Starting phenix.real_space_refine on Mon Oct 14 16:37:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qem_18372/10_2024/8qem_18372.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qem_18372/10_2024/8qem_18372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qem_18372/10_2024/8qem_18372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qem_18372/10_2024/8qem_18372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qem_18372/10_2024/8qem_18372.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qem_18372/10_2024/8qem_18372.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 126 5.49 5 S 288 5.16 5 C 44745 2.51 5 N 12236 2.21 5 O 13659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 71054 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "B" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "E" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "F" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "G" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "H" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "I" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "J" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "K" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "L" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2083 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "M" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3642 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "N" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3630 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 437} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3642 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3613 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 3603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3603 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3622 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 3637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3637 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "T" Number of atoms: 3627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3627 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "U" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3622 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "V" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3618 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 436} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3607 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3612 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 433} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1293 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "Y" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1290 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Time building chain proxies: 29.86, per 1000 atoms: 0.42 Number of scatterers: 71054 At special positions: 0 Unit cell: (171.234, 172.291, 269.535, 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 126 15.00 O 13659 8.00 N 12236 7.00 C 44745 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 - 3.00 Amino acid : True - 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: 12.63 Conformation dependent library (CDL) restraints added in 6.5 seconds 16830 Ramachandran restraints generated. 8415 Oldfield, 0 Emsley, 8415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15746 Finding SS restraints... Secondary structure from input PDB file: 309 helices and 73 sheets defined 45.2% alpha, 15.0% beta 53 base pairs and 98 stacking pairs defined. Time for finding SS restraints: 18.36 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 removed outlier: 4.012A pdb=" N ASN A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 71 through 90 removed outlier: 3.818A pdb=" N TYR A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 220 through 240 removed outlier: 3.820A pdb=" N GLU A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 295 Processing helix chain 'B' and resid 35 through 40 removed outlier: 3.833A pdb=" N ASN B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 71 through 90 removed outlier: 3.771A pdb=" N TYR B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 220 through 240 removed outlier: 3.883A pdb=" N GLU B 224 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 225 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 295 Processing helix chain 'C' and resid 35 through 40 removed outlier: 3.772A pdb=" N ASN C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 71 through 90 removed outlier: 3.785A pdb=" N TYR C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 220 through 240 removed outlier: 3.978A pdb=" N GLU C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN C 225 " --> pdb=" O PRO C 221 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 234 " --> pdb=" O TYR C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 295 Processing helix chain 'D' and resid 35 through 40 removed outlier: 3.810A pdb=" N ASN D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 71 through 90 removed outlier: 3.761A pdb=" N TYR D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 220 through 240 removed outlier: 3.982A pdb=" N GLU D 224 " --> pdb=" O PRO D 220 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU D 234 " --> pdb=" O TYR D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 295 Processing helix chain 'E' and resid 35 through 40 removed outlier: 3.860A pdb=" N ASN E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'E' and resid 48 through 56 Processing helix chain 'E' and resid 71 through 90 removed outlier: 3.762A pdb=" N TYR E 75 " --> pdb=" O GLY E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 112 Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'E' and resid 220 through 240 removed outlier: 3.920A pdb=" N GLU E 224 " --> pdb=" O PRO E 220 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU E 234 " --> pdb=" O TYR E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 295 Processing helix chain 'F' and resid 35 through 40 removed outlier: 3.531A pdb=" N ASN F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 Processing helix chain 'F' and resid 48 through 56 Processing helix chain 'F' and resid 71 through 90 removed outlier: 3.807A pdb=" N TYR F 75 " --> pdb=" O GLY F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 112 Processing helix chain 'F' and resid 142 through 144 No H-bonds generated for 'chain 'F' and resid 142 through 144' Processing helix chain 'F' and resid 220 through 240 removed outlier: 3.875A pdb=" N GLU F 224 " --> pdb=" O PRO F 220 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU F 234 " --> pdb=" O TYR F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 295 Processing helix chain 'G' and resid 35 through 40 removed outlier: 3.851A pdb=" N ASN G 39 " --> pdb=" O SER G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 Processing helix chain 'G' and resid 48 through 56 Processing helix chain 'G' and resid 71 through 90 removed outlier: 3.841A pdb=" N TYR G 75 " --> pdb=" O GLY G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 112 Processing helix chain 'G' and resid 142 through 144 No H-bonds generated for 'chain 'G' and resid 142 through 144' Processing helix chain 'G' and resid 220 through 240 removed outlier: 3.817A pdb=" N GLU G 224 " --> pdb=" O PRO G 220 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN G 225 " --> pdb=" O PRO G 221 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU G 234 " --> pdb=" O TYR G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 295 Processing helix chain 'H' and resid 35 through 40 removed outlier: 3.890A pdb=" N ASN H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 46 Processing helix chain 'H' and resid 48 through 56 Processing helix chain 'H' and resid 71 through 90 removed outlier: 3.786A pdb=" N TYR H 75 " --> pdb=" O GLY H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 142 through 144 No H-bonds generated for 'chain 'H' and resid 142 through 144' Processing helix chain 'H' and resid 220 through 240 removed outlier: 3.831A pdb=" N GLU H 224 " --> pdb=" O PRO H 220 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN H 225 " --> pdb=" O PRO H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 295 Processing helix chain 'I' and resid 35 through 40 