chain 'J' and resid 282 through 297 Processing helix chain 'J' and resid 338 through 355 Processing helix chain 'J' and resid 358 through 375 removed outlier: 4.109A pdb=" N GLY J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 410 Processing helix chain 'J' and resid 416 through 427 removed outlier: 3.731A pdb=" N ILE J 420 " --> pdb=" O GLY J 416 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 458 Proline residue: J 450 - end of helix Processing helix chain 'J' and resid 461 through 472 removed outlier: 3.509A pdb=" N VAL J 465 " --> pdb=" O GLU J 461 " (cutoff:3.500A) Processing helix chain 'J' and resid 497 through 516 Processing helix chain 'K' and resid 9 through 29 removed outlier: 4.235A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 60 removed outlier: 3.549A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 86 Processing helix chain 'K' and resid 88 through 109 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 244 removed outlier: 4.124A pdb=" N MET K 233 " --> pdb=" O ASN K 229 " (cutoff:3.500A) Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 256 through 269 Processing helix chain 'K' and resid 282 through 297 Processing helix chain 'K' and resid 338 through 356 Processing helix chain 'K' and resid 358 through 375 removed outlier: 4.357A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 410 Processing helix chain 'K' and resid 416 through 427 removed outlier: 3.730A pdb=" N ILE K 420 " --> pdb=" O GLY K 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 458 Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 461 through 472 Processing helix chain 'K' and resid 497 through 516 Processing helix chain 'L' and resid 9 through 29 removed outlier: 4.151A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 60 removed outlier: 3.557A pdb=" N VAL L 56 " --> pdb=" O ASP L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 86 Processing helix chain 'L' and resid 88 through 109 Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 170 Processing helix chain 'L' and resid 201 through 205 Processing helix chain 'L' and resid 229 through 244 removed outlier: 4.315A 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 256 through 269 Processing helix chain 'L' and resid 282 through 297 Processing helix chain 'L' and resid 338 through 356 Processing helix chain 'L' and resid 358 through 375 removed outlier: 3.886A pdb=" N GLY L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 410 Processing helix chain 'L' and resid 416 through 427 removed outlier: 3.804A pdb=" N ILE L 420 " --> pdb=" O GLY L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 433 through 459 Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 461 through 472 removed outlier: 3.525A pdb=" N GLY L 472 " --> pdb=" O THR L 468 " (cutoff:3.500A) 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: 4.176A pdb=" N VAL M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 60 removed outlier: 3.635A pdb=" N VAL M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 86 Processing helix chain 'M' and resid 88 through 109 Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 155 through 170 Processing helix chain 'M' and resid 201 through 205 Processing helix chain 'M' and resid 229 through 244 removed outlier: 4.396A pdb=" N MET M 233 " --> pdb=" O ASN M 229 " (cutoff:3.500A) Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 255 through 269 removed outlier: 3.732A pdb=" N LEU M 259 " --> pdb=" O GLU M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 297 Processing helix chain 'M' and resid 338 through 355 Processing helix chain 'M' and resid 358 through 375 removed outlier: 4.021A pdb=" N GLY M 375 " --> pdb=" O LYS M 371 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 410 Processing helix chain 'M' and resid 416 through 427 removed outlier: 3.696A pdb=" N ILE M 420 " --> pdb=" O GLY M 416 " (cutoff:3.500A) Processing helix chain 'M' and resid 433 through 459 Proline residue: M 450 - end of helix Processing helix chain 'M' and resid 461 through 472 removed outlier: 3.562A pdb=" N VAL M 465 " --> pdb=" O GLU M 461 " (cutoff:3.500A) Processing helix chain 'M' and resid 497 through 516 Processing helix chain 'N' and resid 9 through 29 removed outlier: 4.179A 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 85 Processing helix chain 'N' and resid 88 through 110 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 140 through 152 Processing helix chain 'N' and resid 155 through 170 Processing helix chain 'N' and resid 201 through 205 Processing helix chain 'N' and resid 229 through 244 removed outlier: 4.441A pdb=" N MET N 233 " --> pdb=" O ASN N 229 " (cutoff:3.500A) Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 255 through 269 removed outlier: 3.657A pdb=" N LEU N 259 " --> pdb=" O GLU N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 297 Processing helix chain 'N' and resid 338 through 355 Processing helix chain 'N' and resid 358 through 375 removed outlier: 3.949A pdb=" N GLY N 375 " --> pdb=" O LYS N 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 427 removed outlier: 3.752A pdb=" N ILE N 420 " --> pdb=" O GLY N 416 " (cutoff:3.500A) Processing helix chain 'N' and resid 433 through 459 Proline residue: N 450 - end of helix Processing helix chain 'N' and resid 461 through 472 Processing helix chain 'N' and resid 497 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.514A pdb=" N ASN G 37 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS A 519 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.953A pdb=" N ASN A 37 " --> pdb=" O CYS B 519 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N VAL B 521 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 