Starting phenix.real_space_refine on Mon Nov 20 23:19:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yx3_14353/11_2023/7yx3_14353_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yx3_14353/11_2023/7yx3_14353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yx3_14353/11_2023/7yx3_14353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yx3_14353/11_2023/7yx3_14353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yx3_14353/11_2023/7yx3_14353_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yx3_14353/11_2023/7yx3_14353_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 288 5.16 5 C 57906 2.51 5 N 15678 2.21 5 O 17208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 566": "OE1" <-> "OE2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 332": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 566": "OE1" <-> "OE2" Residue "D GLU 607": "OE1" <-> "OE2" Residue "E GLU 254": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E GLU 332": "OE1" <-> "OE2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "F PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 566": "OE1" <-> "OE2" Residue "F GLU 607": "OE1" <-> "OE2" Residue "G GLU 254": "OE1" <-> "OE2" Residue "G GLU 294": "OE1" <-> "OE2" Residue "G GLU 332": "OE1" <-> "OE2" Residue "H GLU 254": "OE1" <-> "OE2" Residue "H GLU 294": "OE1" <-> "OE2" Residue "H PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 566": "OE1" <-> "OE2" Residue "H GLU 607": "OE1" <-> "OE2" Residue "I GLU 254": "OE1" <-> "OE2" Residue "I GLU 294": "OE1" <-> "OE2" Residue "I GLU 332": "OE1" <-> "OE2" Residue "J GLU 254": "OE1" <-> "OE2" Residue "J GLU 294": "OE1" <-> "OE2" Residue "J PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 566": "OE1" <-> "OE2" Residue "J GLU 607": "OE1" <-> "OE2" Residue "K GLU 254": "OE1" <-> "OE2" Residue "K GLU 294": "OE1" <-> "OE2" Residue "K GLU 332": "OE1" <-> "OE2" Residue "L GLU 254": "OE1" <-> "OE2" Residue "L GLU 294": "OE1" <-> "OE2" Residue "L PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 566": "OE1" <-> "OE2" Residue "L GLU 607": "OE1" <-> "OE2" Residue "M GLU 254": "OE1" <-> "OE2" Residue "M GLU 294": "OE1" <-> "OE2" Residue "M GLU 332": "OE1" <-> "OE2" Residue "N GLU 254": "OE1" <-> "OE2" Residue "N GLU 294": "OE1" <-> "OE2" Residue "N PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 566": "OE1" <-> "OE2" Residue "N GLU 607": "OE1" <-> "OE2" Residue "O GLU 254": "OE1" <-> "OE2" Residue "O GLU 294": "OE1" <-> "OE2" Residue "O GLU 332": "OE1" <-> "OE2" Residue "P GLU 254": "OE1" <-> "OE2" Residue "P GLU 294": "OE1" <-> "OE2" Residue "P PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 566": "OE1" <-> "OE2" Residue "P GLU 607": "OE1" <-> "OE2" Residue "Q GLU 254": "OE1" <-> "OE2" Residue "Q GLU 294": "OE1" <-> "OE2" Residue "Q GLU 332": "OE1" <-> "OE2" Residue "R GLU 254": "OE1" <-> "OE2" Residue "R GLU 294": "OE1" <-> "OE2" Residue "R PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 566": "OE1" <-> "OE2" Residue "R GLU 607": "OE1" <-> "OE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 91116 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "B" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "D" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "F" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "H" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "G" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "J" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "I" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "L" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "K" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "N" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "M" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "P" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "O" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "R" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 5009 Classifications: {'peptide': 649} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 39, 'TRANS': 609} Chain: "Q" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 34.97, per 1000 atoms: 0.38 Number of scatterers: 91116 At special positions: 0 Unit cell: (327, 319.37, 154.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 288 16.00 P 36 15.00 O 17208 8.00 N 15678 7.00 C 57906 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: 28.93 Conformation dependent library (CDL) restraints added in 12.5 seconds 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21240 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 423 helices and 117 sheets defined 32.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 69.68 Creating SS restraints... Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 96 through 99 No H-bonds generated for 'chain 'A' and resid 96 through 99' Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 150 through 153 removed outlier: 3.570A pdb=" N MET A 153 " --> pdb=" O GLY A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 153' Processing helix chain 'A' and resid 165 through 168 No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 177 through 191 removed outlier: 5.769A pdb=" N ASN A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TYR A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 220 Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 350 through 359 Proline residue: A 354 - end of helix Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 439 through 442 removed outlier: 4.588A pdb=" N ASN A 442 " --> pdb=" O ALA A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 461 through 467 Processing helix chain 'A' and resid 521 through 558 Proline residue: A 526 - end of helix removed outlier: 3.694A pdb=" N ALA A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) Proline residue: A 534 - end of helix Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.757A pdb=" N TYR A 592 " --> pdb=" O TRP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 598 No H-bonds generated for 'chain 'A' and resid 595 through 598' Processing helix chain 'A' and resid 603 through 621 removed outlier: 4.615A pdb=" N TYR A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR A 618 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Proline residue: A 619 - end of helix Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 668 through 683 removed outlier: 4.206A pdb=" N SER A 672 " --> pdb=" O TRP A 668 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 690 No H-bonds generated for 'chain 'A' and resid 687 through 690' Processing helix chain 'B' and resid 66 through 77 Processing helix chain 'B' and resid 96 through 99 No H-bonds generated for 'chain 'B' and resid 96 through 99' Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 150 through 153 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 177 through 191 removed outlier: 5.654A pdb=" N ASN B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 220 Processing helix chain 'B' and resid 282 through 285 No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 439 through 442 removed outlier: 4.109A pdb=" N ASN B 442 " --> pdb=" O ALA B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 461 through 467 Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'B' and resid 533 through 559 removed outlier: 4.073A pdb=" N GLN B 554 " --> pdb=" O ILE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 592 removed outlier: 7.118A pdb=" N ALA B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN B 588 " --> pdb=" O THR B 584 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP B 589 " --> pdb=" O TYR B 585 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TRP B 590 " --> pdb=" O GLY B 586 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR B 592 " --> pdb=" O ASN B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 598 No H-bonds generated for 'chain 'B' and resid 595 through 598' Processing helix chain 'B' and resid 603 through 621 removed outlier: 4.056A pdb=" N TYR B 617 " --> pdb=" O SER B 613 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR B 618 " --> pdb=" O LYS B 614 " (cutoff:3.500A) Proline residue: B 619 - end of helix Processing helix chain 'B' and resid 656 through 658 No H-bonds generated for 'chain 'B' and resid 656 through 658' Processing helix chain 'B' and resid 668 through 683 removed outlier: 3.519A pdb=" N ASP B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 690 No H-bonds generated for 'chain 'B' and resid 688 through 690' Processing helix chain 'C' and resid 68 through 77 Processing helix chain 'C' and resid 96 through 99 No H-bonds generated for 'chain 'C' and resid 96 through 99' Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 150 through 153 removed outlier: 3.570A pdb=" N MET C 153 " --> pdb=" O GLY C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 150 through 153' Processing helix chain 'C' and resid 165 through 168 No H-bonds generated for 'chain 'C' and resid 165 through 168' Processing helix chain 'C' and resid 177 through 191 removed outlier: 5.770A pdb=" N ASN C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TYR C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 220 Processing helix chain 'C' and resid 283 through 286 No H-bonds generated for 'chain 'C' and resid 283 through 286' Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'C' and resid 350 through 359 Proline residue: C 354 - end of helix Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 439 through 442 removed outlier: 4.588A pdb=" N ASN C 442 " --> pdb=" O ALA C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 461 through 467 Processing helix chain 'C' and resid 521 through 558 Proline residue: C 526 - end of helix removed outlier: 3.693A pdb=" N ALA C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) Proline residue: C 534 - end of helix Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 589 through 593 removed outlier: 3.758A pdb=" N TYR C 592 " --> pdb=" O TRP C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 598 No H-bonds generated for 'chain 'C' and resid 595 through 598' Processing helix chain 'C' and resid 603 through 621 removed outlier: 4.614A pdb=" N TYR C 617 " --> pdb=" O SER C 613 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR C 618 " --> pdb=" O LYS C 614 " (cutoff:3.500A) Proline residue: C 619 - end of helix Processing helix chain 'C' and resid 656 through 658 No H-bonds generated for 'chain 'C' and resid 656 through 658' Processing helix chain 'C' and resid 668 through 683 removed outlier: 4.206A pdb=" N SER C 672 " --> pdb=" O TRP C 668 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 680 " --> pdb=" O ALA C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 690 No H-bonds generated for 'chain 'C' and resid 687 through 690' Processing helix chain 'D' and resid 66 through 77 Processing helix chain 'D' and resid 96 through 99 No H-bonds generated for 'chain 'D' and resid 96 through 99' Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 111 through 113 No H-bonds generated for 'chain 'D' and resid 111 through 113' Processing helix chain 'D' and resid 117 through 119 No H-bonds generated for 'chain 'D' and resid 117 through 119' Processing helix chain 'D' and resid 150 through 153 Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 177 through 191 removed outlier: 5.654A pdb=" N ASN D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 220 Processing helix chain 'D' and resid 282 through 285 No H-bonds generated for 'chain 'D' and resid 282 through 285' Processing helix chain 'D' and resid 300 through 302 No H-bonds generated for 'chain 'D' and resid 300 through 302' Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 403 through 409 Processing helix chain 'D' and resid 439 through 442 removed outlier: 4.109A pdb=" N ASN D 442 " --> pdb=" O ALA D 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 461 through 467 Processing helix chain 'D' and resid 525 through 531 Processing helix chain 'D' and resid 533 through 559 removed outlier: 4.073A pdb=" N GLN D 554 " --> pdb=" O ILE D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 592 removed outlier: 7.118A pdb=" N ALA D 587 " --> pdb=" O ALA D 583 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASN D 588 " --> pdb=" O THR D 584 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP D 589 " --> pdb=" O TYR D 585 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TRP D 590 " --> pdb=" O GLY D 586 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS D 591 " --> pdb=" O ALA D 587 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TYR D 592 " --> pdb=" O ASN D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 598 No H-bonds generated for 'chain 'D' and resid 595 through 598' Processing helix chain 'D' and resid 603 through 621 removed outlier: 4.056A pdb=" N TYR D 617 " --> pdb=" O SER D 613 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR D 618 " --> pdb=" O LYS D 614 " (cutoff:3.500A) Proline residue: D 619 - end of helix Processing helix chain 'D' and resid 656 through 658 No H-bonds generated for 'chain 'D' and resid 656 through 658' Processing helix chain 'D' and resid 668 through 683 removed outlier: 3.519A pdb=" N ASP D 680 " --> pdb=" O ALA D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 690 No H-bonds generated for 'chain 'D' and resid 688 through 690' Processing helix chain 'E' and resid 68 through 77 Processing helix chain 'E' and resid 96 through 99 No H-bonds generated for 'chain 'E' and resid 96 through 99' Processing helix chain 'E' and resid 101 through 105 Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 150 through 153 removed outlier: 3.570A pdb=" N MET E 153 " --> pdb=" O GLY E 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 150 through 153' Processing helix chain 'E' and resid 165 through 168 No H-bonds generated for 'chain 'E' and resid 165 through 168' Processing helix chain 'E' and resid 177 through 191 removed outlier: 5.770A pdb=" N ASN E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TYR E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 220 Processing helix chain 'E' and resid 283 through 286 No H-bonds generated for 'chain 'E' and resid 283 through 286' Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 350 through 359 Proline residue: E 354 - end of helix Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 403 through 409 Processing helix chain 'E' and resid 439 through 442 removed outlier: 4.588A pdb=" N ASN E 442 " --> pdb=" O ALA E 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 439 through 442' Processing helix chain 'E' and resid 461 through 467 Processing helix chain 'E' and resid 521 through 558 Proline residue: E 526 - end of helix removed outlier: 3.693A pdb=" N ALA E 533 " --> pdb=" O GLN E 529 " (cutoff:3.500A) Proline residue: E 534 - end of helix Processing helix chain 'E' and resid 572 through 585 Processing helix chain 'E' and resid 589 through 593 removed outlier: 3.757A pdb=" N TYR E 592 " --> pdb=" O TRP E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 595 through 598 No H-bonds generated for 'chain 'E' and resid 595 through 598' Processing helix chain 'E' and resid 603 through 621 removed outlier: 4.614A pdb=" N TYR E 617 " --> pdb=" O SER E 613 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR E 618 " --> pdb=" O LYS E 614 " (cutoff:3.500A) Proline residue: E 619 - end of helix Processing helix chain 'E' and resid 656 through 658 No H-bonds generated for 'chain 'E' and resid 656 through 658' Processing helix chain 'E' and resid 668 through 683 removed outlier: 4.206A pdb=" N SER E 672 " --> pdb=" O TRP E 668 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP E 680 " --> pdb=" O ALA E 676 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 690 No H-bonds generated for 'chain 'E' and resid 687 through 690' Processing helix chain 'F' and resid 66 through 77 Processing helix chain 'F' and resid 96 through 99 No H-bonds generated for 'chain 'F' and resid 96 through 99' Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'F' and resid 117 through 119 No H-bonds generated for 'chain 'F' and resid 117 through 119' Processing helix chain 'F' and resid 150 through 153 Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'F' and resid 177 through 191 removed outlier: 5.654A pdb=" N ASN F 182 " --> pdb=" O ASP F 178 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR F 183 " --> pdb=" O ASP F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 220 Processing helix chain 'F' and resid 282 through 285 No H-bonds generated for 'chain 'F' and resid 282 through 285' Processing helix chain 'F' and resid 300 through 302 No H-bonds generated for 'chain 'F' and resid 300 through 302' Processing helix chain 'F' and resid 353 through 360 Processing helix chain 'F' and resid 365 through 371 Processing helix chain 'F' and resid 403 through 409 Processing helix chain 'F' and resid 439 through 442 removed outlier: 4.110A pdb=" N ASN F 442 " --> pdb=" O ALA F 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 439 through 442' Processing helix chain 'F' and resid 461 through 467 Processing helix chain 'F' and resid 525 through 531 Processing helix chain 'F' and resid 533 through 559 removed outlier: 4.073A pdb=" N GLN F 554 " --> pdb=" O ILE F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 592 removed outlier: 7.118A pdb=" N ALA F 587 " --> pdb=" O ALA F 583 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASN F 588 " --> pdb=" O THR F 584 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP F 589 " --> pdb=" O TYR F 585 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TRP F 590 " --> pdb=" O GLY F 586 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS F 591 " --> pdb=" O ALA F 587 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR F 592 " --> pdb=" O ASN F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 595 through 598 No H-bonds generated for 'chain 'F' and resid 595 through 598' Processing helix chain 'F' and resid 603 through 621 removed outlier: 4.056A pdb=" N TYR F 617 " --> pdb=" O SER F 613 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR F 618 " --> pdb=" O LYS F 614 " (cutoff:3.500A) Proline residue: F 619 - end of helix Processing helix chain 'F' and resid 656 through 658 No H-bonds generated for 'chain 'F' and resid 656 through 658' Processing helix chain 'F' and resid 668 through 683 removed outlier: 3.520A pdb=" N ASP F 680 " --> pdb=" O ALA F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 688 through 690 No H-bonds generated for 'chain 'F' and resid 688 through 690' Processing helix chain 'G' and resid 68 through 77 Processing helix chain 'G' and resid 96 through 99 No H-bonds generated for 'chain 'G' and resid 96 through 99' Processing helix chain 'G' and resid 101 through 105 Processing helix chain 'G' and resid 133 through 135 No H-bonds generated for 'chain 'G' and resid 133 through 135' Processing helix chain 'G' and resid 150 through 153 removed outlier: 3.570A pdb=" N MET G 153 " --> pdb=" O GLY G 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 150 through 153' Processing helix chain 'G' and resid 165 through 168 No H-bonds generated for 'chain 'G' and resid 165 through 168' Processing helix chain 'G' and resid 177 through 191 removed outlier: 5.769A pdb=" N ASN G 182 " --> pdb=" O ASP G 178 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TYR G 183 " --> pdb=" O ASP G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 220 Processing helix chain 'G' and resid 283 through 286 No H-bonds generated for 'chain 'G' and resid 283 through 286' Processing helix chain 'G' and resid 300 through 302 No H-bonds generated for 'chain 'G' and resid 300 through 302' Processing helix chain 'G' and resid 350 through 359 Proline residue: G 354 - end of helix Processing helix chain 'G' and resid 365 through 371 Processing helix chain 'G' and resid 403 through 409 Processing helix chain 'G' and resid 439 through 442 removed outlier: 4.587A pdb=" N ASN G 442 " --> pdb=" O ALA G 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 439 through 442' Processing helix chain 'G' and resid 461 through 467 Processing helix chain 'G' and resid 521 through 558 Proline residue: G 526 - end of helix removed outlier: 3.694A pdb=" N ALA G 533 " --> pdb=" O GLN G 529 " (cutoff:3.500A) Proline residue: G 534 - end of helix Processing helix chain 'G' and resid 572 through 585 Processing helix chain 'G' and resid 589 through 593 removed outlier: 3.757A pdb=" N TYR G 592 " --> pdb=" O TRP G 589 " (cutoff:3.500A) Processing helix chain 'G' and resid 595 through 598 No H-bonds generated for 'chain 'G' and resid 595 through 598' Processing helix chain 'G' and resid 603 through 621 removed outlier: 4.615A pdb=" N TYR G 617 " --> pdb=" O SER G 613 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR G 618 " --> pdb=" O LYS G 614 " (cutoff:3.500A) Proline residue: G 619 - end of helix Processing helix chain 'G' and resid 656 through 658 No H-bonds generated for 'chain 'G' and resid 656 through 658' Processing helix chain 'G' and resid 668 through 683 removed outlier: 4.206A pdb=" N SER G 672 " --> pdb=" O TRP G 668 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP G 680 " --> pdb=" O ALA G 676 " (cutoff:3.500A) Processing helix chain 'G' and resid 687 through 690 No H-bonds generated for 'chain 'G' and resid 687 through 690' Processing helix chain 'H' and resid 66 through 77 Processing helix chain 'H' and resid 96 through 99 No H-bonds generated for 'chain 'H' and resid 96 through 99' Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 111 through 113 No H-bonds generated for 'chain 'H' and resid 111 through 113' Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 150 through 153 Processing helix chain 'H' and resid 165 through 169 Processing helix chain 'H' and resid 177 through 191 removed outlier: 5.654A pdb=" N ASN H 182 " --> pdb=" O ASP H 178 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR H 183 " --> pdb=" O ASP H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 220 Processing helix chain 'H' and resid 282 through 285 No H-bonds generated for 'chain 'H' and resid 282 through 285' Processing helix chain 'H' and resid 300 through 302 No H-bonds generated for 'chain 'H' and resid 300 through 302' Processing helix chain 'H' and resid 353 through 360 Processing helix chain 'H' and resid 365 through 371 Processing helix chain 'H' and resid 403 through 409 Processing helix chain 'H' and resid 439 through 442 removed outlier: 4.109A pdb=" N ASN H 442 " --> pdb=" O ALA H 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 439 through 442' Processing helix chain 'H' and resid 461 through 467 Processing helix chain 'H' and resid 525 through 531 Processing helix chain 'H' and resid 533 through 559 removed outlier: 4.073A pdb=" N GLN H 554 " --> pdb=" O ILE H 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 572 through 592 removed outlier: 7.117A pdb=" N ALA H 587 " --> pdb=" O ALA H 583 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASN H 588 " --> pdb=" O THR H 584 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP H 589 " --> pdb=" O TYR H 585 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TRP H 590 " --> pdb=" O GLY H 586 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS H 591 " --> pdb=" O ALA H 587 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR H 592 " --> pdb=" O ASN H 588 " (cutoff:3.500A) Processing helix chain 'H' and resid 595 through 598 No H-bonds generated for 'chain 'H' and resid 595 through 598' Processing helix chain 'H' and resid 603 through 621 removed outlier: 4.056A pdb=" N TYR H 617 " --> pdb=" O SER H 613 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR H 618 " --> pdb=" O LYS H 614 " (cutoff:3.500A) Proline residue: H 619 - end of helix Processing helix chain 'H' and resid 656 through 658 No H-bonds generated for 'chain 'H' and resid 656 through 658' Processing helix chain 'H' and resid 668 through 683 removed outlier: 3.519A pdb=" N ASP H 680 " --> pdb=" O ALA H 676 " (cutoff:3.500A) Processing helix chain 'H' and resid 688 through 690 No H-bonds generated for 'chain 'H' and resid 688 through 690' Processing helix chain 'I' and resid 68 through 77 Processing helix chain 'I' and resid 96 through 99 No H-bonds generated for 'chain 'I' and resid 96 through 99' Processing helix chain 'I' and resid 101 through 105 Processing helix chain 'I' and resid 133 through 135 No H-bonds generated for 'chain 'I' and resid 133 through 135' Processing helix chain 'I' and resid 150 through 153 removed outlier: 3.570A pdb=" N MET I 153 " --> pdb=" O GLY I 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 150 through 153' Processing helix chain 'I' and resid 165 through 168 No H-bonds generated for 'chain 'I' and resid 165 through 168' Processing helix chain 'I' and resid 177 through 191 removed outlier: 5.769A pdb=" N ASN I 182 " --> pdb=" O ASP I 178 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TYR I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 220 Processing helix chain 'I' and resid 283 through 286 No H-bonds generated for 'chain 'I' and resid 283 through 286' Processing helix chain 'I' and resid 300 through 302 No H-bonds generated for 'chain 'I' and resid 300 through 302' Processing helix chain 'I' and resid 350 through 359 Proline residue: I 354 - end of helix Processing helix chain 'I' and resid 365 through 371 Processing helix chain 'I' and resid 403 through 409 Processing helix chain 'I' and resid 439 through 442 removed outlier: 4.588A pdb=" N ASN I 442 " --> pdb=" O ALA I 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 439 through 442' Processing helix chain 'I' and resid 461 through 467 Processing helix chain 'I' and resid 521 through 558 