removed outlier: 3.715A pdb=" N ASN I 39 " --> pdb=" O SER I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 46 Processing helix chain 'I' and resid 48 through 56 Processing helix chain 'I' and resid 71 through 90 removed outlier: 3.832A pdb=" N TYR I 75 " --> pdb=" O GLY I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 112 Processing helix chain 'I' and resid 142 through 144 No H-bonds generated for 'chain 'I' and resid 142 through 144' Processing helix chain 'I' and resid 220 through 240 removed outlier: 3.876A pdb=" N GLU I 224 " --> pdb=" O PRO I 220 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN I 225 " --> pdb=" O PRO I 221 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU I 234 " --> pdb=" O TYR I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 295 Processing helix chain 'J' and resid 35 through 40 removed outlier: 3.614A pdb=" N ASN J 39 " --> pdb=" O SER J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 46 Processing helix chain 'J' and resid 48 through 56 Processing helix chain 'J' and resid 71 through 90 removed outlier: 3.777A pdb=" N TYR J 75 " --> pdb=" O GLY J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 112 Processing helix chain 'J' and resid 142 through 144 No H-bonds generated for 'chain 'J' and resid 142 through 144' Processing helix chain 'J' and resid 220 through 240 removed outlier: 3.830A pdb=" N GLU J 224 " --> pdb=" O PRO J 220 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN J 225 " --> pdb=" O PRO J 221 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU J 234 " --> pdb=" O TYR J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 273 through 295 Processing helix chain 'K' and resid 35 through 40 removed outlier: 3.759A pdb=" N ASN K 39 " --> pdb=" O SER K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 46 Processing helix chain 'K' and resid 48 through 56 Processing helix chain 'K' and resid 71 through 90 removed outlier: 3.833A pdb=" N TYR K 75 " --> pdb=" O GLY K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 112 Processing helix chain 'K' and resid 142 through 144 No H-bonds generated for 'chain 'K' and resid 142 through 144' Processing helix chain 'K' and resid 220 through 240 removed outlier: 3.873A pdb=" N GLU K 224 " --> pdb=" O PRO K 220 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN K 225 " --> pdb=" O PRO K 221 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU K 234 " --> pdb=" O TYR K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 295 Processing helix chain 'L' and resid 35 through 40 removed outlier: 3.829A pdb=" N ASN L 39 " --> pdb=" O SER L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 Processing helix chain 'L' and resid 48 through 56 Processing helix chain 'L' and resid 71 through 90 removed outlier: 3.848A pdb=" N TYR L 75 " --> pdb=" O GLY L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 112 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 220 through 240 removed outlier: 3.851A pdb=" N GLU L 224 " --> pdb=" O PRO L 220 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN L 225 " --> pdb=" O PRO L 221 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU L 234 " --> pdb=" O TYR L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 295 Processing helix chain 'M' and resid 83 through 89 Processing helix chain 'M' and resid 90 through 92 No H-bonds generated for 'chain 'M' and resid 90 through 92' Processing helix chain 'M' and resid 94 through 110 removed outlier: 3.781A pdb=" N MET M 110 " --> pdb=" O ASN M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 153 removed outlier: 3.838A pdb=" N GLU M 141 " --> pdb=" O ARG M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 179 Processing helix chain 'M' and resid 202 through 204 No H-bonds generated for 'chain 'M' and resid 202 through 204' Processing helix chain 'M' and resid 250 through 254 Processing helix chain 'M' and resid 259 through 264 Processing helix chain 'M' and resid 264 through 284 removed outlier: 3.820A pdb=" N PHE M 281 " --> pdb=" O PHE M 277 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE M 282 " --> pdb=" O ASN M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 317 Processing helix chain 'M' and resid 347 through 363 Processing helix chain 'M' and resid 365 through 370 Processing helix chain 'M' and resid 394 through 402 removed outlier: 3.533A pdb=" N SER M 398 " --> pdb=" O LYS M 394 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 418 removed outlier: 3.543A pdb=" N LEU M 406 " --> pdb=" O GLY M 402 " (cutoff:3.500A) Processing helix chain 'M' and resid 419 through 423 Processing helix chain 'M' and resid 437 through 452 removed outlier: 3.899A pdb=" N GLN M 450 " --> pdb=" O LYS M 446 " (cutoff:3.500A) Processing helix chain 'M' and resid 454 through 462 Processing helix chain 'M' and resid 475 through 506 Processing helix chain 'N' and resid 83 through 89 Processing helix chain 'N' and resid 90 through 92 No H-bonds generated for 'chain 'N' and resid 90 through 92' Processing helix chain 'N' and resid 94 through 110 removed outlier: 3.748A pdb=" N MET N 110 " --> pdb=" O ASN N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 118 removed outlier: 3.574A pdb=" N TYR N 117 " --> pdb=" O PRO N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 153 removed outlier: 3.771A pdb=" N GLU N 141 " --> pdb=" O ARG N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 163 through 179 Processing helix chain 'N' and resid 202 through 204 No H-bonds generated for 'chain 'N' and resid 202 through 204' Processing helix chain 'N' and resid 250 through 254 Processing helix chain 'N' and resid 259 through 264 Processing helix chain 'N' and resid 264 through 284 removed outlier: 3.983A pdb=" N PHE N 281 " --> pdb=" O PHE N 277 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N PHE N 282 " --> pdb=" O ASN N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 317 Processing helix chain 'N' and resid 347 through 363 Processing helix chain 'N' and resid 365 through 370 Processing helix chain 'N' and resid 394 through 401 Processing helix chain 'N' and resid 402 through 418 Processing helix chain 'N' and resid 419 through 423 Processing helix chain 'N' and resid 437 through 452 removed outlier: 3.898A pdb=" N GLN N 450 " --> pdb=" O LYS N 446 " (cutoff:3.500A) Processing helix chain 'N' and resid 454 through 462 Processing helix chain 'N' and resid 475 through 506 removed outlier: 3.549A pdb=" N GLN N 487 " --> pdb=" O ALA N 483 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 89 Processing helix chain 'O' and resid 90 through 92 No H-bonds generated for 'chain 'O' and resid 90 through 92' Processing helix chain 'O' and resid 94 through 110 removed outlier: 3.790A pdb=" N MET O 110 " --> pdb=" O ASN O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 113 No H-bonds generated for 'chain 'O' and resid 111 through 113' Processing helix chain 'O' and resid 136 through 153 removed outlier: 3.976A pdb=" N GLU O 141 " --> pdb=" O ARG O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 163 through 179 Processing helix chain 'O' and resid 202 through 204 No H-bonds generated for 'chain 'O' and resid 202 through 204' Processing helix chain 'O' and resid 250 through 254 Processing helix chain 'O' and resid 259 through 264 Processing helix chain 'O' and resid 264 through 284 removed outlier: 3.975A pdb=" N PHE O 281 " --> pdb=" O PHE O 277 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE O 282 " --> pdb=" O ASN O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 301 through 317 Processing helix chain 'O' and resid 347 through 363 Processing helix chain 'O' and resid 365 through 370 removed outlier: 3.842A pdb=" N GLY O 370 " --> pdb=" O ALA O 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 392 through 418 removed outlier: 4.483A pdb=" N GLN O 397 " --> pdb=" O LYS O 393 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER O 398 " --> pdb=" O LYS O 394 " (cutoff:3.500A) Proline residue: O 405 - end of helix Processing helix chain 'O' and resid 419 through 423 Processing helix chain 'O' and resid 437 through 452 removed outlier: 3.906A pdb=" N GLN O 450 " --> pdb=" O LYS O 446 " (cutoff:3.500A) Processing helix chain 'O' and resid 454 through 462 Processing helix chain 'O' and resid 475 through 506 Processing