39 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N ASP B 523 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.670A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU A 178 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 195 removed outlier: 6.281A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 192 through 195 removed outlier: 6.281A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'A' and resid 476 through 479 removed outlier: 3.590A pdb=" N GLU A 484 " --> pdb=" O ASN A 479 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.934A pdb=" N ASN B 37 " --> pdb=" O CYS C 519 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N VAL C 521 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B 39 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N ASP C 523 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 174 through 179 Processing sheet with id=AB1, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.236A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.236A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA B 251 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AB4, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.573A pdb=" N GLU B 484 " --> pdb=" O ASN B 479 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.462A pdb=" N ASN C 37 " --> pdb=" O THR D 517 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N CYS D 519 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS D 7 " --> pdb=" O MET D 520 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 174 through 179 removed outlier: 6.654A pdb=" N VAL C 174 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE C 379 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR C 176 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL C 381 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU C 178 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 195 removed outlier: 6.255A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 193 through 195 removed outlier: 6.255A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU C 247 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL C 276 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE C 249 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC1, first strand: chain 'C' and resid 476 through 479 removed outlier: 3.632A pdb=" N GLU C 484 " --> pdb=" O ASN C 479 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 48 through 50 removed outlier: 7.044A pdb=" N ASN D 37 " --> pdb=" O CYS E 519 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N VAL E 521 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 39 " --> pdb=" O VAL E 521 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ASP E 523 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 174 through 179 removed outlier: 6.499A pdb=" N VAL D 174 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE D 379 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU D 178 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.185A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.438A 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: 6.185A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 251 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AC7, first strand: chain 'D' and resid 476 through 478 Processing sheet with id=AC8, first strand: chain 'E' and resid 48 through 50 removed outlier: 7.018A pdb=" N ASN E 37 " --> pdb=" O CYS F 519 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N VAL F 521 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL E 39 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N ASP F 523 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 174 through 179 removed outlier: 6.626A pdb=" N VAL E 174 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE E 379 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR E 176 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL E 381 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU E 178 " --> pdb=" O VAL E 381 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 192 through 195 removed outlier: 6.201A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.461A 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: 6.201A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 3.565A 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 478 Processing sheet with id=AD5, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.983A pdb=" N ASN F 37 " --> pdb=" O CYS G 519 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N VAL G 521 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL F 39 " --> pdb=" O VAL G 521 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ASP G 523 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 174 through 179 removed outlier: 6.487A pdb=" N VAL F 174 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE F 379 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR F 176 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL F 381 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU F 178 " --> pdb=" O VAL F 381 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 193 through 195 removed outlier: 6.180A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA F 251 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 213 through 216 removed outlier: 8.393A pdb=" N ILE F 301 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU F 222 " --> pdb=" O ILE F 301 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AE1, first strand: chain 'F' and resid 476 through 479 removed outlier: 3.595A pdb=" N GLU F 484 " --> pdb=" O ASN F 479 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 174 through 179 removed outlier: 6.508A pdb=" N VAL G 174 