Proline residue: I 526 - end of helix removed outlier: 3.693A pdb=" N ALA I 533 " --> pdb=" O GLN I 529 " (cutoff:3.500A) Proline residue: I 534 - end of helix Processing helix chain 'I' and resid 572 through 585 Processing helix chain 'I' and resid 589 through 593 removed outlier: 3.757A pdb=" N TYR I 592 " --> pdb=" O TRP I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 595 through 598 No H-bonds generated for 'chain 'I' and resid 595 through 598' Processing helix chain 'I' and resid 603 through 621 removed outlier: 4.615A pdb=" N TYR I 617 " --> pdb=" O SER I 613 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR I 618 " --> pdb=" O LYS I 614 " (cutoff:3.500A) Proline residue: I 619 - end of helix Processing helix chain 'I' and resid 656 through 658 No H-bonds generated for 'chain 'I' and resid 656 through 658' Processing helix chain 'I' and resid 668 through 683 removed outlier: 4.207A pdb=" N SER I 672 " --> pdb=" O TRP I 668 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP I 680 " --> pdb=" O ALA I 676 " (cutoff:3.500A) Processing helix chain 'I' and resid 687 through 690 No H-bonds generated for 'chain 'I' and resid 687 through 690' Processing helix chain 'J' and resid 66 through 77 Processing helix chain 'J' and resid 96 through 99 No H-bonds generated for 'chain 'J' and resid 96 through 99' Processing helix chain 'J' and resid 101 through 105 Processing helix chain 'J' and resid 111 through 113 No H-bonds generated for 'chain 'J' and resid 111 through 113' Processing helix chain 'J' and resid 117 through 119 No H-bonds generated for 'chain 'J' and resid 117 through 119' Processing helix chain 'J' and resid 150 through 153 Processing helix chain 'J' and resid 165 through 169 Processing helix chain 'J' and resid 177 through 191 removed outlier: 5.654A pdb=" N ASN J 182 " --> pdb=" O ASP J 178 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR J 183 " --> pdb=" O ASP J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 220 Processing helix chain 'J' and resid 282 through 285 No H-bonds generated for 'chain 'J' and resid 282 through 285' Processing helix chain 'J' and resid 300 through 302 No H-bonds generated for 'chain 'J' and resid 300 through 302' Processing helix chain 'J' and resid 353 through 360 Processing helix chain 'J' and resid 365 through 371 Processing helix chain 'J' and resid 403 through 409 Processing helix chain 'J' and resid 439 through 442 removed outlier: 4.109A pdb=" N ASN J 442 " --> pdb=" O ALA J 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 439 through 442' Processing helix chain 'J' and resid 461 through 467 Processing helix chain 'J' and resid 525 through 531 Processing helix chain 'J' and resid 533 through 559 removed outlier: 4.073A pdb=" N GLN J 554 " --> pdb=" O ILE J 550 " (cutoff:3.500A) Processing helix chain 'J' and resid 572 through 592 removed outlier: 7.118A pdb=" N ALA J 587 " --> pdb=" O ALA J 583 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN J 588 " --> pdb=" O THR J 584 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP J 589 " --> pdb=" O TYR J 585 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TRP J 590 " --> pdb=" O GLY J 586 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS J 591 " --> pdb=" O ALA J 587 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR J 592 " --> pdb=" O ASN J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 595 through 598 No H-bonds generated for 'chain 'J' and resid 595 through 598' Processing helix chain 'J' and resid 603 through 621 removed outlier: 4.056A pdb=" N TYR J 617 " --> pdb=" O SER J 613 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR J 618 " --> pdb=" O LYS J 614 " (cutoff:3.500A) Proline residue: J 619 - end of helix Processing helix chain 'J' and resid 656 through 658 No H-bonds generated for 'chain 'J' and resid 656 through 658' Processing helix chain 'J' and resid 668 through 683 removed outlier: 3.519A pdb=" N ASP J 680 " --> pdb=" O ALA J 676 " (cutoff:3.500A) Processing helix chain 'J' and resid 688 through 690 No H-bonds generated for 'chain 'J' and resid 688 through 690' Processing helix chain 'K' and resid 68 through 77 Processing helix chain 'K' and resid 96 through 99 No H-bonds generated for 'chain 'K' and resid 96 through 99' Processing helix chain 'K' and resid 101 through 105 Processing helix chain 'K' and resid 133 through 135 No H-bonds generated for 'chain 'K' and resid 133 through 135' Processing helix chain 'K' and resid 150 through 153 removed outlier: 3.570A pdb=" N MET K 153 " --> pdb=" O GLY K 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 150 through 153' Processing helix chain 'K' and resid 165 through 168 No H-bonds generated for 'chain 'K' and resid 165 through 168' Processing helix chain 'K' and resid 177 through 191 removed outlier: 5.769A pdb=" N ASN K 182 " --> pdb=" O ASP K 178 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TYR K 183 " --> pdb=" O ASP K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 220 Processing helix chain 'K' and resid 283 through 286 No H-bonds generated for 'chain 'K' and resid 283 through 286' Processing helix chain 'K' and resid 300 through 302 No H-bonds generated for 'chain 'K' and resid 300 through 302' Processing helix chain 'K' and resid 350 through 359 Proline residue: K 354 - end of helix Processing helix chain 'K' and resid 365 through 371 Processing helix chain 'K' and resid 403 through 409 Processing helix chain 'K' and resid 439 through 442 removed outlier: 4.588A pdb=" N ASN K 442 " --> pdb=" O ALA K 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 439 through 442' Processing helix chain 'K' and resid 461 through 467 Processing helix chain 'K' and resid 521 through 558 Proline residue: K 526 - end of helix removed outlier: 3.693A pdb=" N ALA K 533 " --> pdb=" O GLN K 529 " (cutoff:3.500A) Proline residue: K 534 - end of helix Processing helix chain 'K' and resid 572 through 585 Processing helix chain 'K' and resid 589 through 593 removed outlier: 3.757A pdb=" N TYR K 592 " --> pdb=" O TRP K 589 " (cutoff:3.500A) Processing helix chain 'K' and resid 595 through 598 No H-bonds generated for 'chain 'K' and resid 595 through 598' Processing helix chain 'K' and resid 603 through 621 removed outlier: 4.615A pdb=" N TYR K 617 " --> pdb=" O SER K 613 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR K 618 " --> pdb=" O LYS K 614 " (cutoff:3.500A) Proline residue: K 619 - end of helix Processing helix chain 'K' and resid 656 through 658 No H-bonds generated for 'chain 'K' and resid 656 through 658' Processing helix chain 'K' and resid 668 through 683 removed outlier: 4.206A pdb=" N SER K 672 " --> pdb=" O TRP K 668 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP K 680 " --> pdb=" O ALA K 676 " (cutoff:3.500A) Processing helix chain 'K' and resid 687 through 690 No H-bonds generated for 'chain 'K' and resid 687 through 690' Processing helix chain 'L' and resid 66 through 77 Processing helix chain 'L' and resid 96 through 99 No H-bonds generated for 'chain 'L' and resid 96 through 99' Processing helix chain 'L' and resid 101 through 105 Processing helix chain 'L' and resid 111 through 113 No H-bonds generated for 'chain 'L' and resid 111 through 113' Processing helix chain 'L' and resid 117 through 119 No H-bonds generated for 'chain 'L' and resid 117 through 119' Processing helix chain 'L' and resid 150 through 153 Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'L' and resid 177 through 191 removed outlier: 5.654A pdb=" N ASN L 182 " --> pdb=" O ASP L 178 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR L 183 " --> pdb=" O ASP L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 220 Processing helix chain 'L' and resid 282 through 285 No H-bonds generated for 'chain 'L' and resid 282 through 285' Processing helix chain 'L' and resid 300 through 302 No H-bonds generated for 'chain 'L' and resid 300 through 302' Processing helix chain 'L' and resid 353 through 360 Processing helix chain 'L' and resid 365 through 371 Processing helix chain 'L' and resid 403 through 409 Processing helix chain 'L' and resid 439 through 442 removed outlier: 4.110A pdb=" N ASN L 442 " --> pdb=" O ALA L 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 439 through 442' Processing helix chain 'L' and resid 461 through 467 Processing helix chain 'L' and resid 525 through 531 Processing helix chain 'L' and resid 533 through 559 removed outlier: 4.072A pdb=" N GLN L 554 " --> pdb=" O ILE L 550 " (cutoff:3.500A) Processing helix chain 'L' and resid 572 through 592 removed outlier: 7.118A pdb=" N ALA L 587 " --> pdb=" O ALA L 583 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN L 588 " --> pdb=" O THR L 584 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP L 589 " --> pdb=" O TYR L 585 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TRP L 590 " --> pdb=" O GLY L 586 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS L 591 " --> pdb=" O ALA L 587 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR L 592 " --> pdb=" O ASN L 588 " (cutoff:3.500A) Processing helix chain 'L' and resid 595 through 598 No H-bonds generated for 'chain 'L' and resid 595 through 598' Processing helix chain 'L' and resid 603 through 621 removed outlier: 4.056A pdb=" N TYR L 617 " --> pdb=" O SER L 613 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR L 618 " --> pdb=" O LYS L 614 " (cutoff:3.500A) Proline residue: L 619 - end of helix Processing helix chain 'L' and resid 656 through 658 No H-bonds generated for 'chain 'L' and resid 656 through 658' Processing helix chain 'L' and resid 668 through 683 removed outlier: 3.519A pdb=" N ASP L 680 " --> pdb=" O ALA L 676 " (cutoff:3.500A) Processing helix chain 'L' and resid 688 through 690 No H-bonds generated for 'chain 'L' and resid 688 through 690' Processing helix chain 'M' and resid 68 through 77 Processing helix chain 'M' and resid 96 through 99 No H-bonds generated for 'chain 'M' and resid 96 through 99' Processing helix chain 'M' and resid 101 through 105 Processing helix chain 'M' and resid 133 through 135 No H-bonds generated for 'chain 'M' and resid 133 through 135' Processing helix chain 'M' and resid 150 through 153 removed outlier: 3.570A pdb=" N MET M 153 " --> pdb=" O GLY M 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 150 through 153' Processing helix chain 'M' and resid 165 through 168 No H-bonds generated for 'chain 'M' and resid 165 through 168' Processing helix chain 'M' and resid 177 through 191 removed outlier: 5.770A pdb=" N ASN M 182 " --> pdb=" O ASP M 178 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N TYR M 183 " --> pdb=" O ASP M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 220 Processing helix chain 'M' and resid 283 through 286 No H-bonds generated for 'chain 'M' and resid 283 through 286' Processing helix chain 'M' and resid 300 through 302 No H-bonds generated for 'chain 'M' and resid 300 through 302' Processing helix chain 'M' and resid 350 through 359 Proline residue: M 354 - end of helix Processing helix chain 'M' and resid 365 through 371 Processing helix chain 'M' and resid 403 through 409 Processing helix chain 'M' and resid 439 through 442 removed outlier: 4.587A pdb=" N ASN M 442 " --> pdb=" O ALA M 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 439 through 442' Processing helix chain 'M' and resid 461 through 467 Processing helix chain 'M' and resid 521 through 558 Proline residue: M 526 - end of helix removed outlier: 3.693A pdb=" N ALA M 533 " --> pdb=" O GLN M 529 " (cutoff:3.500A) Proline residue: M 534 - end of helix Processing helix chain 'M' and resid 572 through 585 Processing helix chain 'M' and resid 589 through 593 removed outlier: 3.757A pdb=" N TYR M 592 " --> pdb=" O TRP M 589 " (cutoff:3.500A) Processing helix chain 'M' and resid 595 through 598 No H-bonds generated for 'chain 'M' and resid 595 through 598' Processing helix chain 'M' and resid 603 through 621 removed outlier: 4.614A pdb=" N TYR M 617 " --> pdb=" O SER M 613 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR M 618 " --> pdb=" O LYS M 614 " (cutoff:3.500A) Proline residue: M 619 - end of helix Processing helix chain 'M' and resid 656 through 658 No H-bonds generated for 'chain 'M' and resid 656 through 658' Processing helix chain 'M' and resid 668 through 683 removed outlier: 4.207A pdb=" N SER M 672 " --> pdb=" O TRP M 668 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP M 680 " --> pdb=" O ALA M 676 " (cutoff:3.500A) Processing helix chain 'M' and resid 687 through 690 No H-bonds generated for 'chain 'M' and resid 687 through 690' Processing helix chain 'N' and resid 66 through 77 Processing helix chain 'N' and resid 96 through 99 No H-bonds generated for 'chain 'N' and resid 96 through 99' Processing helix chain 'N' and resid 101 through 105 Processing helix chain 'N' and