helix chain 'P' and resid 83 through 89 Processing helix chain 'P' and resid 90 through 92 No H-bonds generated for 'chain 'P' and resid 90 through 92' Processing helix chain 'P' and resid 94 through 110 removed outlier: 3.824A pdb=" N MET P 110 " --> pdb=" O ASN P 106 " (cutoff:3.500A) 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 136 through 153 removed outlier: 3.905A pdb=" N GLU P 141 " --> pdb=" O ARG P 137 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 179 Processing helix chain 'P' and resid 202 through 204 No H-bonds generated for 'chain 'P' and resid 202 through 204' Processing helix chain 'P' and resid 250 through 254 Processing helix chain 'P' and resid 259 through 264 Processing helix chain 'P' and resid 264 through 284 removed outlier: 3.932A pdb=" N PHE P 281 " --> pdb=" O PHE P 277 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE P 282 " --> pdb=" O ASN P 278 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 317 Processing helix chain 'P' and resid 347 through 363 Processing helix chain 'P' and resid 365 through 370 Processing helix chain 'P' and resid 392 through 418 removed outlier: 3.794A pdb=" N GLN P 396 " --> pdb=" O GLY P 392 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN P 404 " --> pdb=" O ASN P 400 " (cutoff:3.500A) Proline residue: P 405 - end of helix Processing helix chain 'P' and resid 419 through 423 Processing helix chain 'P' and resid 437 through 452 removed outlier: 3.979A pdb=" N GLN P 450 " --> pdb=" O LYS P 446 " (cutoff:3.500A) Processing helix chain 'P' and resid 454 through 462 Processing helix chain 'P' and resid 475 through 506 Processing helix chain 'Q' and resid 83 through 89 Processing helix chain 'Q' and resid 90 through 92 No H-bonds generated for 'chain 'Q' and resid 90 through 92' Processing helix chain 'Q' and resid 94 through 110 removed outlier: 3.917A pdb=" N MET Q 110 " --> pdb=" O ASN Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 153 removed outlier: 3.781A pdb=" N GLU Q 141 " --> pdb=" O ARG Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 179 Processing helix chain 'Q' and resid 202 through 204 No H-bonds generated for 'chain 'Q' and resid 202 through 204' Processing helix chain 'Q' and resid 250 through 254 Processing helix chain 'Q' and resid 259 through 264 Processing helix chain 'Q' and resid 264 through 284 removed outlier: 3.891A pdb=" N PHE Q 281 " --> pdb=" O PHE Q 277 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N PHE Q 282 " --> pdb=" O ASN Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 317 Processing helix chain 'Q' and resid 347 through 363 Processing helix chain 'Q' and resid 365 through 370 removed outlier: 3.543A pdb=" N GLY Q 370 " --> pdb=" O ALA Q 367 " (cutoff:3.500A) Processing helix chain 'Q' and resid 392 through 402 Processing helix chain 'Q' and resid 402 through 418 removed outlier: 3.686A pdb=" N LEU Q 406 " --> pdb=" O GLY Q 402 " (cutoff:3.500A) Processing helix chain 'Q' and resid 419 through 423 Processing helix chain 'Q' and resid 437 through 452 removed outlier: 3.947A pdb=" N GLN Q 450 " --> pdb=" O LYS Q 446 " (cutoff:3.500A) Processing helix chain 'Q' and resid 454 through 462 Processing helix chain 'Q' and resid 475 through 506 Processing helix chain 'R' and resid 83 through 89 Processing helix chain 'R' and resid 90 through 92 No H-bonds generated for 'chain 'R' and resid 90 through 92' Processing helix chain 'R' and resid 94 through 110 removed outlier: 3.906A pdb=" N MET R 110 " --> pdb=" O ASN R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 153 removed outlier: 4.025A pdb=" N GLU R 141 " --> pdb=" O ARG R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 179 Processing helix chain 'R' and resid 202 through 204 No H-bonds generated for 'chain 'R' and resid 202 through 204' Processing helix chain 'R' and resid 250 through 254 Processing helix chain 'R' and resid 259 through 264 Processing helix chain 'R' and resid 264 through 284 removed outlier: 3.970A pdb=" N PHE R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N PHE R 282 " --> pdb=" O ASN R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 317 Processing helix chain 'R' and resid 347 through 363 Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 392 through 402 Processing helix chain 'R' and resid 402 through 418 Processing helix chain 'R' and resid 419 through 423 Processing helix chain 'R' and resid 437 through 452 removed outlier: 3.946A pdb=" N GLN R 450 " --> pdb=" O LYS R 446 " (cutoff:3.500A) Processing helix chain 'R' and resid 454 through 462 Processing helix chain 'R' and resid 475 through 506 Processing helix chain 'S' and resid 83 through 89 Processing helix chain 'S' and resid 90 through 92 No H-bonds generated for 'chain 'S' and resid 90 through 92' Processing helix chain 'S' and resid 94 through 110 removed outlier: 3.845A pdb=" N MET S 110 " --> pdb=" O ASN S 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 153 removed outlier: 3.740A pdb=" N GLU S 141 " --> pdb=" O ARG S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 163 through 179 Processing helix chain 'S' and resid 202 through 204 No H-bonds generated for 'chain 'S' and resid 202 through 204' Processing helix chain 'S' and resid 250 through 254 Processing helix chain 'S' and resid 259 through 264 Processing helix chain 'S' and resid 264 through 284 removed outlier: 3.861A pdb=" N PHE S 281 " --> pdb=" O PHE S 277 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N PHE S 282 " --> pdb=" O ASN S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 317 removed outlier: 3.525A pdb=" N SER S 317 " --> pdb=" O LYS S 313 " (cutoff:3.500A) Processing helix chain 'S' and resid 347 through 363 Processing helix chain 'S' and resid 365 through 370 removed outlier: 3.644A pdb=" N GLY S 370 " --> pdb=" O ALA S 367 " (cutoff:3.500A) Processing helix chain 'S' and resid 392 through 402 Processing helix chain 'S' and resid 402 through 418 removed outlier: 3.710A pdb=" N LEU S 406 " --> pdb=" O GLY S 402 " (cutoff:3.500A) Processing helix chain 'S' and resid 419 through 423 Processing helix chain 'S' and resid 437 through 452 removed outlier: 3.955A pdb=" N GLN S 450 " --> pdb=" O LYS S 446 " (cutoff:3.500A) Processing helix chain 'S' and resid 454 through 462 Processing helix chain 'S' and resid 475 through 506 Processing helix chain 'T' and resid 83 through 89 Processing helix chain 'T' and resid 90 through 92 No H-bonds generated for 'chain 'T' and resid 90 through 92' Processing helix chain 'T' and resid 94 through 110 removed outlier: 3.691A pdb=" N MET T 110 " --> pdb=" O ASN T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 136 through 153 removed outlier: 3.540A pdb=" N GLU T 141 " --> pdb=" O ARG T 137 " (cutoff:3.500A) Processing helix chain 'T' and resid 163 through 179 Processing helix chain 'T' and resid 202 through 204 No H-bonds generated for 'chain 'T' and resid 202 through 204' Processing helix chain 'T' and resid 250 through 254 Processing helix chain 'T' and resid 259 through 264 Processing helix chain 'T' and resid 264 through 284 removed outlier: 3.962A pdb=" N PHE T 281 " --> pdb=" O PHE T 277 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE T 282 " --> pdb=" O ASN T 278 " (cutoff:3.500A) Processing helix chain 'T' and resid 301 through 317 Processing helix chain 'T' and resid 347 through 363 Processing helix chain 'T' and resid 365 through 370 Processing helix chain 'T' and resid 395 through 418 removed outlier: 4.171A pdb=" N GLN T 399 " --> pdb=" O GLN T 395 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLN T 404 " --> pdb=" O ASN T 400 " (cutoff:3.500A) Proline residue: T 405 - end of helix Processing helix chain 'T' and resid 419 through 423 Processing helix chain 'T' and resid 437 through 452 removed outlier: 3.909A pdb=" N GLN T 450 " --> pdb=" O LYS T 446 " (cutoff:3.500A) Processing helix chain 'T' and resid 454 through 462 Processing helix chain 'T' and resid 475 through 506 removed outlier: 3.503A pdb=" N GLN T 487 " --> pdb=" O ALA T 483 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 89 Processing helix chain 'U' and resid 90 through 92 No H-bonds generated for 'chain 'U' and resid 90 through 92' Processing helix chain 'U' and resid 94 through 110 removed outlier: 3.765A pdb=" N MET U 110 " --> pdb=" O ASN