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE G 379 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR G 176 " --> pdb=" O ILE G 379 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL G 381 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU G 178 " --> pdb=" O VAL G 381 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 192 through 195 removed outlier: 6.165A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 192 through 195 removed outlier: 6.165A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU G 247 " --> pdb=" O ALA G 274 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL G 276 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE G 249 " --> pdb=" O VAL G 276 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AE6, first strand: chain 'G' and resid 476 through 478 Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.511A pdb=" N LYS H 7 " --> pdb=" O MET H 520 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASN N 37 " --> pdb=" O THR H 517 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N CYS H 519 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 48 through 50 removed outlier: 7.061A pdb=" N ASN H 37 " --> pdb=" O CYS I 519 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N VAL I 521 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL H 39 " --> pdb=" O VAL I 521 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ASP I 523 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 174 through 179 Processing sheet with id=AF1, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.230A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.230A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA H 251 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AF4, first strand: chain 'H' and resid 476 through 479 removed outlier: 3.691A pdb=" N GLU H 484 " --> pdb=" O ASN H 479 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.929A pdb=" N ASN I 37 " --> pdb=" O CYS J 519 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL J 521 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL I 39 " --> pdb=" O VAL J 521 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ASP J 523 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 174 through 179 removed outlier: 6.713A pdb=" N VAL I 174 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE I 379 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR I 176 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL I 381 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU I 178 " --> pdb=" O VAL I 381 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.235A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL I 323 " --> pdb=" O LEU I 215 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.235A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AG1, first strand: chain 'I' and resid 476 through 479 removed outlier: 3.600A pdb=" N GLU I 484 " --> pdb=" O ASN I 479 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 48 through 50 removed outlier: 7.048A pdb=" N ASN J 37 " --> pdb=" O CYS K 519 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL K 521 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL J 39 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N ASP K 523 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 174 through 179 Processing sheet with id=AG4, first strand: chain 'J' and resid 193 through 195 removed outlier: 6.235A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 193 through 195 removed outlier: 6.235A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA J 251 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AG7, first strand: chain 'J' and resid 476 through 479 removed outlier: 3.606A pdb=" N GLU J 484 " --> pdb=" O ASN J 479 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 48 through 50 removed outlier: 7.024A pdb=" N ASN K 37 " --> pdb=" O CYS L 519 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N VAL L 521 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL K 39 " --> pdb=" O VAL L 521 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N ASP L 523 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 174 through 179 removed outlier: 3.600A pdb=" N GLU K 186 " --> pdb=" O LYS K 380 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 192 through 195 removed outlier: 6.202A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 192 through 195 removed outlier: 6.202A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU K 247 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL K 276 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE K 249 " --> pdb=" O VAL K 276 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AH4, first strand: chain 'K' and resid 476 through 479 removed outlier: 3.517A pdb=" N GLU K 484 " --> pdb=" O ASN K 479 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 48 through 50 removed outlier: 6.947A pdb=" N ASN L 37 " --> pdb=" O CYS M 519 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N VAL M 521 " --> pdb=" O ASN L 37 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL L 39 " --> pdb=" O VAL M 521 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ASP M 523 " --> pdb=" O VAL L 39 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 174 through 179 Processing sheet with id=AH7, first strand: chain 'L' and resid 193 through 195 removed outlier: 3.767A pdb=" N ARG L 322 " --> pdb=" O ILE L 333 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 193 through 195 removed outlier: 3.767A pdb=" N ARG L 322 " --> pdb=" O ILE L 333 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA L 251 " --> pdb=" O VAL L 276 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AI1, first strand: chain 'L' and resid 476 through 