Starting phenix.real_space_refine on Mon Jun 24 20:01:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xol_33351/06_2024/7xol_33351.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xol_33351/06_2024/7xol_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_33351/06_2024/7xol_33351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xol_33351/06_2024/7xol_33351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xol_33351/06_2024/7xol_33351.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xol_33351/06_2024/7xol_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: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 20.91, per 1000 atoms: 0.39 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: 16.87 Conformation dependent library (CDL) restraints added in 8.3 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: 4.92 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: 20.36 Time building geometry restraints manager: 18.61 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 6.350 Check model and map are aligned: 0.300 Set scattering table: 0.360 Process input model: 110.460 Find NCS groups from input model: 2.950 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.860 ------------------------------------------------------------------------------- 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 : 4.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8316 (tm-30) REVERT: F 233 MET cc_start: 0.8445 (ppp) cc_final: 0.8204 (tmm) REVERT: F 389 MET cc_start: 0.9191 (tmm) cc_final: 0.8787 (tmm) REVERT: G 10 ASN cc_start: 0.8623 (t0) cc_final: 0.8360 (t0) REVERT: G 307 MET cc_start: 0.9037 (pmm) cc_final: 0.8829 (pmm) REVERT: G 389 MET cc_start: 0.8818 (tmm) cc_final: 0.8338 (tmm) REVERT: H 166 MET cc_start: 0.7838 (tpt) cc_final: 0.7577 (tpt) REVERT: H 288 MET cc_start: 0.9004 (mtm) cc_final: 0.8688 (mtm) REVERT: H 488 MET cc_start: 0.8856 (mmm) cc_final: 0.8483 (mmm) REVERT: I 288 MET cc_start: 0.8926 (mtm) cc_final: 0.8599 (mtm) REVERT: I 307 MET cc_start: 0.8696 (ppp) cc_final: 0.8369 (ppp) REVERT: J 69 MET cc_start: 0.8533 (mtt) cc_final: 0.8324 (mtt) REVERT: J 488 MET cc_start: 0.9248 (mmm) cc_final: 0.8855 (mmm) REVERT: K 233 MET cc_start: 0.8707 (ppp) cc_final: 0.8142 (tmm) REVERT: K 288 MET cc_start: 0.8562 (mpp) cc_final: 0.7780 (mpp) REVERT: K 389 MET cc_start: 0.8797 (tmm) cc_final: 0.8573 (tmm) REVERT: L 288 MET cc_start: 0.8813 (mpp) cc_final: 0.8249 (mpp) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.4722 time to fit residues: 245.3322 Evaluate side-chains 278 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 4.558 ------------------------------------------------------------------------------- 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: 0.8668 moved from start: 0.0660 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= 0.238 Angle : 0.489 8.420 73402 Z= 0.268 Chirality : 0.040 0.195 8932 Planarity : 0.003 0.036 9618 Dihedral : 3.834 19.457 7728 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.48 % Allowed : 5.30 % Favored : 94.22 % 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: 2.44 (0.10), residues: 7308 helix: 2.47 (0.08), residues: 4242 sheet: 1.12 (0.15), residues: 1176 loop : -0.03 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.017 0.001 PHE N 195 TYR 0.008 0.001 TYR L 476 ARG 0.004 0.000 ARG F 345 *********************** 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 308 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 281 time to evaluate : 4.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8402 (tm-30) REVERT: B 234 LEU cc_start: 0.9041 (mt) cc_final: 0.8794 (mt) REVERT: D 69 MET cc_start: 0.8646 (mmt) cc_final: 0.7936 (mmt) REVERT: D 389 MET cc_start: 0.9055 (tmm) cc_final: 0.8774 (tmm) REVERT: D 520 MET cc_start: 0.8398 (mpp) cc_final: 0.8037 (mtm) REVERT: F 389 MET cc_start: 0.9214 (tmm) cc_final: 0.8771 (tmm) REVERT: G 10 ASN cc_start: 0.8712 (t0) cc_final: 0.8448 (t0) REVERT: G 389 MET cc_start: 0.8770 (tmm) cc_final: 0.8279 (tmm) REVERT: H 164 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8780 (pm20) REVERT: H 288 MET cc_start: 0.9100 (mtm) cc_final: 0.8730 (mtm) REVERT: H 488 MET cc_start: 0.8794 (mmm) cc_final: 0.8406 (mmm) REVERT: I 288 MET cc_start: 0.8936 (mtm) cc_final: 0.8604 (mtt) REVERT: I 307 MET cc_start: 0.8661 (ppp) cc_final: 0.8315 (ppp) REVERT: K 233 MET cc_start: 0.8756 (ppp) cc_final: 0.8180 (tmm) REVERT: K 307 MET cc_start: 0.9199 (pmm) cc_final: 0.8670 (pmm) REVERT: K 389 MET cc_start: 0.8872 (tmm) cc_final: 0.8621 (tmm) outliers start: 27 outliers final: 9 residues processed: 298 average time/residue: 0.4838 time to fit residues: 254.5767 Evaluate side-chains 290 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 280 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 351 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 550 optimal