resid 111 through 113 No H-bonds generated for 'chain 'N' and resid 111 through 113' Processing helix chain 'N' and resid 117 through 119 No H-bonds generated for 'chain 'N' and resid 117 through 119' Processing helix chain 'N' and resid 150 through 153 Processing helix chain 'N' and resid 165 through 169 Processing helix chain 'N' and resid 177 through 191 removed outlier: 5.654A pdb=" N ASN N 182 " --> pdb=" O ASP N 178 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR N 183 " --> pdb=" O ASP N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 220 Processing helix chain 'N' and resid 282 through 285 No H-bonds generated for 'chain 'N' and resid 282 through 285' Processing helix chain 'N' and resid 300 through 302 No H-bonds generated for 'chain 'N' and resid 300 through 302' Processing helix chain 'N' and resid 353 through 360 Processing helix chain 'N' and resid 365 through 371 Processing helix chain 'N' and resid 403 through 409 Processing helix chain 'N' and resid 439 through 442 removed outlier: 4.109A pdb=" N ASN N 442 " --> pdb=" O ALA N 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 439 through 442' Processing helix chain 'N' and resid 461 through 467 Processing helix chain 'N' and resid 525 through 531 Processing helix chain 'N' and resid 533 through 559 removed outlier: 4.073A pdb=" N GLN N 554 " --> pdb=" O ILE N 550 " (cutoff:3.500A) Processing helix chain 'N' and resid 572 through 592 removed outlier: 7.118A pdb=" N ALA N 587 " --> pdb=" O ALA N 583 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ASN N 588 " --> pdb=" O THR N 584 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP N 589 " --> pdb=" O TYR N 585 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TRP N 590 " --> pdb=" O GLY N 586 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS N 591 " --> pdb=" O ALA N 587 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR N 592 " --> pdb=" O ASN N 588 " (cutoff:3.500A) Processing helix chain 'N' and resid 595 through 598 No H-bonds generated for 'chain 'N' and resid 595 through 598' Processing helix chain 'N' and resid 603 through 621 removed outlier: 4.056A pdb=" N TYR N 617 " --> pdb=" O SER N 613 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR N 618 " --> pdb=" O LYS N 614 " (cutoff:3.500A) Proline residue: N 619 - end of helix Processing helix chain 'N' and resid 656 through 658 No H-bonds generated for 'chain 'N' and resid 656 through 658' Processing helix chain 'N' and resid 668 through 683 removed outlier: 3.519A pdb=" N ASP N 680 " --> pdb=" O ALA N 676 " (cutoff:3.500A) Processing helix chain 'N' and resid 688 through 690 No H-bonds generated for 'chain 'N' and resid 688 through 690' Processing helix chain 'O' and resid 68 through 77 Processing helix chain 'O' and resid 96 through 99 No H-bonds generated for 'chain 'O' and resid 96 through 99' Processing helix chain 'O' and resid 101 through 105 Processing helix chain 'O' and resid 133 through 135 No H-bonds generated for 'chain 'O' and resid 133 through 135' Processing helix chain 'O' and resid 150 through 153 removed outlier: 3.570A pdb=" N MET O 153 " --> pdb=" O GLY O 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 150 through 153' Processing helix chain 'O' and resid 165 through 168 No H-bonds generated for 'chain 'O' and resid 165 through 168' Processing helix chain 'O' and resid 177 through 191 removed outlier: 5.770A pdb=" N ASN O 182 " --> pdb=" O ASP O 178 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TYR O 183 " --> pdb=" O ASP O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 201 through 220 Processing helix chain 'O' and resid 283 through 286 No H-bonds generated for 'chain 'O' and resid 283 through 286' Processing helix chain 'O' and resid 300 through 302 No H-bonds generated for 'chain 'O' and resid 300 through 302' Processing helix chain 'O' and resid 350 through 359 Proline residue: O 354 - end of helix Processing helix chain 'O' and resid 365 through 371 Processing helix chain 'O' and resid 403 through 409 Processing helix chain 'O' and resid 439 through 442 removed outlier: 4.588A pdb=" N ASN O 442 " --> pdb=" O ALA O 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 439 through 442' Processing helix chain 'O' and resid 461 through 467 Processing helix chain 'O' and resid 521 through 558 Proline residue: O 526 - end of helix removed outlier: 3.694A pdb=" N ALA O 533 " --> pdb=" O GLN O 529 " (cutoff:3.500A) Proline residue: O 534 - end of helix Processing helix chain 'O' and resid 572 through 585 Processing helix chain 'O' and resid 589 through 593 removed outlier: 3.757A pdb=" N TYR O 592 " --> pdb=" O TRP O 589 " (cutoff:3.500A) Processing helix chain 'O' and resid 595 through 598 No H-bonds generated for 'chain 'O' and resid 595 through 598' Processing helix chain 'O' and resid 603 through 621 removed outlier: 4.615A pdb=" N TYR O 617 " --> pdb=" O SER O 613 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR O 618 " --> pdb=" O LYS O 614 " (cutoff:3.500A) Proline residue: O 619 - end of helix Processing helix chain 'O' and resid 656 through 658 No H-bonds generated for 'chain 'O' and resid 656 through 658' Processing helix chain 'O' and resid 668 through 683 removed outlier: 4.206A pdb=" N SER O 672 " --> pdb=" O TRP O 668 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP O 680 " --> pdb=" O ALA O 676 " (cutoff:3.500A) Processing helix chain 'O' and resid 687 through 690 No H-bonds generated for 'chain 'O' and resid 687 through 690' Processing helix chain 'P' and resid 66 through 77 Processing helix chain 'P' and resid 96 through 99 No H-bonds generated for 'chain 'P' and resid 96 through 99' Processing helix chain 'P' and resid 101 through 105 Processing helix chain 'P' and resid 111 through 113 No H-bonds generated for 'chain 'P' and resid 111 through 113' Processing helix chain 'P' and resid 117 through 119 No H-bonds generated for 'chain 'P' and resid 117 through 119' Processing helix chain 'P' and resid 150 through 153 Processing helix chain 'P' and resid 165 through 169 Processing helix chain 'P' and resid 177 through 191 removed outlier: 5.655A pdb=" N ASN P 182 " --> pdb=" O ASP P 178 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR P 183 " --> pdb=" O ASP P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 220 Processing helix chain 'P' and resid 282 through 285 No H-bonds generated for 'chain 'P' and resid 282 through 285' Processing helix chain 'P' and resid 300 through 302 No H-bonds generated for 'chain 'P' and resid 300 through 302' Processing helix chain 'P' and resid 353 through 360 Processing helix chain 'P' and resid 365 through 371 Processing helix chain 'P' and resid 403 through 409 Processing helix chain 'P' and resid 439 through 442 removed outlier: 4.109A pdb=" N ASN P 442 " --> pdb=" O ALA P 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 439 through 442' Processing helix chain 'P' and resid 461 through 467 Processing helix chain 'P' and resid 525 through 531 Processing helix chain 'P' and resid 533 through 559 removed outlier: 4.073A pdb=" N GLN P 554 " --> pdb=" O ILE P 550 " (cutoff:3.500A) Processing helix chain 'P' and resid 572 through 592 removed outlier: 7.119A pdb=" N ALA P 587 " --> pdb=" O ALA P 583 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ASN P 588 " --> pdb=" O THR P 584 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP P 589 " --> pdb=" O TYR P 585 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TRP P 590 " --> pdb=" O GLY P 586 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS P 591 " --> pdb=" O ALA P 587 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR P 592 " --> pdb=" O ASN P 588 " (cutoff:3.500A) Processing helix chain 'P' and resid 595 through 598 No H-bonds generated for 'chain 'P' and resid 595 through 598' Processing helix chain 'P' and resid 603 through 621 removed outlier: 4.055A pdb=" N TYR P 617 " --> pdb=" O SER P 613 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N TYR P 618 " --> pdb=" O LYS P 614 " (cutoff:3.500A) Proline residue: P 619 - end of helix Processing helix chain 'P' and resid 656 through 658 No H-bonds generated for 'chain 'P' and resid 656 through 658' Processing helix chain 'P' and resid 668 through 683 removed outlier: 3.519A pdb=" N ASP P 680 " --> pdb=" O ALA P 676 " (cutoff:3.500A) Processing helix chain 'P' and resid 688 through 690 No H-bonds generated for 'chain 'P' and resid 688 through 690' Processing helix chain 'Q' and resid 68 through 77 Processing helix chain 'Q' and resid 96 through 99 No H-bonds generated for 'chain 'Q' and resid 96 through 99' Processing helix chain 'Q' and resid 101 through 105 Processing helix chain 'Q' and resid 133 through 135 No H-bonds generated for 'chain 'Q' and resid 133 through 135' Processing helix chain 'Q' and resid 150 through 153 removed outlier: 3.570A pdb=" N MET Q 153 " --> pdb=" O GLY Q 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 150 through 153' Processing helix chain 'Q' and resid 165 through 168 No H-bonds generated for 'chain 'Q' and resid 165 through 168' Processing helix chain 'Q' and resid 177 through 191 removed outlier: 5.769A pdb=" N ASN Q 182 " --> pdb=" O ASP Q 178 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N TYR Q 183 " --> pdb=" O ASP Q 179 " (cutoff:3.500A) Processing helix chain 'Q' and resid 201 through 220 Processing helix chain 'Q' and resid 283 through 286 No H-bonds generated for 'chain 'Q' and resid 283 through 286' Processing helix chain 'Q' and resid 300 through 302 No H-bonds generated for 'chain 'Q' and resid 300 through 302' Processing helix chain 'Q' and resid 350 through 359 Proline residue: Q 354 - end of helix Processing helix chain 'Q' and resid 365 through 371 Processing helix chain 'Q' and resid 403 through 409 Processing helix chain 'Q' and resid 439 through 442 removed outlier: 4.588A pdb=" N ASN Q 442 " --> pdb=" O ALA Q 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 439 through 442' Processing helix chain 'Q' and resid 461 through 467 Processing helix chain 'Q' and resid 521 through 558 Proline residue: Q 526 - end of helix removed outlier: 3.695A pdb=" N ALA Q 533 " --> pdb=" O GLN Q 529 " (cutoff:3.500A) Proline residue: Q 534 - end of helix Processing helix chain 'Q' and resid 572 through 585 Processing helix chain 'Q' and resid 589 through 593 removed outlier: 3.757A pdb=" N TYR Q 592 " --> pdb=" O TRP Q 589 " (cutoff:3.500A) Processing helix chain 'Q' and resid 595 through 598 No H-bonds generated for 'chain 'Q' and resid 595 through 598' Processing helix chain 'Q' and resid 603 through 621 removed outlier: 4.615A pdb=" N TYR Q 617 " --> pdb=" O SER Q 613 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N TYR Q 618 " --> pdb=" O LYS Q 614 " (cutoff:3.500A) Proline residue: Q 619 - end of helix Processing helix chain 'Q' and resid 656 through 658 No H-bonds generated for 'chain 'Q' and resid 656 through 658' Processing helix chain 'Q' and resid 668 through 683 removed outlier: 4.206A pdb=" N SER Q 672 " --> pdb=" O TRP Q 668 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP Q 680 " --> pdb=" O ALA Q 676 " (cutoff:3.500A) Processing helix chain 'Q' and resid 687 through 690 No H-bonds generated for 'chain 'Q' and resid 687 through 690' Processing helix chain 'R' and resid 66 through 77 Processing helix chain 'R' and resid 96 through 99 No H-bonds generated for 'chain 'R' and resid 96 through 99' Processing helix chain 'R' and resid 101 through 105 Processing helix chain 'R' and resid 111 through 113 No H-bonds generated for 'chain 'R' and resid 111 through 113' Processing helix chain 'R' and resid 117 through 119 No H-bonds generated for 'chain 'R' and resid 117 through 119' Processing helix chain 'R' and resid 150 through 153 Processing helix chain 'R' and resid 165 through 169 Processing helix chain 'R' and resid 177 through 191 removed outlier: 5.654A pdb=" N ASN R 182 " --> pdb=" O ASP R 178 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR R 183 " --> pdb=" O ASP R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 220 Processing helix chain 'R' and resid 282 through 285 No H-bonds generated for 'chain 'R' and resid 282 through 285' Processing helix chain 'R' and resid 300 through 302 No H-bonds generated for 'chain 'R' and resid 300 through 302' Processing helix chain 'R' and resid 353 through 360 Processing helix chain 'R' and resid 365 through 371 Processing helix chain 'R' and resid 403 through 409 Processing helix chain 'R' and resid 439 through 442 removed outlier: 4.108A pdb=" N ASN R 442 " --> pdb=" O ALA R 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 439 through 442' Processing helix chain 'R' and resid 461 through 467 Processing helix chain 'R' and resid 525 through 531 Processing helix chain 'R' and resid 533 through 559 removed outlier: 4.073A pdb=" N GLN R 554 " --> pdb=" O ILE R 550 " (cutoff:3.500A) Processing helix chain 'R' and resid 572 through 592 removed outlier: 7.118A pdb=" N ALA R 587 " --> pdb=" O ALA R 583 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ASN R 588 " --> pdb=" O THR R 584 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP R 589 " --> pdb=" O TYR R 585 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N TRP R 590 " --> pdb=" O GLY R 586 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS R 591 " --> pdb=" O ALA R 587 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TYR R 592 " --> pdb=" O ASN R 588 " (cutoff:3.500A) Processing helix chain 'R' and resid 595 through 598 No H-bonds generated for 'chain 'R' and resid 595 through 598' Processing helix chain 'R' and resid 603 through 621 removed outlier: 4.056A pdb=" N TYR R 617 " --> pdb=" O SER R 613 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR R 618 " --> pdb=" O LYS R 614 " (cutoff:3.500A) Proline residue: R 619 - end of helix Processing helix chain 'R' and resid 656 through 658 No H-bonds generated for 'chain 'R' and resid 656 through 658' Processing helix chain 'R' and resid 668 through 683 removed outlier: 3.519A pdb=" N ASP R 680 " --> pdb=" O ALA R 676 " (cutoff:3.500A) Processing helix chain 'R' and resid 688 through 690 No H-bonds generated for 'chain 'R' and resid 688 through 690' Processing sheet with id= A, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.059A pdb=" N VAL A 344 " --> pdb=" O ARG A 652 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 124 through 128 removed outlier: 3.576A pdb=" N HIS A 144 " --> pdb=" O TRP A 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 269 through 271 Processing sheet with id= D, first strand: chain 'A' and resid 335 through 339 removed outlier: 3.738A pdb=" N GLY A 325 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 327 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG A 315 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE A 329 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 313 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 564 through 567 removed outlier: 3.700A pdb=" N SER A 564 " --> pdb=" O HIS A 400 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 479 " --> pdb=" O THR A 395 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 490 through 493 Processing sheet with id= G, first strand: chain 'B' and resid 55 through 57 removed outlier: 4.332A pdb=" N LEU B 55 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR B 328 " --> pdb=" O HIS B 336 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL B 324 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE B 317 " --> pdb=" O VAL B 324 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 343 through 346 removed outlier: 3.794A pdb=" N ILE B 84 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 124 through 128 removed outlier: 3.525A pdb=" N HIS B 144 " --> pdb=" O TRP B 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 142 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 269 through 271 Processing sheet with id= K, first strand: chain 'B' and resid 391 through 393 removed outlier: 3.650A pdb=" N ALA B 481 " --> pdb=" O PRO B 393 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 476 through 478 Processing sheet with id= M, first strand: chain 'B' and resid 491 through 493 removed outlier: 3.637A pdb=" N TYR B 491 " --> pdb=" O PHE B 507 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 651 through 653 removed outlier: 6.058A pdb=" N VAL C 344 " --> pdb=" O ARG C 652 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 124 through 128 removed outlier: 3.576A pdb=" N HIS C 144 " --> pdb=" O TRP C 125 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 269 through 271 Processing sheet with id= Q, first strand: chain 'C' and resid 335 through 339 removed outlier: 3.738A pdb=" N GLY C 325 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN C 327 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG C 315 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE C 329 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 313 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 564 through 567 removed outlier: 3.700A pdb=" N SER C 564 " --> pdb=" O HIS C 400 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 479 " --> pdb=" O THR C 395 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 490 through 493 Processing sheet with id= T, first strand: chain 'D' and resid 55 through 57 removed outlier: 4.332A pdb=" N LEU D 55 " --> pdb=" O TYR D 337 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR D 328 " --> pdb=" O HIS D 336 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL D 324 " --> pdb=" O VAL D 340 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE D 317 " --> pdb=" O VAL D 324 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 343 through 346 removed outlier: 3.794A pdb=" N ILE D 84 " --> pdb=" O ILE D 59 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 124 through 128 removed outlier: 3.525A pdb=" N HIS D 144 " --> pdb=" O TRP D 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 142 " --> pdb=" O GLY D 127 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 269 through 271 Processing sheet with id= X, first strand: chain 'D' and resid 391 through 393 removed outlier: 3.650A pdb=" N ALA D 481 " --> pdb=" O PRO D 393 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 476 through 478 Processing sheet with id= Z, first strand: chain 'D' and resid 491 through 493 removed outlier: 3.636A pdb=" N TYR D 491 " --> pdb=" O PHE D 507 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 651 through 653 removed outlier: 6.059A pdb=" N VAL E 344 " --> pdb=" O ARG E 652 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 124 through 128 removed outlier: 3.576A pdb=" N HIS E 144 " --> pdb=" O TRP E 125 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 269 through 271 Processing sheet with id= AD, first strand: chain 'E' and resid 335 through 339 removed outlier: 3.738A pdb=" N GLY E 325 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN E 327 " --> pdb=" O ARG E 315 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG E 315 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE E 329 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL E 313 " --> pdb=" O ILE E 329 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 564 through 567 removed outlier: 3.700A pdb=" N SER E 564 " --> pdb=" O HIS E 400 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 479 " --> pdb=" O THR E 395 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 490 through 493 Processing sheet with id= AG, first strand: chain 'F' and resid 55 through 57 removed outlier: 4.333A pdb=" N LEU F 55 " --> pdb=" O TYR F 337 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR F 328 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL F 324 " --> pdb=" O VAL F 340 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE F 317 " --> pdb=" O VAL F 324 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 343 through 346 removed outlier: 3.793A pdb=" N ILE F 84 " --> pdb=" O ILE F 59 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 124 through 128 removed outlier: 3.525A pdb=" N HIS F 144 " --> pdb=" O TRP F 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 142 " --> pdb=" O GLY F 127 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 269 through 271 Processing sheet with id= AK, first strand: chain 'F' and resid 391 through 393 removed outlier: 3.650A pdb=" N ALA F 481 " --> pdb=" O PRO F 393 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'F' and resid 476 through 478 Processing sheet with id= AM, first strand: chain 'F' and resid 491 through 493 removed outlier: 3.637A pdb=" N TYR F 491 " --> pdb=" O PHE F 507 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 651 through 653 removed outlier: 6.060A pdb=" N VAL G 344 " --> pdb=" O ARG G 652 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'G' and resid 124 through 128 removed outlier: 3.576A pdb=" N HIS G 144 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 269 through 271 Processing sheet with id= AQ, first strand: chain 'G' and resid 335 through 339 removed outlier: 3.738A pdb=" N GLY G 325 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN G 327 " --> pdb=" O ARG G 315 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG G 315 " --> pdb=" O ASN G 327 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE G 329 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL G 313 " --> pdb=" O ILE G 329 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'G' and resid 564 through 567 removed outlier: 3.699A pdb=" N SER G 564 " --> pdb=" O HIS G 400 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU G 479 " --> pdb=" O THR G 395 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'G' and resid 490 through 493 Processing sheet with id= AT, first strand: chain 'H' and resid 55 through 57 removed outlier: 4.332A pdb=" N LEU H 55 " --> pdb=" O TYR H 337 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR H 328 " --> pdb=" O HIS H 336 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL H 324 " --> pdb=" O VAL H 340 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE H 317 " --> pdb=" O VAL H 324 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'H' and resid 343 through 346 removed outlier: 3.793A pdb=" N ILE H 84 " --> pdb=" O ILE H 59 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.526A pdb=" N HIS H 144 " --> pdb=" O TRP H 125 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE H 142 " --> pdb=" O GLY H 127 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 269 through 271 Processing sheet with id= AX, first strand: chain 'H' and resid 391 through 393 removed outlier: 3.650A pdb=" N ALA H 481 " --> pdb=" O PRO H 393 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'H' and resid 476 through 478 Processing sheet with id= AZ, first strand: chain 'H' and resid 491 through 493 removed outlier: 3.636A pdb=" N TYR H 491 " --> pdb=" O PHE H 507 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'I' and resid 651 through 653 removed outlier: 6.060A pdb=" N VAL I 344 " --> pdb=" O ARG I 652 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'I' and resid 124 through 128 removed outlier: 3.576A pdb=" N HIS I 144 " --> pdb=" O TRP I 125 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'I' and resid 269 through 271 Processing sheet with id= BD, first strand: chain 'I' and resid 335 through 339 removed outlier: 3.738A pdb=" N GLY I 325 " --> pdb=" O ILE I 317 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN I 327 " --> pdb=" O ARG I 315 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG I 315 " --> pdb=" O ASN I 327 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE I 329 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL I 313 " --> pdb=" O ILE I 329 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'I' and resid 564 through 567 removed outlier: 3.700A pdb=" N SER I 564 " --> pdb=" O HIS I 400 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU I 479 " --> pdb=" O THR I 395 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'I' and resid 490 through 493 Processing sheet with id= BG, first strand: chain 'J' and resid 55 through 57 removed outlier: 4.332A pdb=" N LEU J 55 " --> pdb=" O TYR J 337 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR J 328 " --> pdb=" O HIS J 336 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL J 324 " --> pdb=" O VAL J 340 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE J 317 " --> pdb=" O VAL J 324 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'J' and resid 343 through 346 removed outlier: 3.793A pdb=" N ILE J 84 " --> pdb=" O ILE J 59 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'J' and resid 124 through 128 removed outlier: 3.525A pdb=" N HIS J 144 " --> pdb=" O TRP J 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE J 142 " --> pdb=" O GLY J 127 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'J' and resid 269 through 271 Processing sheet with id= BK, first strand: chain 'J' and resid 391 through 393 removed outlier: 3.649A pdb=" N ALA J 481 " --> pdb=" O PRO J 393 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'J' and resid 476 through 478 Processing sheet with id= BM, first strand: chain 'J' and resid 491 through 493 removed outlier: 3.636A pdb=" N TYR J 491 " --> pdb=" O PHE J 507 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'K' and resid 651 through 653 removed outlier: 6.059A pdb=" N VAL K 344 " --> pdb=" O ARG K 652 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'K' and resid 124 through 128 removed outlier: 3.576A pdb=" N HIS K 144 " --> pdb=" O TRP K 125 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'K' and resid 269 through 271 Processing sheet with id= BQ, first