479 removed outlier: 3.649A pdb=" N GLU L 484 " --> pdb=" O ASN L 479 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 48 through 50 removed outlier: 6.370A pdb=" N ASN M 37 " --> pdb=" O THR N 517 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N CYS N 519 " --> pdb=" O ASN M 37 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 174 through 179 removed outlier: 6.623A pdb=" N VAL M 174 " --> pdb=" O ALA M 377 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE M 379 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR M 176 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL M 381 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU M 178 " --> pdb=" O VAL M 381 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 193 through 195 removed outlier: 6.328A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 213 through 216 removed outlier: 8.187A pdb=" N ILE M 301 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU M 222 " --> pdb=" O ILE M 301 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AI7, first strand: chain 'M' and resid 476 through 478 Processing sheet with id=AI8, first strand: chain 'N' and resid 174 through 179 Processing sheet with id=AI9, first strand: chain 'N' and resid 193 through 195 Processing sheet with id=AJ1, first strand: chain 'N' and resid 273 through 277 removed outlier: 3.601A pdb=" N ALA N 251 " --> pdb=" O VAL N 276 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AJ3, first strand: chain 'N' and resid 476 through 479 removed outlier: 3.620A pdb=" N GLU N 484 " --> pdb=" O ASN N 479 " (cutoff:3.500A) 3834 hydrogen bonds defined for protein. 11121 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: 20.96 Time building geometry restraints manager: 17.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18504 1.34 - 1.46: 5277 1.46 - 1.58: 30063 1.58 - 1.70: 0 1.70 - 1.82: 518 Bond restraints: 54362 Sorted by residual: bond pdb=" SD MET D 16 " pdb=" CE MET D 16 " ideal model delta sigma weight residual 1.791 1.757 0.034 2.50e-02 1.60e+03 1.90e+00 bond pdb=" CD GLU C 164 " pdb=" OE1 GLU C 164 " ideal model delta sigma weight residual 1.249 1.227 0.022 1.90e-02 2.77e+03 1.39e+00 bond pdb=" N GLY H 198 " pdb=" CA GLY H 198 " ideal model delta sigma weight residual 1.442 1.451 -0.009 7.70e-03 1.69e+04 1.36e+00 bond pdb=" N VAL G 336 " pdb=" CA VAL G 336 " ideal model delta sigma weight residual 1.474 1.459 0.016 1.57e-02 4.06e+03 9.99e-01 bond pdb=" CB MET D 16 " pdb=" CG MET D 16 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.55e-01 ... (remaining 54357 not shown) Histogram of bond angle deviations from ideal: 97.70 - 104.41: 658 104.41 - 111.12: 21755 111.12 - 117.82: 20225 117.82 - 124.53: 30521 124.53 - 131.23: 243 Bond angle restraints: 73402 Sorted by residual: angle pdb=" N GLU C 164 " pdb=" CA GLU C 164 " pdb=" CB GLU C 164 " ideal model delta sigma weight residual 110.39 116.87 -6.48 1.66e+00 3.63e-01 1.52e+01 angle pdb=" N GLN G 351 " pdb=" CA GLN G 351 " pdb=" CB GLN G 351 " ideal model delta sigma weight residual 110.28 115.96 -5.68 1.55e+00 4.16e-01 1.34e+01 angle pdb=" N GLN B 351 " pdb=" CA GLN B 351 " pdb=" CB GLN B 351 " ideal model delta sigma weight residual 110.28 115.94 -5.66 1.55e+00 4.16e-01 1.33e+01 angle pdb=" CA MET H 166 " pdb=" CB MET H 166 " pdb=" CG MET H 166 " ideal model delta sigma weight residual 114.10 121.11 -7.01 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA GLU C 164 " pdb=" CB GLU C 164 " pdb=" CG GLU C 164 " ideal model delta sigma weight residual 114.10 121.00 -6.90 2.00e+00 2.50e-01 1.19e+01 ... (remaining 73397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 30525 17.84 - 35.69: 2701 35.69 - 53.53: 448 53.53 - 71.37: 74 71.37 - 89.22: 20 Dihedral angle restraints: 33768 sinusoidal: 13076 harmonic: 20692 Sorted by residual: dihedral pdb=" CA ILE M 60 " pdb=" C ILE M 60 " pdb=" N GLU M 61 " pdb=" CA GLU M 61 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLU L 61 " pdb=" C GLU L 61 " pdb=" N LEU L 62 " pdb=" CA LEU L 62 " ideal model delta harmonic sigma weight residual 180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ILE F 60 " pdb=" C ILE F 60 " pdb=" N GLU F 61 " pdb=" CA GLU F 61 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 33765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 6252 0.033 - 0.065: 1757 0.065 - 0.098: 601 0.098 - 0.130: 310 0.130 - 0.163: 12 Chirality restraints: 8932 Sorted by residual: chirality pdb=" CG LEU B 234 " pdb=" CB LEU B 234 " pdb=" CD1 LEU B 234 " pdb=" CD2 LEU B 234 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA GLU F 164 " pdb=" N GLU F 164 " pdb=" C GLU F 164 " pdb=" CB GLU F 164 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA MET M 288 " pdb=" N MET M 288 " pdb=" C MET M 288 " pdb=" CB MET M 288 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 8929 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET M 288 " -0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C MET M 288 " 0.020 2.00e-02 2.50e+03 pdb=" O MET M 288 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU M 289 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN L 112 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO L 113 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO L 113 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO L 113 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU M 461 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO M 462 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO M 462 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO M 462 " -0.015 5.00e-02 4.00e+02 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 8771 2.76 - 3.29: 57767 3.29 - 3.83: 95658 3.83 - 4.36: 