U 106 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 153 removed outlier: 3.788A pdb=" N GLU U 141 " --> pdb=" O ARG U 137 " (cutoff:3.500A) Processing helix chain 'U' and resid 163 through 179 Processing helix chain 'U' and resid 202 through 204 No H-bonds generated for 'chain 'U' and resid 202 through 204' Processing helix chain 'U' and resid 250 through 254 Processing helix chain 'U' and resid 259 through 264 Processing helix chain 'U' and resid 264 through 284 removed outlier: 3.894A pdb=" N PHE U 281 " --> pdb=" O PHE U 277 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE U 282 " --> pdb=" O ASN U 278 " (cutoff:3.500A) Processing helix chain 'U' and resid 301 through 317 Processing helix chain 'U' and resid 347 through 363 Processing helix chain 'U' and resid 365 through 370 Processing helix chain 'U' and resid 393 through 418 removed outlier: 3.543A pdb=" N GLN U 397 " --> pdb=" O LYS U 393 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER U 398 " --> pdb=" O LYS U 394 " (cutoff:3.500A) Proline residue: U 405 - end of helix Processing helix chain 'U' and resid 419 through 423 Processing helix chain 'U' and resid 437 through 452 removed outlier: 3.800A pdb=" N GLN U 450 " --> pdb=" O LYS U 446 " (cutoff:3.500A) Processing helix chain 'U' and resid 454 through 462 Processing helix chain 'U' and resid 475 through 506 Processing helix chain 'V' and resid 83 through 89 Processing helix chain 'V' and resid 90 through 92 No H-bonds generated for 'chain 'V' and resid 90 through 92' Processing helix chain 'V' and resid 94 through 110 removed outlier: 3.853A pdb=" N MET V 110 " --> pdb=" O ASN V 106 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 153 removed outlier: 3.785A pdb=" N GLU V 141 " --> pdb=" O ARG V 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 163 through 179 Processing helix chain 'V' and resid 202 through 204 No H-bonds generated for 'chain 'V' and resid 202 through 204' Processing helix chain 'V' and resid 250 through 254 Processing helix chain 'V' and resid 259 through 264 Processing helix chain 'V' and resid 264 through 284 removed outlier: 3.860A pdb=" N PHE V 281 " --> pdb=" O PHE V 277 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N PHE V 282 " --> pdb=" O ASN V 278 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 317 Processing helix chain 'V' and resid 347 through 363 Processing helix chain 'V' and resid 365 through 370 Processing helix chain 'V' and resid 393 through 418 Proline residue: V 405 - end of helix Processing helix chain 'V' and resid 419 through 423 Processing helix chain 'V' and resid 437 through 452 removed outlier: 3.902A pdb=" N GLN V 450 " --> pdb=" O LYS V 446 " (cutoff:3.500A) Processing helix chain 'V' and resid 454 through 462 Processing helix chain 'V' and resid 475 through 506 Processing helix chain 'W' and resid 83 through 89 Processing helix chain 'W' and resid 90 through 92 No H-bonds generated for 'chain 'W' and resid 90 through 92' Processing helix chain 'W' and resid 94 through 110 removed outlier: 3.841A pdb=" N MET W 110 " --> pdb=" O ASN W 106 " (cutoff:3.500A) Processing helix chain 'W' and resid 136 through 153 removed outlier: 3.854A pdb=" N GLU W 141 " --> pdb=" O ARG W 137 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 179 Processing helix chain 'W' and resid 202 through 204 No H-bonds generated for 'chain 'W' and resid 202 through 204' Processing helix chain 'W' and resid 250 through 254 Processing helix chain 'W' and resid 259 through 264 Processing helix chain 'W' and resid 264 through 284 removed outlier: 3.879A pdb=" N PHE W 281 " --> pdb=" O PHE W 277 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE W 282 " --> pdb=" O ASN W 278 " (cutoff:3.500A) Processing helix chain 'W' and resid 301 through 317 Processing helix chain 'W' and resid 347 through 363 Processing helix chain 'W' and resid 366 through 370 Processing helix chain 'W' and resid 393 through 401 removed outlier: 3.572A pdb=" N GLN W 397 " --> pdb=" O LYS W 393 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER W 398 " --> pdb=" O LYS W 394 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN W 399 " --> pdb=" O GLN W 395 " (cutoff:3.500A) Processing helix chain 'W' and resid 402 through 418 Processing helix chain 'W' and resid 419 through 423 Processing helix chain 'W' and resid 437 through 452 removed outlier: 3.899A pdb=" N GLN W 450 " --> pdb=" O LYS W 446 " (cutoff:3.500A) Processing helix chain 'W' and resid 454 through 462 Processing helix chain 'W' and resid 475 through 506 removed outlier: 3.517A pdb=" N GLN W 487 " --> pdb=" O ALA W 483 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 89 Processing helix chain 'X' and resid 90 through 92 No H-bonds generated for 'chain 'X' and resid 90 through 92' Processing helix chain 'X' and resid 94 through 110 removed outlier: 3.884A pdb=" N MET X 110 " --> pdb=" O ASN X 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 136 through 153 removed outlier: 3.807A pdb=" N GLU X 141 " --> pdb=" O ARG X 137 " (cutoff:3.500A) Processing helix chain 'X' and resid 163 through 179 Processing helix chain 'X' and resid 202 through 204 No H-bonds generated for 'chain 'X' and resid 202 through 204' Processing helix chain 'X' and resid 250 through 254 Processing helix chain 'X' and resid 259 through 264 Processing helix chain 'X' and resid 264 through 284 removed outlier: 3.954A pdb=" N PHE X 281 " --> pdb=" O PHE X 277 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N PHE X 282 " --> pdb=" O ASN X 278 " (cutoff:3.500A) Processing helix chain 'X' and resid 301 through 317 Processing helix chain 'X' and resid 347 through 363 Processing helix chain 'X' and resid 365 through 370 Processing helix chain 'X' and resid 393 through 418 Proline residue: X 405 - end of helix Processing helix chain 'X' and resid 419 through 423 Processing helix chain 'X' and resid 437 through 452 removed outlier: 3.783A pdb=" N GLN X 450 " --> pdb=" O LYS X 446 " (cutoff:3.500A) Processing helix chain 'X' and resid 454 through 462 Processing helix chain 'X' and resid 475 through 506 removed outlier: 3.501A pdb=" N GLN X 487 " --> pdb=" O ALA X 483 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 106 removed outlier: 6.656A pdb=" N TYR A 105 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN A 195 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N MET A 196 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 202 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL A 126 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N LEU A 129 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LYS A 140 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU A 131 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 255 removed outlier: 7.096A pdb=" N ALA A 249 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A 264 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ALA B 249 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR B 264 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR B 259 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LEU C 253 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B 261 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS C 251 " --> pdb=" O THR B 261 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY B 263 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA C 249 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR C 264 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR C 259 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU D 253 " --> pdb=" O THR C 259 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR C 261 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS D 251 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLY C 263 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ALA D 249 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR D 264 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA E 249 " --> pdb=" O THR E 264 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR E 264 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA F 249 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR F 264 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR F 259 " --> pdb=" O LEU G 253 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU G 253 