strand: chain 'K' and resid 335 through 339 removed outlier: 3.738A pdb=" N GLY K 325 " --> pdb=" O ILE K 317 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN K 327 " --> pdb=" O ARG K 315 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG K 315 " --> pdb=" O ASN K 327 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE K 329 " --> pdb=" O VAL K 313 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL K 313 " --> pdb=" O ILE K 329 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'K' and resid 564 through 567 removed outlier: 3.701A pdb=" N SER K 564 " --> pdb=" O HIS K 400 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU K 479 " --> pdb=" O THR K 395 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'K' and resid 490 through 493 Processing sheet with id= BT, first strand: chain 'L' and resid 55 through 57 removed outlier: 4.332A pdb=" N LEU L 55 " --> pdb=" O TYR L 337 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR L 328 " --> pdb=" O HIS L 336 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL L 324 " --> pdb=" O VAL L 340 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE L 317 " --> pdb=" O VAL L 324 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'L' and resid 343 through 346 removed outlier: 3.794A pdb=" N ILE L 84 " --> pdb=" O ILE L 59 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'L' and resid 124 through 128 removed outlier: 3.525A pdb=" N HIS L 144 " --> pdb=" O TRP L 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE L 142 " --> pdb=" O GLY L 127 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'L' and resid 269 through 271 Processing sheet with id= BX, first strand: chain 'L' and resid 391 through 393 removed outlier: 3.650A pdb=" N ALA L 481 " --> pdb=" O PRO L 393 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'L' and resid 476 through 478 Processing sheet with id= BZ, first strand: chain 'L' and resid 491 through 493 removed outlier: 3.637A pdb=" N TYR L 491 " --> pdb=" O PHE L 507 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'M' and resid 651 through 653 removed outlier: 6.059A pdb=" N VAL M 344 " --> pdb=" O ARG M 652 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'M' and resid 124 through 128 removed outlier: 3.576A pdb=" N HIS M 144 " --> pdb=" O TRP M 125 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'M' and resid 269 through 271 Processing sheet with id= CD, first strand: chain 'M' and resid 335 through 339 removed outlier: 3.739A pdb=" N GLY M 325 " --> pdb=" O ILE M 317 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN M 327 " --> pdb=" O ARG M 315 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG M 315 " --> pdb=" O ASN M 327 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE M 329 " --> pdb=" O VAL M 313 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL M 313 " --> pdb=" O ILE M 329 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'M' and resid 564 through 567 removed outlier: 3.700A pdb=" N SER M 564 " --> pdb=" O HIS M 400 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU M 479 " --> pdb=" O THR M 395 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'M' and resid 490 through 493 Processing sheet with id= CG, first strand: chain 'N' and resid 55 through 57 removed outlier: 4.332A pdb=" N LEU N 55 " --> pdb=" O TYR N 337 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR N 328 " --> pdb=" O HIS N 336 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL N 324 " --> pdb=" O VAL N 340 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE N 317 " --> pdb=" O VAL N 324 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'N' and resid 343 through 346 removed outlier: 3.793A pdb=" N ILE N 84 " --> pdb=" O ILE N 59 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'N' and resid 124 through 128 removed outlier: 3.525A pdb=" N HIS N 144 " --> pdb=" O TRP N 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE N 142 " --> pdb=" O GLY N 127 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'N' and resid 269 through 271 Processing sheet with id= CK, first strand: chain 'N' and resid 391 through 393 removed outlier: 3.650A pdb=" N ALA N 481 " --> pdb=" O PRO N 393 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'N' and resid 476 through 478 Processing sheet with id= CM, first strand: chain 'N' and resid 491 through 493 removed outlier: 3.637A pdb=" N TYR N 491 " --> pdb=" O PHE N 507 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'O' and resid 651 through 653 removed outlier: 6.060A pdb=" N VAL O 344 " --> pdb=" O ARG O 652 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'O' and resid 124 through 128 removed outlier: 3.576A pdb=" N HIS O 144 " --> pdb=" O TRP O 125 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'O' and resid 269 through 271 Processing sheet with id= CQ, first strand: chain 'O' and resid 335 through 339 removed outlier: 3.738A pdb=" N GLY O 325 " --> pdb=" O ILE O 317 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN O 327 " --> pdb=" O ARG O 315 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG O 315 " --> pdb=" O ASN O 327 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE O 329 " --> pdb=" O VAL O 313 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL O 313 " --> pdb=" O ILE O 329 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'O' and resid 564 through 567 removed outlier: 3.700A pdb=" N SER O 564 " --> pdb=" O HIS O 400 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU O 479 " --> pdb=" O THR O 395 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'O' and resid 490 through 493 Processing sheet with id= CT, first strand: chain 'P' and resid 55 through 57 removed outlier: 4.332A pdb=" N LEU P 55 " --> pdb=" O TYR P 337 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR P 328 " --> pdb=" O HIS P 336 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL P 324 " --> pdb=" O VAL P 340 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE P 317 " --> pdb=" O VAL P 324 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'P' and resid 343 through 346 removed outlier: 3.794A pdb=" N ILE P 84 " --> pdb=" O ILE P 59 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'P' and resid 124 through 128 removed outlier: 3.526A pdb=" N HIS P 144 " --> pdb=" O TRP P 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE P 142 " --> pdb=" O GLY P 127 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'P' and resid 269 through 271 Processing sheet with id= CX, first strand: chain 'P' and resid 391 through 393 removed outlier: 3.650A pdb=" N ALA P 481 " --> pdb=" O PRO P 393 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'P' and resid 476 through 478 Processing sheet with id= CZ, first strand: chain 'P' and resid 491 through 493 removed outlier: 3.636A pdb=" N TYR P 491 " --> pdb=" O PHE P 507 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'Q' and resid 651 through 653 removed outlier: 6.059A pdb=" N VAL Q 344 " --> pdb=" O ARG Q 652 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'Q' and resid 124 through 128 removed outlier: 3.576A pdb=" N HIS Q 144 " --> pdb=" O TRP Q 125 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'Q' and resid 269 through 271 Processing sheet with id= DD, first strand: chain 'Q' and resid 335 through 339 removed outlier: 3.738A pdb=" N GLY Q 325 " --> pdb=" O ILE Q 317 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN Q 327 " --> pdb=" O ARG Q 315 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG Q 315 " --> pdb=" O ASN Q 327 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE Q 329 " --> pdb=" O VAL Q 313 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL Q 313 " --> pdb=" O ILE Q 329 " (cutoff:3.500A) Processing sheet with id= DE, first strand: chain 'Q' and resid 564 through 567 removed outlier: 3.700A pdb=" N SER Q 564 " --> pdb=" O HIS Q 400 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU Q 479 " --> pdb=" O THR Q 395 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'Q' and resid 490 through 493 Processing sheet with id= DG, first strand: chain 'R' and resid 55 through 57 removed outlier: 4.333A pdb=" N LEU R 55 " --> pdb=" O TYR R 337 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR R 328 " --> pdb=" O HIS R 336 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL R 324 " --> pdb=" O VAL R 340 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE R 317 " --> pdb=" O VAL R 324 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'R' and resid 343 through 346 removed outlier: 3.794A pdb=" N ILE R 84 " --> pdb=" O ILE R 59 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain 'R' and resid 124 through 128 removed outlier: 3.526A pdb=" N HIS R 144 " --> pdb=" O TRP R 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE R 142 " --> pdb=" O GLY R 127 " (cutoff:3.500A) Processing sheet with id= DJ, first strand: chain 'R' and resid 269 through 271 Processing sheet with id= DK, first strand: chain 'R' and resid 391 through 393 removed outlier: 3.650A pdb=" N ALA R 481 " --> pdb=" O PRO R 393 " (cutoff:3.500A) Processing sheet with id= DL, first strand: chain 'R' and resid 476 through 478 Processing sheet with id= DM, first strand: chain 'R' and resid 491 through 493 removed outlier: 3.637A pdb=" N TYR R 491 " --> pdb=" O PHE R 507 " (cutoff:3.500A) 2475 hydrogen bonds defined for protein. 7101 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: 40.44 Time building geometry restraints manager: 31.72 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: 29116 1.34 - 1.46: 14258 1.46 - 1.57: 49446 1.57 - 1.69: 60 1.69 - 1.81: 540 Bond restraints: 93420 Sorted by residual: bond pdb=" O3P FAD G 901 " pdb=" P FAD G 901 " ideal model delta sigma weight residual 1.660 1.582 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O3P FAD K 901 " pdb=" P FAD K 901 " ideal model delta sigma weight residual 1.660 1.582 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O3P FAD E 901 " pdb=" P FAD E 901 " ideal model delta sigma weight residual 1.660 1.582 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O3P FAD C 901 " pdb=" P FAD C 901 " ideal model delta sigma weight residual 1.660 1.582 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O3P FAD A 901 " pdb=" P FAD A 901 " ideal model delta sigma weight residual 1.660 1.582 0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 93415 not shown) Histogram of bond angle deviations from ideal: 97.53 - 104.86: 2233 104.86 - 112.19: 45077 112.19 - 119.52: 31606 119.52 - 126.86: 47298 126.86 - 134.19: 1388 Bond angle restraints: 127602 Sorted by residual: angle pdb=" N LEU B 476 " pdb=" CA LEU B 476 " pdb=" C LEU B 476 " ideal model delta sigma weight residual 109.46 115.92 -6.46 1.66e+00 3.63e-01 1.51e+01 angle pdb=" N LEU L 476 " pdb=" CA LEU L 476 " pdb=" C LEU L 476 " ideal model delta sigma weight residual 109.46 115.92 -6.46 1.66e+00 3.63e-01 1.51e+01 angle pdb=" N LEU P 476 " pdb=" CA LEU P 476 " pdb=" C LEU P 476 " ideal model delta sigma weight residual 109.46 115.92 -6.46 1.66e+00 3.63e-01 1.51e+01 angle pdb=" N LEU F 476 " pdb=" CA LEU F 476 " pdb=" C LEU F 476 " ideal model delta sigma weight residual 109.46 115.91 -6.45 1.66e+00 3.63e-01 1.51e+01 angle pdb=" N LEU N 476 " pdb=" CA LEU N 476 " pdb=" C LEU N 476 " ideal model delta sigma weight residual 109.46 115.91 -6.45 1.66e+00 3.63e-01 1.51e+01 ... (remaining 127597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.29: 51566 26.29 - 52.58: 2718 52.58 - 78.87: 184 78.87 - 105.16: 63 105.16 - 131.45: 9 Dihedral angle restraints: 54540 sinusoidal: 21060 harmonic: 33480 Sorted by residual: dihedral pdb=" O5' FAD J 901 " pdb=" O3P FAD J 901 " pdb=" P FAD J 901 " pdb=" PA FAD J 901 " ideal model delta sinusoidal sigma weight residual 298.23 166.78 131.45 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" O5' FAD B 901 " pdb=" O3P FAD B 901 " pdb=" P FAD B 901 " pdb=" PA FAD B 901 " ideal model delta sinusoidal sigma weight residual 298.23 166.78 131.45 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" O5' FAD L 901 " pdb=" O3P FAD L 901 " pdb=" P FAD L 901 " pdb=" PA FAD L 901 " ideal model delta sinusoidal sigma weight residual 298.23 166.78 131.45 1 3.00e+01 1.11e-03 1.77e+01 ... (remaining 54537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 10100 0.045 - 0.091: 2866 0.091 - 0.136: 1089 0.136 - 0.181: 75 0.181 - 0.227: 18 Chirality restraints: 14148 Sorted by residual: chirality pdb=" CA ASN H 475 " pdb=" N ASN H 475 " pdb=" C ASN H 475 " pdb=" CB ASN H 475 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN N 475 " pdb=" N ASN N 475 " pdb=" C ASN N 475 " pdb=" CB ASN N 475 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ASN F 475 " pdb=" N ASN F 475 " pdb=" C ASN F 475 " pdb=" CB ASN F 475 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 14145 not shown) Planarity restraints: 16596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 475 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" C ASN F 475 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN F 475 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU F 476 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN N 475 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" C ASN N 475 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN N 475 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU N 476 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 475 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C ASN L 475 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN L 475 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU L 476 " -0.015 2.00e-02 2.50e+03 ... (remaining 16593 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 111 2.30 - 2.95: 43106 2.95 - 3.60: 134155 3.60 - 4.25: 211868 4.25 - 4.90: 356817 Nonbonded interactions: 746057 Sorted by model distance: nonbonded pdb=" OD2 ASP K 274 " pdb=" CG PRO N 110 " model vdw 1.650 3.440 nonbonded pdb=" CG PRO D 110 " pdb=" OD2 ASP Q 274 " model vdw 1.651 3.440 nonbonded pdb=" OD2 ASP E 274 " pdb=" CG PRO H 110 " model vdw 1.651 3.440 nonbonded pdb=" ND2 ASN E 112 " pdb=" O ASP H 274 " model vdw 1.657 2.520 nonbonded pdb=" ND2 ASN K 112 " pdb=" O ASP N 274 " model vdw 1.657 2.520 ... (remaining 746052 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' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.860 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: 0.070 Extract box with map and model: 16.340 Check model and map are aligned: 1.080 Set scattering table: 0.640 Process input model: 195.290 Find NCS groups from input model: 5.280 Set up NCS constraints: 0.590 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:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 226.