106362 4.36 - 4.90: 185068 Nonbonded interactions: 453626 Sorted by model distance: nonbonded pdb=" OH TYR L 478 " pdb=" OE1 GLU L 483 " model vdw 2.224 2.440 nonbonded pdb=" OG SER E 463 " pdb=" OG SER H 463 " model vdw 2.225 2.440 nonbonded pdb=" OD1 ASP H 291 " pdb=" NH2 ARG H 345 " model vdw 2.227 2.520 nonbonded pdb=" OH TYR D 478 " pdb=" OE1 GLU D 483 " model vdw 2.234 2.440 nonbonded pdb=" O VAL M 263 " pdb=" OG1 THR M 266 " model vdw 2.241 2.440 ... (remaining 453621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.490 Check model and map are aligned: 0.620 Set scattering table: 0.370 Process input model: 111.070 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 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 0.034 54362 Z= 0.143 Angle : 0.486 9.444 73402 Z= 0.269 Chirality : 0.039 0.163 8932 Planarity : 0.003 0.028 9618 Dihedral : 13.498 89.215 20496 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.10), residues: 7308 helix: 2.44 (0.08), residues: 4214 sheet: 1.25 (0.15), residues: 1260 loop : -0.18 (0.15), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.015 0.001 PHE A 44 TYR 0.017 0.001 TYR L 360 ARG 0.007 0.000 ARG D 18 *********************** 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 296 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 4.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.4912 time to fit residues: 254.2820 Evaluate side-chains 276 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 4.582 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1921 ------------------------------------------------------------------------------- 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: 10.0000 chunk 551 optimal weight: 40.0000 chunk 306 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 372 optimal weight: 20.0000 chunk 294 optimal weight: 20.0000 chunk 570 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 346 optimal weight: 20.0000 chunk 424 optimal weight: 20.0000 chunk 661 optimal weight: 0.6980 overall best weight: 4.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 54362 Z= 0.239 Angle : 0.497 8.491 73402 Z= 0.270 Chirality : 0.040 0.189 8932 Planarity : 0.003 0.040 9618 Dihedral : 3.852 19.491 7728 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.51 % Allowed : 5.66 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.10), residues: 7308 helix: 2.46 (0.08), residues: 4242 sheet: 1.11 (0.15), residues: 1176 loop : -0.04 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.012 0.001 PHE N 195 TYR 0.008 0.001 TYR L 476 ARG 0.008 0.000 ARG K 284 *********************** 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 310 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 281 time to evaluate : 4.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 8 residues processed: 300 average time/residue: 0.4938 time to fit residues: 260.9808 Evaluate side-chains 288 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 280 time to evaluate : 4.607 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4338 time to fit residues: 12.5388 ------------------------------------------------------------------------------- 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: 9.9990 chunk 205 optimal weight: 8.9990 chunk 550 optimal weight: 20.0000 chunk 450 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 662 optimal weight: 9.9990 chunk 715 optimal weight: 6.9990 chunk 589 optimal weight: 30.0000 chunk 656 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 chunk 531 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 479 ASN ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 GLN ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 366 GLN ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 475 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 54362 Z= 0.272 Angle : 0.502 10.088 73402 Z= 0.272 Chirality : 0.040 0.187 8932 Planarity : 0.003 0.036 9618 Dihedral : 3.891 19.603 7728 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.53 % Allowed : 9.35 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.10), residues: 7308 helix: 2.43 (0.08), residues: 4228 sheet: 0.87 (0.15), residues: 1176 loop : -0.14 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.011 0.001 PHE F 204 TYR 0.015 0.001 TYR M 360 ARG 0.004 0.000 ARG G 345 *********************** 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 312 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 282 time to evaluate : 4.654 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 outliers start: 30 outliers final: 9 residues processed: 303 average time/residue: 0.4919 time to fit residues: 264.2626 Evaluate side-chains 288 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 279 time to evaluate : 4.570 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4192 time to fit residues: 13.0895 ------------------------------------------------------------------------------- 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: 0.7980 chunk 497 optimal weight: 10.0000 chunk 343 optimal weight: 40.0000 chunk 73 optimal weight: 1.9990 chunk 316 optimal weight: 9.9990 chunk 444 optimal weight: 20.0000 chunk 664 optimal weight: 10.0000 chunk 703 optimal weight: 30.0000 chunk 347 optimal weight: 8.9990 chunk 629 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 54362 Z= 0.265 Angle : 0.503 10.526 73402 Z= 0.271 Chirality : 0.040 0.180 8932 Planarity : 0.003 0.035 9618 Dihedral : 3.905 19.485 7728 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.60 % Allowed : 11.09 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.10), residues: 7308 helix: 2.42 (0.08), residues: 4228 sheet: 0.79 (0.15), residues: 1176 loop : -0.17 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.010 0.001 PHE N 195 TYR 0.015 0.001 TYR M 360 ARG 0.004 0.000 ARG G 345 *********************** 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 320 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 286 time to evaluate : 4.