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR F 261 " --> pdb=" O LYS G 251 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS G 251 " --> pdb=" O THR F 261 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLY F 263 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ALA G 249 " --> pdb=" O THR G 264 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR G 264 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR G 259 " --> pdb=" O LEU H 253 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU H 253 " --> pdb=" O THR G 259 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR G 261 " --> pdb=" O LYS H 251 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS H 251 " --> pdb=" O THR G 261 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLY G 263 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA H 249 " --> pdb=" O THR H 264 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR H 264 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR H 259 " --> pdb=" O LEU I 253 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LEU I 253 " --> pdb=" O THR H 259 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR H 261 " --> pdb=" O LYS I 251 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS I 251 " --> pdb=" O THR H 261 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLY H 263 " --> pdb=" O ALA I 249 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA I 249 " --> pdb=" O THR I 264 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR I 264 " --> pdb=" O ALA I 249 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR I 259 " --> pdb=" O LEU J 253 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU J 253 " --> pdb=" O THR I 259 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR I 261 " --> pdb=" O LYS J 251 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS J 251 " --> pdb=" O THR I 261 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLY I 263 " --> pdb=" O ALA J 249 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA J 249 " --> pdb=" O THR J 264 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR J 264 " --> pdb=" O ALA J 249 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA K 249 " --> pdb=" O THR K 264 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR K 264 " --> pdb=" O ALA K 249 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA L 249 " --> pdb=" O THR L 264 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR L 264 " --> pdb=" O ALA L 249 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR L 259 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU A 253 " --> pdb=" O THR L 259 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR L 261 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS A 251 " --> pdb=" O THR L 261 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLY L 263 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 302 Processing sheet with id=AA5, first strand: chain 'B' and resid 97 through 106 removed outlier: 6.570A pdb=" N TYR B 105 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN B 195 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N MET B 196 " --> pdb=" O GLN B 132 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 202 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL B 126 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE B 133 " --> pdb=" O PRO B 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AA7, first strand: chain 'B' and resid 299 through 302 Processing sheet with id=AA8, first strand: chain 'C' and resid 97 through 106 removed outlier: 6.652A pdb=" N TYR C 105 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN C 195 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N MET C 196 " --> pdb=" O GLN C 132 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL C 202 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL C 126 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE C 133 " --> pdb=" O PRO C 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AB1, first strand: chain 'C' and resid 299 through 302 Processing sheet with id=AB2, first strand: chain 'D' and resid 97 through 106 removed outlier: 6.652A pdb=" N TYR D 105 " --> pdb=" O GLN D 195 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN D 195 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE D 133 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N MET D 196 " --> pdb=" O LEU D 131 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU D 131 " --> pdb=" O MET D 196 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG D 198 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU D 129 " --> pdb=" O ARG D 198 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU D 200 " --> pdb=" O GLU D 127 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 125 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE D 133 " --> pdb=" O PRO D 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 116 through 117 Processing sheet with id=AB4, first strand: chain 'D' and resid 299 through 302 removed outlier: 3.521A pdb=" N ILE P 294 " --> pdb=" O VAL Q 328 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP P 332 " --> pdb=" O ARG P 295 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 97 through 106 removed outlier: 6.582A pdb=" N TYR E 105 " --> pdb=" O GLN E 195 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN E 195 " --> pdb=" O TYR E 105 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N MET E 196 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL E 202 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL E 126 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N PHE E 133 " --> pdb=" O PRO E 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 116 through 117 Processing sheet with id=AB7, first strand: chain 'E' and resid 299 through 302 removed outlier: 3.757A pdb=" N ASP Q 332 " --> pdb=" O ARG Q 295 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 97 through 106 removed outlier: 6.641A pdb=" N TYR F 105 " --> pdb=" O GLN F 195 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLN F 195 " --> pdb=" O TYR F 105 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N PHE F 133 " --> pdb=" O PRO F 194 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N MET F 196 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU F 131 " --> pdb=" O MET F 196 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG F 198 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU F 129 " --> pdb=" O ARG F 198 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU F 200 " --> pdb=" O GLU F 127 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N LEU F 129 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS F 140 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU F 131 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 116 through 117 Processing sheet with id=AC1, first strand: chain 'F' and resid 299 through 302 removed outlier: 3.527A pdb=" N ILE F 300 " --> pdb=" O VAL S 327 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP R 332 " --> pdb=" O ARG R 295 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 97 through 106 removed outlier: 6.503A pdb=" N TYR G 105 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN G 195 " --> pdb=" O TYR G 105 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N MET G 196 " --> pdb=" O GLN G 132 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL G 202 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL G 126 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE G 133 " --> pdb=" O PRO G 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 116 through 117 Processing sheet with id=AC4, first strand: chain 'G' and resid 299 through 302 removed outlier: 3.507A pdb=" N ILE G 300 " --> pdb=" O VAL T 327 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP S 332 " --> pdb=" O ARG S 295 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 97 through 106 removed outlier: 6.617A pdb=" N TYR H 105 " --> pdb=" O GLN H 195 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN H 195 " --> pdb=" O TYR H 105 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N MET H 196 " --> pdb=" O GLN H 132 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL H 202 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL H 126 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N LEU H 129 " --> pdb=" O LYS H 140 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LYS H 140 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU H 131 " --> pdb=" O ILE H 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 116 through 117 Processing sheet with id=AC7, first strand: chain 'H' and resid 299 through 302 removed outlier: 3.516A pdb=" N ASP T 332 " --> pdb=" O ARG T 295 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 97 through 106 removed outlier: 6.570A pdb=" N TYR I 105 " --> pdb=" O GLN I 195 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN I 195 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLN I 132 " --> pdb=" O PRO I 194 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N MET I 196 " --> pdb=" O GLN I 130 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN I 130 " --> pdb=" O MET I 196 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG I 198 " --> pdb=" O ASN I 128 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN I 128 " --> pdb=" O ARG I 198 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLU I 200 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL I 126 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL I 202 " --> pdb=" O LEU I 124 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE I 133 " --> pdb=" O PRO I 137 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 116 through 117 Processing sheet with id=AD1, first strand: chain 'I' and resid 299 through 302 removed outlier: 3.626A pdb=" N ASP U 332 " --> pdb=" O ARG U 295 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 97 through 106 removed outlier: 6.603A pdb=" N TYR J 105 " --> pdb=" O GLN J 195 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN J 195 " --> pdb=" O TYR J 105 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N PHE J 133 " --> pdb=" O PRO J 194 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N MET J 196 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU J 131 " --> pdb=" O MET J 196 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG J 198 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU J 129 " --> pdb=" O ARG J 198 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU J 200 " --> pdb=" O GLU J 127 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LEU J 129 " --> pdb=" O LYS J 140 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS J 140 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU J 131 " --> pdb=" O ILE J 138 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 116 through 117 Processing sheet with id=AD4, first strand: chain 'J' and resid 299 through 302 removed outlier: 3.514A pdb=" N ILE V 294 " --> pdb=" O VAL W 328 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP V 332 " --> pdb=" O ARG V 295 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 97 through 106 removed outlier: 6.728A pdb=" N TYR K 105 " --> pdb=" O GLN K 195 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN K 195 " --> pdb=" O TYR K 105 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N MET K 196 " --> pdb=" O GLN K 132 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL K 202 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL K 126 " --> pdb=" O VAL K 202 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LEU K 129 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LYS K 140 " --> pdb=" O LEU K 129 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU K 131 " --> pdb=" O ILE K 138 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 116 through 117 Processing sheet with id=AD7, first strand: chain 'K' and resid 299 through 302 removed outlier: 3.520A pdb=" N ASP W 332 " --> pdb=" O ARG W 295 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 97 through 106 removed outlier: 6.602A pdb=" N TYR L 105 " --> pdb=" O GLN L 195 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN L 195 " --> pdb=" O TYR L 105 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N MET L 196 " --> pdb=" O GLN L 132 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL L 202 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL L 126 " --> pdb=" O VAL L 202 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N LEU L 129 " --> pdb=" O LYS L 140 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LYS L 140 " --> pdb=" O LEU L 129 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU L 131 " --> pdb=" O ILE L 138 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 116 through 117 Processing sheet with id=AE1, first strand: chain 'L' and resid 299 through 302 removed outlier: 7.276A pdb=" N ILE X 294 " --> pdb=" O PRO M 326 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL M 328 " --> pdb=" O ILE X 294 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP X 332 " --> pdb=" O ARG X 295 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 123 through 128 Processing sheet with id=AE3, first strand: chain 'M' and resid 195 through 201 removed outlier: 6.961A pdb=" N VAL M 186 " --> pdb=" O GLU M 196 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE M 198 " --> pdb=" O GLU M 184 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU M 184 " --> pdb=" O PHE M 198 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ALA M 200 " --> pdb=" O ASN M 182 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASN M 182 " --> pdb=" O ALA M 200 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE M 183 " --> pdb=" O ALA M 241 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 206 through 208 removed outlier: 6.328A pdb=" N VAL M 227 " --> pdb=" O VAL M 231 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL M 231 " --> pdb=" O VAL M 227 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 123 through 128 Processing sheet with id=AE6, first strand: chain 'N' and resid 195 through 201 removed outlier: 4.447A pdb=" N ASN N 182 " --> pdb=" O VAL N 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE N 183 " --> pdb=" O ALA N 241 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 206 through 208 removed outlier: 3.524A pdb=" N ALA N 233 " --> pdb=" O GLN N 225 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL N 227 " --> pdb=" O VAL N 231 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N VAL N 231 " --> pdb=" O VAL N 227 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 123 through 128 Processing sheet with id=AE9, first strand: chain 'O' and resid 195 through 201 removed outlier: 6.939A pdb=" N VAL O 186 " --> pdb=" O GLU O 196 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE O 198 " --> pdb=" O GLU O 184 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLU O 184 " --> pdb=" O PHE O 198 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ALA O 200 " --> pdb=" O ASN O 182 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASN O 182 " --> pdb=" O ALA O 200 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE O 183 " --> pdb=" O ALA O 241 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 206 through 208 removed outlier: 3.540A pdb=" N ALA O 233 " --> pdb=" O GLN O 225 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL O 227 " --> pdb=" O VAL O 231 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL O 231 " --> pdb=" O VAL O 227 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 123 through 128 Processing sheet with id=AF3, first strand: chain 'P' and resid 195 through 201 removed outlier: 4.544A pdb=" N ASN P 182 " --> pdb=" O VAL P 201 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE P 183 " --> pdb=" O ALA P 241 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 206 through 208 removed outlier: 6.354A pdb=" N VAL P 227 " --> pdb=" O VAL P 231 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL P 231 " --> pdb=" O VAL P 227 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 123 through 128 Processing sheet with id=AF6, first strand: chain 'Q' and resid 195 through 201 removed outlier: 4.385A pdb=" N ASN Q 182 " --> pdb=" O VAL Q 201 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE Q 183 " --> pdb=" O ALA Q 241 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 206 through 208 removed outlier: 3.647A pdb=" N ALA Q 233 " --> pdb=" O GLN Q 225 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL Q 227 " --> pdb=" O VAL Q 231 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL Q 231 " --> pdb=" O VAL Q 227 