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 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 : 0.004 0.078 93420 Z= 0.254 Angle : 0.660 8.893 127602 Z= 0.362 Chirality : 0.047 0.227 14148 Planarity : 0.005 0.049 16596 Dihedral : 15.047 131.447 33300 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.61 % Allowed : 24.32 % Favored : 75.08 % 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: -0.90 (0.08), residues: 11646 helix: 0.38 (0.09), residues: 3627 sheet: -0.14 (0.14), residues: 1611 loop : -1.32 (0.08), residues: 6408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2332 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 2273 time to evaluate : 9.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 15 residues processed: 2302 average time/residue: 0.8755 time to fit residues: 3396.6616 Evaluate side-chains 1492 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1477 time to evaluate : 7.838 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.6799 time to fit residues: 29.6173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 972 optimal weight: 5.9990 chunk 873 optimal weight: 0.3980 chunk 484 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 chunk 588 optimal weight: 0.0270 chunk 466 optimal weight: 2.9990 chunk 902 optimal weight: 3.9990 chunk 349 optimal weight: 0.9980 chunk 549 optimal weight: 10.0000 chunk 672 optimal weight: 9.9990 chunk 1046 optimal weight: 10.0000 overall best weight: 1.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 431 HIS B 666 ASN C 73 HIS ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 ASN C 529 GLN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN D 295 ASN D 440 ASN D 464 GLN D 666 ASN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 ASN E 588 ASN E 628 HIS E 642 ASN ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN F 270 ASN F 295 ASN F 358 GLN F 666 ASN G 73 HIS ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 ASN G 588 ASN G 628 HIS G 694 ASN H 112 ASN H 217 GLN H 295 ASN H 464 GLN H 580 ASN H 666 ASN I 144 HIS I 251 ASN I 524 GLN ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 217 GLN J 229 ASN J 271 GLN J 295 ASN J 389 ASN ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 591 HIS K 112 ASN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 237 ASN ** K 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 375 ASN K 380 ASN K 529 GLN ** K 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 464 GLN L 591 HIS L 624 HIS L 666 ASN ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 182 ASN M 375 ASN ** M 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 524 GLN M 649 GLN M 702 ASN N 169 ASN N 217 GLN N 389 ASN N 591 HIS N 649 GLN O 73 HIS O 92 HIS ** O 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 524 GLN ** P 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 217 GLN ** P 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 666 ASN ** Q 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 276 ASN Q 327 ASN Q 375 ASN ** R 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 464 GLN ** R 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 93420 Z= 0.230 Angle : 0.606 11.482 127602 Z= 0.308 Chirality : 0.047 0.310 14148 Planarity : 0.005 0.073 16596 Dihedral : 6.579 122.893 12852 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.87 % Allowed : 23.49 % Favored : 71.65 % 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: -0.86 (0.08), residues: 11646 helix: 0.37 (0.09), residues: 3732 sheet: 0.07 (0.14), residues: 1628 loop : -1.35 (0.08), residues: 6286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2024 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 474 poor density : 1550 time to evaluate : 7.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 474 outliers final: 253 residues processed: 1906 average time/residue: 0.8389 time to fit residues: 2757.2067 Evaluate side-chains 1602 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1349 time to evaluate : 7.938 Switching outliers to nearest non-outliers outliers start: 253 outliers final: 0 residues processed: 253 average time/residue: 0.6835 time to fit residues: 335.2256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 581 optimal weight: 7.9990 chunk 324 optimal weight: 10.0000 chunk 870 optimal weight: 0.0670 chunk 712 optimal weight: 0.0030 chunk 288 optimal weight: 0.8980 chunk 1048 optimal weight: 8.9990 chunk 1132 optimal weight: 5.9990 chunk 933 optimal weight: 0.1980 chunk 1039 optimal weight: 5.9990 chunk 357 optimal weight: 7.9990 chunk 840 optimal weight: 0.0010 overall best weight: 0.2334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 HIS B 464 GLN B 666 ASN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN D 321 ASN D 327 ASN D 464 GLN ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 588 ASN ** F 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 GLN G 73 HIS ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 HIS H 284 ASN H 290 ASN H 389 ASN I 129 GLN I 251 ASN ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 464 GLN ** K 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 ASN K 375 ASN ** K 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 217 GLN L 251 ASN M 92 HIS ** M 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 390 HIS ** M 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 529 GLN M 591 HIS N 169 ASN N 464 GLN P 321 ASN P 327 ASN P 464 GLN ** P 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 649 GLN P 666 ASN ** Q 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 290 ASN R 327 ASN R 450 GLN ** R 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 93420 Z= 0.148 Angle : 0.542 10.665 127602 Z= 0.271 Chirality : 0.045 0.237 14148 Planarity : 0.004 0.068 16596 Dihedral : 6.373 124.758 12852 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.37 % Allowed : 24.61 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.08), residues: 11646 helix: 0.84 (0.09), residues: 3488 sheet: -0.15 (0.13), residues: 1850 loop : -1.17 (0.08), residues: 6308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1710 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1479 time to evaluate : 7.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 231 outliers final: 87 residues processed: 1649 average time/residue: 0.8357 time to fit residues: 2388.4414 Evaluate side-chains 1410 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1323 time to evaluate : 8.650 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 0.6975 time to fit residues: 124.0400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 1035 optimal weight: 9.9990 chunk 787 optimal weight: 0.0670 chunk 543 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 500 optimal weight: 2.9990 chunk 703 optimal weight: 1.9990 chunk 1051 optimal weight: 10.0000 chunk 1113 optimal weight: 10.0000 chunk 549 optimal weight: 10.0000 chunk 996 optimal weight: 1.9990 chunk 300 optimal weight: 4.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN B 217 GLN B 251 ASN B 464 GLN B 666 ASN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN F 129 GLN ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 ASN F 464 GLN ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 412 ASN ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 379 ASN H 431 HIS H 464 GLN ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 591 HIS I 119 GLN I 251 ASN I 412 ASN ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 HIS J 216 GLN K 144 HIS K 380 ASN K 628 HIS ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 229 ASN L 284 ASN L 524 GLN ** M 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 327 ASN M 463 GLN M 524 GLN M 591 HIS O 144 HIS ** P 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 284 ASN ** Q 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 169 ASN ** R 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 284 ASN ** R 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 93420 Z= 0.246 Angle : 0.650 24.213 127602 Z= 0.329 Chirality : 0.049 0.350 14148 Planarity : 0.005 0.083 16596 Dihedral : 6.418 117.407 12852 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.27 % Allowed : 24.16 % Favored : 71.57 % 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: -0.88 (0.08), residues: 11646 helix: 0.40 (0.09), residues: 3656 sheet: -0.06 (0.14), residues: 1494 loop : -1.31 (0.07), residues: 6496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1848 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 416 poor density : 1432 time to evaluate : 9.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 416 outliers final: 214 residues processed: 1716 average time/residue: 0.8565 time to fit residues: 2544.1429 Evaluate side-chains 1467 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1253 time to evaluate : 7.994 Switching outliers to nearest non-outliers outliers start: 214 outliers final: 0 residues processed: 214 average time/residue: 0.6921 time to fit residues: 290.6667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 927 optimal weight: 1.9990 chunk 632 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 829 optimal weight: 20.0000 chunk 459 optimal weight: 9.9990 chunk 950 optimal weight: 1.9990 chunk 769 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 568 optimal weight: 0.8980 chunk 999 optimal weight: 6.9990 chunk 280 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN B 431 HIS B 666 ASN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 GLN ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 642 ASN ** F 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 GLN G 702 ASN I 251 ASN I 375 ASN I 412 ASN ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 474 ASN K 380 ASN ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 216 GLN L 284 ASN L 524 GLN M 73 HIS M 588 ASN O 270 ASN ** P 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 290 ASN P 474 ASN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 93420 Z= 0.184 Angle : 0.567 9.907 127602 Z= 0.284 Chirality : 0.046 0.220 14148 Planarity : 0.004 0.054 16596 Dihedral : 6.222 123.622 12852 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.25 % Allowed : 26.05 % Favored : 71.70 % 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: -0.75 (0.08), residues: 11646 helix: 0.55 (0.09), residues: 3666 sheet: -0.10 (0.14), residues: 1530 loop : -1.24 (0.08), residues: 6450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1581 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1362 time to evaluate : 8.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 219 outliers final: 101 residues processed: 1518 average time/residue: 0.8689 time to fit residues: 2271.3285 Evaluate side-chains 1364 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1263 time to evaluate : 7.891 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 0 residues processed: 101 average time/residue: 0.7039 time to fit residues: 142.9654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 374 optimal weight: 0.0270 chunk 1002 optimal weight: 4.9990 chunk 220 optimal weight: 0.8980 chunk 653 optimal weight: 0.7980 chunk 274 optimal weight: 8.9990 chunk 1114 optimal weight: 4.9990 chunk 925 optimal weight: 6.9990 chunk 516 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 368 optimal weight: 8.9990 chunk 585 optimal weight: 8.9990 overall best weight: 2.