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 13 residues processed: 306 average time/residue: 0.5024 time to fit residues: 270.6433 Evaluate side-chains 292 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 279 time to evaluate : 4.619 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4361 time to fit residues: 16.4261 ------------------------------------------------------------------------------- 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: 20.0000 chunk 399 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 523 optimal weight: 9.9990 chunk 290 optimal weight: 6.9990 chunk 600 optimal weight: 6.9990 chunk 486 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 359 optimal weight: 10.0000 chunk 631 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 54362 Z= 0.261 Angle : 0.506 8.936 73402 Z= 0.273 Chirality : 0.040 0.182 8932 Planarity : 0.003 0.037 9618 Dihedral : 3.923 19.283 7728 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.53 % Allowed : 12.43 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.10), residues: 7308 helix: 2.40 (0.08), residues: 4228 sheet: 0.75 (0.15), residues: 1176 loop : -0.18 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.012 0.001 PHE N 195 TYR 0.016 0.001 TYR M 360 ARG 0.006 0.000 ARG J 284 *********************** 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 311 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 281 time to evaluate : 4.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 12 residues processed: 305 average time/residue: 0.5013 time to fit residues: 269.7610 Evaluate side-chains 293 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 281 time to evaluate : 4.608 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4110 time to fit residues: 15.3792 ------------------------------------------------------------------------------- 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: 9.9990 chunk 633 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 413 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 704 optimal weight: 7.9990 chunk 584 optimal weight: 3.9990 chunk 326 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 232 optimal weight: 3.9990 chunk 369 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 54362 Z= 0.236 Angle : 0.498 9.561 73402 Z= 0.267 Chirality : 0.039 0.194 8932 Planarity : 0.003 0.034 9618 Dihedral : 3.916 19.018 7728 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.57 % Allowed : 13.22 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.10), residues: 7308 helix: 2.40 (0.08), residues: 4228 sheet: 0.73 (0.15), residues: 1176 loop : -0.18 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.011 0.001 PHE N 195 TYR 0.017 0.001 TYR M 360 ARG 0.003 0.000 ARG G 345 *********************** 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 317 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 285 time to evaluate : 4.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 304 average time/residue: 0.5110 time to fit residues: 273.0632 Evaluate side-chains 300 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 283 time to evaluate : 4.676 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4306 time to fit residues: 19.5838 ------------------------------------------------------------------------------- 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: 5.9990 chunk 79 optimal weight: 7.9990 chunk 401 optimal weight: 6.9990 chunk 514 optimal weight: 0.9980 chunk 398 optimal weight: 5.9990 chunk 592 optimal weight: 4.9990 chunk 393 optimal weight: 40.0000 chunk 701 optimal weight: 30.0000 chunk 439 optimal weight: 6.9990 chunk 427 optimal weight: 5.9990 chunk 323 optimal weight: 0.8980 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN E 479 ASN ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1274 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= 0.199 Angle : 0.491 10.581 73402 Z= 0.263 Chirality : 0.039 0.194 8932 Planarity : 0.003 0.031 9618 Dihedral : 3.882 18.720 7728 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.50 % Allowed : 13.60 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.10), residues: 7308 helix: 2.42 (0.08), residues: 4228 sheet: 0.72 (0.15), residues: 1176 loop : -0.16 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.023 0.001 PHE B 195 TYR 0.017 0.001 TYR M 360 ARG 0.003 0.000 ARG G 345 *********************** 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 313 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 285 time to evaluate : 5.157 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 outliers start: 28 outliers final: 14 residues processed: 306 average time/residue: 0.5162 time to fit residues: 277.1241 Evaluate side-chains 295 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 281 time to evaluate : 4.699 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4236 time to fit residues: 17.2419 ------------------------------------------------------------------------------- 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: 6.9990 chunk 280 optimal weight: 3.9990 chunk 419 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 446 optimal weight: 10.0000 chunk 478 optimal weight: 5.9990 chunk 346 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 551 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN E 479 ASN ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 479 ASN ** H 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 366 GLN ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 366 GLN ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 54362 Z= 0.305 Angle : 0.546 12.597 73402 Z= 0.290 Chirality : 0.040 0.183 8932 Planarity : 0.003 0.038 9618 Dihedral : 3.948 19.455 7728 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.50 % Allowed : 13.99 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.10), residues: 7308 helix: 2.35 (0.08), residues: 4228 sheet: 0.67 (0.15), residues: 1176 loop : -0.24 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.012 0.001 PHE B 195 TYR 0.017 0.001 TYR M 360 ARG 0.003 0.000 ARG G 345 *********************** 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 310 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 282 time to evaluate : 4.