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 123 through 128 Processing sheet with id=AF9, first strand: chain 'R' and resid 195 through 201 removed outlier: 4.419A pdb=" N ASN R 182 " --> pdb=" O VAL R 201 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE R 183 " --> pdb=" O ALA R 241 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'R' and resid 206 through 208 removed outlier: 3.637A pdb=" N ALA R 233 " --> pdb=" O GLN R 225 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL R 227 " --> pdb=" O VAL R 231 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL R 231 " --> pdb=" O VAL R 227 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 123 through 128 Processing sheet with id=AG3, first strand: chain 'S' and resid 195 through 201 removed outlier: 4.426A pdb=" N ASN S 182 " --> pdb=" O VAL S 201 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE S 183 " --> pdb=" O ALA S 241 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 206 through 208 removed outlier: 3.573A pdb=" N ALA S 233 " --> pdb=" O GLN S 225 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL S 227 " --> pdb=" O VAL S 231 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL S 231 " --> pdb=" O VAL S 227 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 123 through 128 Processing sheet with id=AG6, first strand: chain 'T' and resid 195 through 201 removed outlier: 4.360A pdb=" N ASN T 182 " --> pdb=" O VAL T 201 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE T 183 " --> pdb=" O ALA T 241 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'T' and resid 206 through 208 removed outlier: 3.532A pdb=" N ALA T 233 " --> pdb=" O GLN T 225 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL T 227 " --> pdb=" O VAL T 231 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N VAL T 231 " --> pdb=" O VAL T 227 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 123 through 128 Processing sheet with id=AG9, first strand: chain 'U' and resid 195 through 201 removed outlier: 6.970A pdb=" N VAL U 186 " --> pdb=" O GLU U 196 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE U 198 " --> pdb=" O GLU U 184 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLU U 184 " --> pdb=" O PHE U 198 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA U 200 " --> pdb=" O ASN U 182 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ASN U 182 " --> pdb=" O ALA U 200 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE U 183 " --> pdb=" O ALA U 241 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'U' and resid 206 through 208 removed outlier: 6.791A pdb=" N PHE U 223 " --> pdb=" O SER U 234 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER U 234 " --> pdb=" O PHE U 223 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN U 225 " --> pdb=" O VAL U 232 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 123 through 128 Processing sheet with id=AH3, first strand: chain 'V' and resid 195 through 201 removed outlier: 4.441A pdb=" N ASN V 182 " --> pdb=" O VAL V 201 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE V 183 " --> pdb=" O ALA V 241 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'V' and resid 206 through 208 removed outlier: 6.837A pdb=" N PHE V 223 " --> pdb=" O SER V 234 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER V 234 " --> pdb=" O PHE V 223 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN V 225 " --> pdb=" O VAL V 232 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'W' and resid 123 through 128 Processing sheet with id=AH6, first strand: chain 'W' and resid 182 through 187 removed outlier: 7.649A pdb=" N ASN W 182 " --> pdb=" O ALA W 200 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALA W 200 " --> pdb=" O ASN W 182 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU W 184 " --> pdb=" O PHE W 198 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE W 198 " --> pdb=" O GLU W 184 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL W 186 " --> pdb=" O GLU W 196 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'W' and resid 206 through 208 removed outlier: 3.560A pdb=" N ALA W 233 " --> pdb=" O GLN W 225 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL W 227 " --> pdb=" O VAL W 231 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N VAL W 231 " --> pdb=" O VAL W 227 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 123 through 128 Processing sheet with id=AH9, first strand: chain 'X' and resid 195 through 201 removed outlier: 4.352A pdb=" N ASN X 182 " --> pdb=" O VAL X 201 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE X 183 " --> pdb=" O ALA X 241 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'X' and resid 206 through 208 removed outlier: 6.358A pdb=" N VAL X 227 " --> pdb=" O VAL X 231 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N VAL X 231 " --> pdb=" O VAL X 227 " (cutoff:3.500A) 3242 hydrogen bonds defined for protein. 9063 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 122 hydrogen bonds 244 hydrogen bond angles 0 basepair planarities 53 basepair parallelities 98 stacking parallelities Total time for adding SS restraints: 29.64 Time building geometry restraints manager: 15.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 21510 1.33 - 1.45: 10912 1.45 - 1.57: 39594 1.57 - 1.69: 250 1.69 - 1.81: 552 Bond restraints: 72818 Sorted by residual: bond pdb=" C3' DC Y 45 " pdb=" O3' DC Y 45 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" C1' DT Y 4 " pdb=" N1 DT Y 4 " ideal model delta sigma weight residual 1.490 1.530 -0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" C1' DT Y 58 " pdb=" N1 DT Y 58 " ideal model delta sigma weight residual 1.490 1.529 -0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" C1' DT Z 38 " pdb=" N1 DT Z 38 " ideal model delta sigma weight residual 1.490 1.527 -0.037 3.00e-02 1.11e+03 1.53e+00 bond pdb=" CG ARG L 88 " pdb=" CD ARG L 88 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.52e+00 ... (remaining 72813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 96647 1.90 - 3.79: 1796 3.79 - 5.69: 279 5.69 - 7.59: 11 7.59 - 9.49: 2 Bond angle restraints: 98735 Sorted by residual: angle pdb=" CA GLN S 404 " pdb=" CB GLN S 404 " pdb=" CG GLN S 404 " ideal model delta sigma weight residual 114.10 122.26 -8.16 2.00e+00 2.50e-01 1.66e+01 angle pdb=" CB LEU I 79 " pdb=" CG LEU I 79 " pdb=" CD1 LEU I 79 " ideal model delta sigma weight residual 110.70 120.19 -9.49 3.00e+00 1.11e-01 1.00e+01 angle pdb=" CA MET D 114 " pdb=" CB MET D 114 " pdb=" CG MET D 114 " ideal model delta sigma weight residual 114.10 119.77 -5.67 2.00e+00 2.50e-01 8.04e+00 angle pdb=" C PHE N 452 " pdb=" CA PHE N 452 " pdb=" CB PHE N 452 " ideal model delta sigma weight residual 110.42 104.88 5.54 1.99e+00 2.53e-01 7.74e+00 angle pdb=" CA MET B 114 " pdb=" CB MET B 114 " pdb=" CG MET B 114 " ideal model delta sigma weight residual 114.10 119.66 -5.56 2.00e+00 2.50e-01 7.73e+00 ... (remaining 98730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 42635 35.47 - 70.95: 986 70.95 - 106.42: 45 106.42 - 141.90: 0 141.90 - 177.37: 2 Dihedral angle restraints: 43668 sinusoidal: 19075 harmonic: 24593 Sorted by residual: dihedral pdb=" CA GLY Q 321 " pdb=" C GLY Q 321 " pdb=" N SER Q 322 " pdb=" CA SER Q 322 " ideal model delta harmonic sigma weight residual -180.00 -150.32 -29.68 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLY T 321 " pdb=" C GLY T 321 " pdb=" N SER T 322 " pdb=" CA SER T 322 " ideal model delta harmonic sigma weight residual -180.00 -150.33 -29.67 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA GLY O 321 " pdb=" C GLY O 321 " pdb=" N SER O 322 " pdb=" CA SER O 322 " ideal model delta harmonic sigma weight residual -180.00 -150.37 -29.63 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 43665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 8666 0.057 - 0.114: 1536 0.114 - 0.172: 223 0.172 - 0.229: 15 0.229 - 0.286: 1 Chirality restraints: 10441 Sorted by residual: chirality pdb=" CA GLN S 404 " pdb=" N GLN S 404 " pdb=" C GLN S 404 " pdb=" CB GLN S 404 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ARG H 88 " pdb=" N ARG H 88 " pdb=" C ARG H 88 " pdb=" CB ARG H 88 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ARG C 88 " pdb=" N ARG C 88 " pdb=" C ARG C 88 " pdb=" CB ARG C 