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN B 217 GLN B 450 GLN ** C 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 GLN ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 379 ASN D 474 ASN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 HIS ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 474 ASN I 119 GLN ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 412 ASN ** K 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 216 GLN L 284 ASN L 474 ASN L 529 GLN M 90 HIS M 529 GLN N 284 ASN ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 290 ASN P 554 GLN P 694 ASN ** Q 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 217 GLN ** R 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 93420 Z= 0.216 Angle : 0.608 11.384 127602 Z= 0.305 Chirality : 0.047 0.208 14148 Planarity : 0.005 0.058 16596 Dihedral : 6.134 119.564 12852 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.83 % Allowed : 26.10 % Favored : 71.06 % 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: -0.73 (0.08), residues: 11646 helix: 0.70 (0.09), residues: 3507 sheet: -0.15 (0.14), residues: 1530 loop : -1.26 (0.08), residues: 6609 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1633 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1357 time to evaluate : 8.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 276 outliers final: 139 residues processed: 1537 average time/residue: 0.8720 time to fit residues: 2307.9753 Evaluate side-chains 1402 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1263 time to evaluate : 8.510 Switching outliers to nearest non-outliers outliers start: 139 outliers final: 0 residues processed: 139 average time/residue: 0.7193 time to fit residues: 198.6700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 1074 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 635 optimal weight: 9.9990 chunk 813 optimal weight: 6.9990 chunk 630 optimal weight: 7.9990 chunk 938 optimal weight: 5.9990 chunk 622 optimal weight: 6.9990 chunk 1110 optimal weight: 10.0000 chunk 694 optimal weight: 20.0000 chunk 676 optimal weight: 6.9990 chunk 512 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 HIS B 591 HIS ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 547 GLN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 642 ASN F 80 ASN F 169 ASN F 591 HIS ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 ASN ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 GLN H 572 ASN I 92 HIS I 412 ASN ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 562 GLN ** I 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 702 ASN J 90 HIS ** J 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 251 ASN J 358 GLN J 379 ASN ** J 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 524 GLN ** K 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 440 ASN ** K 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 524 GLN L 529 GLN L 554 GLN M 336 HIS M 529 GLN ** M 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 524 GLN O 336 HIS O 562 GLN ** P 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 284 ASN ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 412 ASN ** Q 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 591 HIS ** Q 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 GLN R 290 ASN ** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 400 HIS ** R 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.6826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 93420 Z= 0.512 Angle : 0.880 13.634 127602 Z= 0.448 Chirality : 0.056 0.360 14148 Planarity : 0.007 0.096 16596 Dihedral : 7.139 121.005 12852 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.33 % Favored : 91.61 % Rotamer: Outliers : 3.36 % Allowed : 26.03 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.07), residues: 11646 helix: -0.24 (0.08), residues: 3465 sheet: -0.76 (0.13), residues: 1566 loop : -1.71 (0.07), residues: 6615 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1622 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 1295 time to evaluate : 8.100 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 327 outliers final: 193 residues processed: 1520 average time/residue: 0.8837 time to fit residues: 2301.7600 Evaluate side-chains 1364 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1171 time to evaluate : 8.113 Switching outliers to nearest non-outliers outliers start: 193 outliers final: 0 residues processed: 193 average time/residue: 0.7017 time to fit residues: 264.9618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 686 optimal weight: 3.9990 chunk 443 optimal weight: 5.9990 chunk 663 optimal weight: 9.9990 chunk 334 optimal weight: 9.9990 chunk 218 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 705 optimal weight: 0.9990 chunk 756 optimal weight: 1.9990 chunk 548 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 872 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 ASN B 217 GLN ** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 547 GLN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 375 ASN ** E 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 642 ASN F 358 GLN F 474 ASN ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 ASN G 588 ASN G 642 ASN ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 HIS ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 509 ASN J 524 GLN K 92 HIS K 380 ASN K 524 GLN K 591 HIS L 284 ASN M 474 ASN N 80 ASN ** N 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 GLN R 129 GLN ** R 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.6842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 93420 Z= 0.200 Angle : 0.634 13.556 127602 Z= 0.319 Chirality : 0.047 0.231 14148 Planarity : 0.005 0.070 16596 Dihedral : 6.464 126.264 12852 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.46 % Favored : 94.52 % Rotamer: Outliers : 1.16 % Allowed : 27.38 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.08), residues: 11646 helix: 0.18 (0.09), residues: 3546 sheet: -0.65 (0.13), residues: 1620 loop : -1.47 (0.08), residues: 6480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1410 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1297 time to evaluate : 8.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 71 residues processed: 1370 average time/residue: 0.8933 time to fit residues: 2091.2752 Evaluate side-chains 1267 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1196 time to evaluate : 8.054 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.7220 time to fit residues: 105.5717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 1010 optimal weight: 9.9990 chunk 1063 optimal weight: 10.0000 chunk 970 optimal weight: 0.9990 chunk 1034 optimal weight: 9.9990 chunk 622 optimal weight: 0.0670 chunk 450 optimal weight: 0.0470 chunk 812 optimal weight: 0.0050 chunk 317 optimal weight: 0.6980 chunk 934 optimal weight: 8.9990 chunk 978 optimal weight: 0.9980 chunk 1031 optimal weight: 3.9990 overall best weight: 0.3630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN ** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 ASN ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 ASN E 251 ASN ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN E 642 ASN F 290 ASN F 327 ASN F 358 GLN F 580 ASN ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 440 ASN K 524 GLN ** K 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 591 HIS L 284 ASN L 524 GLN N 400 HIS P 284 ASN P 450 GLN P 700 ASN ** Q 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 93420 Z= 0.159 Angle : 0.596 15.701 127602 Z= 0.298 Chirality : 0.046 0.218 14148 Planarity : 0.005 0.068 16596 Dihedral : 6.072 127.193 12852 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.49 % Allowed : 28.24 % Favored : 71.27 % 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: -0.79 (0.08), residues: 11646 helix: 0.62 (0.09), residues: 3450 sheet: -0.37 (0.13), residues: 1620 loop : -1.22 (0.08), residues: 6576 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1298 time to evaluate : 8.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 24 residues processed: 1325 average time/residue: 0.9088 time to fit residues: 2055.8301 Evaluate side-chains 1226 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1202 time to evaluate : 8.055 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.7062 time to fit residues: 42.7171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 679 optimal weight: 8.9990 chunk 1094 optimal weight: 0.0040 chunk 667 optimal weight: 10.0000 chunk 519 optimal weight: 10.0000 chunk 760 optimal weight: 2.9990 chunk 1147 optimal weight: 5.9990 chunk 1056 optimal weight: 0.0470 chunk 913 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 705 optimal weight: 0.9990 chunk 560 optimal weight: 1.9990 overall best weight: 1.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN E 642 ASN F 169 ASN F 358 GLN ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 GLN ** I 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 ASN K 327 ASN K 440 ASN K 524 GLN ** K 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 464 GLN N 474 ASN P 284 ASN P 464 GLN ** Q 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN ** R 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 93420 Z= 0.172 Angle : 0.596 15.925 127602 Z= 0.296 Chirality : 0.046 0.300 14148 Planarity : 0.005 0.073 16596 Dihedral : 5.978 126.092 12852 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.11 % Favored : 94.88 % Rotamer: Outliers : 0.32 % Allowed : 28.91 % Favored : 70.77 % 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: -0.78 (0.08), residues: 11646 helix: 0.74 (0.09), residues: 3384 sheet: -0.47 (0.13), residues: 1620 loop : -1.21 (0.08), residues: 6642 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23292 Ramachandran restraints generated. 11646 Oldfield, 0 Emsley, 11646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1257 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1226 time to evaluate : 8.124 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 17 residues processed: 1245 average time/residue: 0.9191 time to fit residues: 1955.6835 Evaluate side-chains 1208 residues out of total 9738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1191 time to evaluate : 8.129 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.7645 time to fit residues: 34.2996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.8585 > 50: distance: 58 - 71: 12.806 distance: 66 - 71: 11.132 distance: 71 - 72: 6.114 distance: 72 - 73: 7.913 distance: 72 - 75: 5.651 distance: 73 - 74: 7.557 distance: 73 - 79: 12.210 distance: 75 - 76: 9.228 distance: 76 - 77: 12.770 distance: 77 - 78: 7.559 distance: 79 - 80: 18.982 distance: 80 - 81: 3.751 distance: 80 - 83: 5.889 distance: 81 - 82: 18.018 distance: 81 - 87: 17.527 distance: 83 - 84: 14.091 distance: 83 - 85: 6.581 distance: 84 - 86: 13.807 distance: 87 - 88: 15.657 distance: 88 - 89: 28.196 distance: 88 - 91: 7.080 distance: 89 - 90: 27.120 distance: 89 - 95: 10.336 distance: 91 - 92: 6.911 distance: 92 - 93: 22.902 distance: 92 - 94: 8.399 distance: 95 - 96: 4.433 distance: 96 - 97: 32.920 distance: 96 - 99: 24.324 distance: 97 - 98: 14.415 distance: 97 - 106: 27.227 distance: 99 - 100: 36.382 distance: 101 - 102: 14.492 distance: 102 - 103: 11.721 distance: 103 - 104: 8.359 distance: 103 - 105: 12.485 distance: 106 - 107: 8.230 distance: 107 - 108: 14.151 distance: 108 - 109: 19.588 distance: 108 - 114: 13.703 distance: 110 - 111: 15.784 distance: 111 - 112: 10.359 distance: 111 - 113: 13.165 distance: 114 - 115: 4.330 distance: 115 - 116: 3.543 distance: 115 - 118: 9.420 distance: 116 - 117: 5.153 distance: 116 - 122: 6.473 distance: 118 - 119: 17.073 distance: 119 - 120: 14.921 distance: 119 - 121: 23.906 distance: 122 - 123: 14.723 distance: 123 - 124: 17.242 distance: 123 - 126: 16.599 distance: 124 - 125: 16.781 distance: 124 - 130: 6.662 distance: 126 - 127: 26.903 distance: 127 - 128: 25.545 distance: 127 - 129: 26.187 distance: 131 - 132: 12.219 distance: 131 - 134: 8.489 distance: 132 - 133: 10.500 distance: 132 - 137: 9.441 distance: 134 - 135: 8.686 distance: 134 - 136: 10.454 distance: 137 - 138: 11.293 distance: 138 - 139: 10.698 distance: 138 - 141: 11.080 distance: 139 - 140: 13.270 distance: 139 - 144: 9.468 distance: 141 - 142: 20.842 distance: 141 - 143: 26.491 distance: 144 - 145: 14.208 distance: 145 - 146: 8.782 distance: 146 - 147: 4.869 distance: 146 - 148: 4.351