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 303 average time/residue: 0.5048 time to fit residues: 269.9547 Evaluate side-chains 290 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 280 time to evaluate : 4.663 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4167 time to fit residues: 13.9231 ------------------------------------------------------------------------------- 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: 0.9990 chunk 672 optimal weight: 7.9990 chunk 613 optimal weight: 10.0000 chunk 653 optimal weight: 40.0000 chunk 393 optimal weight: 7.9990 chunk 284 optimal weight: 0.0170 chunk 513 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 590 optimal weight: 20.0000 chunk 618 optimal weight: 2.9990 chunk 651 optimal weight: 6.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN E 479 ASN ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 479 ASN ** H 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 505 GLN ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 54362 Z= 0.171 Angle : 0.523 12.145 73402 Z= 0.277 Chirality : 0.039 0.194 8932 Planarity : 0.003 0.029 9618 Dihedral : 3.907 18.897 7728 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.18 % Allowed : 14.41 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.10), residues: 7308 helix: 2.41 (0.08), residues: 4228 sheet: 0.68 (0.15), residues: 1176 loop : -0.13 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.019 0.001 PHE B 195 TYR 0.018 0.001 TYR M 360 ARG 0.004 0.000 ARG I 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14616 Ramachandran restraints generated. 7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 286 time to evaluate : 4.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 293 average time/residue: 0.5171 time to fit residues: 265.3020 Evaluate side-chains 287 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 282 time to evaluate : 4.760 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4120 time to fit residues: 10.1575 ------------------------------------------------------------------------------- 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: 7.9990 chunk 691 optimal weight: 5.9990 chunk 422 optimal weight: 10.0000 chunk 328 optimal weight: 6.9990 chunk 480 optimal weight: 5.9990 chunk 725 optimal weight: 5.9990 chunk 667 optimal weight: 3.9990 chunk 577 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 446 optimal weight: 30.0000 chunk 354 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN E 479 ASN ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 479 ASN ** H 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54362 Z= 0.230 Angle : 0.540 13.145 73402 Z= 0.285 Chirality : 0.039 0.181 8932 Planarity : 0.003 0.033 9618 Dihedral : 3.906 18.923 7728 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.12 % Allowed : 14.66 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.10), residues: 7308 helix: 2.38 (0.08), residues: 4228 sheet: 0.66 (0.15), residues: 1176 loop : -0.17 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.015 0.001 PHE B 195 TYR 0.016 0.001 TYR M 360 ARG 0.004 0.000 ARG I 368 ********************** 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 291 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 284 time to evaluate : 4.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 288 average time/residue: 0.5048 time to fit residues: 258.3103 Evaluate side-chains 287 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 283 time to evaluate : 4.625 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4617 time to fit residues: 9.4959 ------------------------------------------------------------------------------- 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: 8.9990 chunk 615 optimal weight: 8.9990 chunk 176 optimal weight: 0.9980 chunk 532 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 578 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 593 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 479 ASN ** G 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.057773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.041631 restraints weight = 238927.521| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.70 r_work: 0.2804 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 54362 Z= 0.177 Angle : 0.526 12.693 73402 Z= 0.278 Chirality : 0.039 0.186 8932 Planarity : 0.003 0.028 9618 Dihedral : 3.882 21.442 7728 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.09 % Allowed : 14.85 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.10), residues: 7308 helix: 2.42 (0.08), residues: 4200 sheet: 0.67 (0.15), residues: 1176 loop : -0.16 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.017 0.001 PHE B 195 TYR 0.017 0.001 TYR M 360 ARG 0.003 0.000 ARG I 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7047.40 seconds wall clock time: 128 minutes 21.82 seconds (7701.82 seconds total)