weight: 40.0000 chunk 450 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 662 optimal weight: 6.9990 chunk 715 optimal weight: 5.9990 chunk 589 optimal weight: 4.9990 chunk 656 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 531 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 54362 Z= 0.249 Angle : 0.483 7.850 73402 Z= 0.264 Chirality : 0.040 0.173 8932 Planarity : 0.003 0.035 9618 Dihedral : 3.867 19.429 7728 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.67 % Allowed : 9.02 % Favored : 90.31 % 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: 2.34 (0.10), residues: 7308 helix: 2.46 (0.08), residues: 4242 sheet: 0.87 (0.15), residues: 1176 loop : -0.08 (0.14), residues: 1890 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 F 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 321 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 283 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.8933 (ppp) cc_final: 0.8694 (ppp) REVERT: C 69 MET cc_start: 0.8982 (mmt) cc_final: 0.8464 (mmt) REVERT: D 389 MET cc_start: 0.9064 (tmm) cc_final: 0.8739 (tmm) REVERT: E 233 MET cc_start: 0.8859 (ppp) cc_final: 0.8608 (ppp) REVERT: F 389 MET cc_start: 0.9246 (tmm) cc_final: 0.8892 (tmm) REVERT: G 10 ASN cc_start: 0.8757 (t0) cc_final: 0.8491 (t0) REVERT: G 351 GLN cc_start: 0.9467 (OUTLIER) cc_final: 0.8996 (pp30) REVERT: G 389 MET cc_start: 0.8722 (tmm) cc_final: 0.8229 (tmm) REVERT: H 164 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8760 (pm20) REVERT: H 288 MET cc_start: 0.9137 (mtm) cc_final: 0.8759 (mtm) REVERT: H 488 MET cc_start: 0.8818 (mmm) cc_final: 0.8407 (mmm) REVERT: I 288 MET cc_start: 0.8903 (mtm) cc_final: 0.8529 (mtt) REVERT: I 307 MET cc_start: 0.8695 (ppp) cc_final: 0.8392 (ppp) REVERT: K 233 MET cc_start: 0.8783 (ppp) cc_final: 0.8211 (tmm) REVERT: K 307 MET cc_start: 0.9224 (pmm) cc_final: 0.8699 (pmm) REVERT: K 389 MET cc_start: 0.8923 (tmm) cc_final: 0.8639 (tmm) REVERT: L 233 MET cc_start: 0.8887 (ppp) cc_final: 0.8633 (ppp) REVERT: L 288 MET cc_start: 0.8596 (mmm) cc_final: 0.7857 (mpp) REVERT: M 114 MET cc_start: 0.8541 (mmm) cc_final: 0.8334 (mmm) REVERT: M 389 MET cc_start: 0.8728 (tmm) cc_final: 0.8046 (tmm) outliers start: 38 outliers final: 16 residues processed: 308 average time/residue: 0.4817 time to fit residues: 259.8184 Evaluate side-chains 297 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 279 time to evaluate : 4.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain F residue 266 THR Chi-restraints excluded: chain G residue 16 MET Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 351 GLN Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 355 GLU Chi-restraints excluded: chain L residue 354 GLU Chi-restraints excluded: chain M residue 111 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.5102 > 50: distance: 18 - 105: 4.701 distance: 21 - 102: 7.794 distance: 63 - 113: 12.090 distance: 66 - 110: 8.668 distance: 77 - 98: 17.555 distance: 80 - 95: 7.107 distance: 90 - 95: 8.165 distance: 95 - 96: 5.763 distance: 96 - 97: 10.434 distance: 96 - 99: 7.213 distance: 97 - 98: 15.330 distance: 97 - 102: 6.882 distance: 99 - 100: 4.694 distance: 99 - 101: 7.677 distance: 102 - 103: 4.043 distance: 103 - 104: 4.881 distance: 104 - 105: 6.659 distance: 104 - 110: 4.972 distance: 106 - 107: 4.129 distance: 106 - 108: 6.398 distance: 107 - 109: 6.269 distance: 110 - 111: 3.695 distance: 111 - 112: 9.201 distance: 111 - 114: 3.125 distance: 112 - 113: 12.513 distance: 112 - 118: 8.380 distance: 114 - 115: 5.106 distance: 114 - 116: 4.133 distance: 115 - 117: 12.010 distance: 118 - 119: 7.198 distance: 119 - 120: 17.139 distance: 119 - 122: 4.373 distance: 120 - 121: 19.164 distance: 120 - 126: 31.369 distance: 122 - 123: 24.920 distance: 123 - 124: 5.316 distance: 123 - 125: 12.066 distance: 126 - 127: 22.896 distance: 127 - 128: 19.655 distance: 128 - 129: 25.070 distance: 128 - 130: 14.882 distance: 130 - 131: 3.080 distance: 131 - 132: 5.663 distance: 131 - 134: 3.468 distance: 132 - 133: 8.524 distance: 132 - 137: 5.672 distance: 134 - 135: 14.614 distance: 134 - 136: 11.172 distance: 137 - 138: 11.419 distance: 138 - 139: 14.819 distance: 139 - 140: 13.342 distance: 139 - 141: 3.843 distance: 141 - 142: 6.549 distance: 142 - 143: 5.620 distance: 143 - 144: 3.130 distance: 143 - 150: 3.691 distance: 144 - 169: 4.503 distance: 145 - 146: 12.895 distance: 146 - 147: 5.850 distance: 147 - 148: 9.158 distance: 147 - 149: 8.688 distance: 150 - 151: 6.193 distance: 151 - 152: 4.218 distance: 151 - 154: 3.507 distance: 152 - 159: 3.191 distance: 153 - 177: 10.481 distance: 154 - 155: 14.678 distance: 155 - 156: 9.434 distance: 156 - 157: 9.282 distance: 156 - 158: 5.133 distance: 159 - 160: 10.517 distance: 160 - 161: 5.608 distance: 160 - 163: 10.220 distance: 161 - 162: 8.865 distance: 162 - 186: 12.884