88 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 10438 not shown) Planarity restraints: 12510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC Z 32 " 0.016 2.00e-02 2.50e+03 2.83e-02 1.80e+01 pdb=" N1 DC Z 32 " -0.061 2.00e-02 2.50e+03 pdb=" C2 DC Z 32 " 0.053 2.00e-02 2.50e+03 pdb=" O2 DC Z 32 " -0.013 2.00e-02 2.50e+03 pdb=" N3 DC Z 32 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DC Z 32 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC Z 32 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC Z 32 " 0.009 2.00e-02 2.50e+03 pdb=" C6 DC Z 32 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT Z 21 " 0.036 2.00e-02 2.50e+03 2.61e-02 1.70e+01 pdb=" N1 DT Z 21 " -0.066 2.00e-02 2.50e+03 pdb=" C2 DT Z 21 " 0.031 2.00e-02 2.50e+03 pdb=" O2 DT Z 21 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT Z 21 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT Z 21 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT Z 21 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DT Z 21 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT Z 21 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT Z 21 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN S 399 " 0.019 2.00e-02 2.50e+03 3.87e-02 1.49e+01 pdb=" C GLN S 399 " -0.067 2.00e-02 2.50e+03 pdb=" O GLN S 399 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN S 400 " 0.023 2.00e-02 2.50e+03 ... (remaining 12507 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1575 2.70 - 3.25: 71291 3.25 - 3.80: 110054 3.80 - 4.35: 149486 4.35 - 4.90: 247695 Nonbonded interactions: 580101 Sorted by model distance: nonbonded pdb=" NH2 ARG F 103 " pdb=" OE1 GLU R 306 " model vdw 2.149 3.120 nonbonded pdb=" NH2 ARG H 103 " pdb=" OE1 GLU T 306 " model vdw 2.163 3.120 nonbonded pdb=" NH2 ARG I 103 " pdb=" OE1 GLU U 306 " model vdw 2.171 3.120 nonbonded pdb=" NH2 ARG B 103 " pdb=" OE1 GLU N 306 " model vdw 2.172 3.120 nonbonded pdb=" NH2 ARG A 103 " pdb=" OE1 GLU M 306 " model vdw 2.175 3.120 ... (remaining 580096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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' } ncs_group { reference = (chain 'M' and (resid 49 through 377 or resid 392 through 506)) selection = (chain 'N' and (resid 49 through 377 or resid 392 through 506)) selection = (chain 'O' and (resid 49 through 377 or resid 392 through 506)) selection = (chain 'P' and (resid 49 through 377 or resid 392 through 506)) selection = (chain 'Q' and (resid 49 through 377 or resid 392 through 506)) selection = (chain 'R' and (resid 49 through 377 or resid 392 through 506)) selection = (chain 'S' and (resid 49 through 377 or resid 392 through 506)) selection = (chain 'T' and (resid 49 through 377 or resid 392 through 506)) selection = (chain 'U' and (resid 49 through 377 or resid 392 through 506)) selection = (chain 'V' and (resid 49 through 377 or resid 392 through 506)) selection = (chain 'W' and (resid 49 through 377 or resid 392 through 506)) selection = (chain 'X' and (resid 49 through 377 or resid 392 through 506)) } 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: 4.100 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: 0.080 Extract box with map and model: 1.990 Check model and map are aligned: 0.410 Set scattering table: 0.500 Process input model: 132.840 Find NCS groups from input model: 3.280 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 0.057 72818 Z= 0.251 Angle : 0.675 9.485 98735 Z= 0.382 Chirality : 0.045 0.286 10441 Planarity : 0.008 0.100 12510 Dihedral : 14.358 177.374 27922 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 0.01 % Favored : 99.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: -0.22 (0.09), residues: 8415 helix: -0.41 (0.08), residues: 3208 sheet: -0.09 (0.13), residues: 1150 loop : 0.28 (0.10), residues: 4057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 239 HIS 0.011 0.002 HIS M 85 PHE 0.039 0.002 PHE S 452 TYR 0.038 0.004 TYR L 270 ARG 0.021 0.003 ARG Q 222 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16830 Ramachandran restraints generated. 8415 Oldfield, 0 Emsley, 8415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16830 Ramachandran restraints generated. 8415 Oldfield, 0 Emsley, 8415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1380 residues out of total 7363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1380 time to evaluate : 6.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.9176 (mt) cc_final: 0.8817 (mt) REVERT: A 107 GLU cc_start: 0.8441 (tt0) cc_final: 0.8193 (tp30) REVERT: A 198 ARG cc_start: 0.7956 (ttt-90) cc_final: 0.7644 (ttp-170) REVERT: B 112 SER cc_start: 0.8741 (m) cc_final: 0.8379 (t) REVERT: B 120 ARG cc_start: 0.8304 (mmm160) cc_final: 0.6877 (mmm160) REVERT: C 70 MET cc_start: 0.8375 (ttp) cc_final: 0.8168 (ttp) REVERT: C 78 ILE cc_start: 0.9054 (mm) cc_final: 0.8830 (tp) REVERT: D 147 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8527 (mptt) REVERT: F 302 LEU cc_start: 0.7822 (mt) cc_final: 0.7388 (mt) REVERT: G 26 SER cc_start: 0.9329 (m) cc_final: 0.9129 (p) REVERT: G 251 LYS cc_start: 0.8916 (ptpt) cc_final: 0.8159 (tttt) REVERT: H 33 ASP cc_start: 0.8252 (t70) cc_final: 0.7943 (t0) REVERT: H 297 TYR cc_start: 0.6937 (m-10) cc_final: 0.6685 (m-80) REVERT: I 70 MET cc_start: 0.8370 (ttp) cc_final: 0.8167 (ttp) REVERT: I 85 LYS cc_start: 0.9181 (ttmt) cc_final: 0.8885 (ttpp) REVERT: I 251 LYS cc_start: 0.8659 (ptpt) cc_final: 0.8222 (tttt) REVERT: I 292 ARG cc_start: 0.9023 (mtt180) cc_final: 0.8706 (mtt90) REVERT: J 225 GLN cc_start: 0.8400 (tt0) cc_final: 0.8043 (tt0) REVERT: K 72 ASP cc_start: 0.8695 (m-30) cc_final: 0.8244 (p0) REVERT: K 280 ILE cc_start: 0.9479 (mt) cc_final: 0.9200 (mt) REVERT: L 33 ASP cc_start: 0.8255 (t70) cc_final: 0.7746 (t0) REVERT: L 61 VAL cc_start: 0.8890 (t) cc_final: 0.8622 (t) REVERT: L 93 SER cc_start: 0.8923 (t) cc_final: 0.8246 (p) REVERT: L 97 ASP cc_start: 0.8700 (t0) cc_final: 0.8487 (t0) REVERT: L 254 GLU cc_start: 0.8014 (tt0) cc_final: 0.7786 (tm-30) REVERT: M 82 HIS cc_start: 0.6114 (m-70) cc_final: 0.5725 (m-70) REVERT: N 353 TYR cc_start: 0.8788 (t80) cc_final: 0.8368 (t80) REVERT: N 503 MET cc_start: 0.2131 (ttm) cc_final: 0.1837 (tmm) REVERT: N 506 LEU cc_start: 0.7379 (tp) cc_final: 0.7044 (pp) REVERT: O 485 LEU cc_start: 0.8306 (mt) cc_final: 0.8028 (pp) REVERT: Q 65 MET cc_start: 0.6673 (mmp) cc_final: 0.5743 (mtm) REVERT: Q 345 MET cc_start: 0.8903 (ptm) cc_final: 0.8606 (ptm) REVERT: Q 445 LEU cc_start: 0.8879 (tp) cc_final: 0.8572 (mm) REVERT: Q 462 GLN cc_start: 0.5642 (mm-40) cc_final: 0.5407 (tm-30) REVERT: Q 478 PHE cc_start: 0.8870 (t80) cc_final: 0.8571 (t80) REVERT: R 502 MET cc_start: 0.7162 (ttt) cc_final: 0.6877 (ppp) REVERT: S 110 MET cc_start: 0.9278 (mmp) cc_final: 0.8789 (mmm) REVERT: S 143 MET cc_start: 0.8981 (mtm) cc_final: 0.8722 (mtt) REVERT: S 267 GLU cc_start: 0.8744 (mp0) cc_final: 0.8425 (mp0) REVERT: S 324 GLN cc_start: 0.8354 (mt0) cc_final: 0.8049 (mt0) REVERT: T 64 MET cc_start: 0.6609 (mmt) cc_final: 0.6193 (tpt) REVERT: U 65 MET cc_start: 0.4682 (mmp) cc_final: 0.3737 (tmm) REVERT: U 300 GLN cc_start: 0.7852 (mt0) cc_final: 0.6879 (mt0) REVERT: U 317 SER cc_start: 0.8985 (m) cc_final: 0.8784 (t) REVERT: U 503 MET cc_start: 0.6481 (ttm) cc_final: 0.6224 (mmm) REVERT: V 331 ASP cc_start: 0.7089 (m-30) cc_final: 0.6005 (m-30) REVERT: W 143 MET cc_start: 0.8739 (mtm) cc_final: 0.8102 (ptp) REVERT: W 451 ILE cc_start: 0.8326 (mm) cc_final: 0.7880 (mm) REVERT: X 503 MET cc_start: -0.0365 (ttm) cc_final: -0.0622 (ttm) outliers start: 0 outliers final: 0 residues processed: 1380 average time/residue: 0.7849 time to fit residues: 1770.2157 Evaluate side-chains 624 residues out of total 7363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 624 time to evaluate : 6.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 716 optimal weight: 1.9990 chunk 642 optimal weight: 0.0040 chunk 356 optimal weight: 9.9990 chunk 219 optimal weight: 0.6980 chunk 433 optimal weight: 9.9990 chunk 343 optimal weight: 20.0000 chunk 664 optimal weight: 0.0980 chunk 257 optimal weight: 5.9990 chunk 404 optimal weight: 9.9990 chunk 494 optimal weight: 0.0070 chunk 770 optimal weight: 6.9990 overall best weight: 0.5612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN B 39 ASN B 68 GLN D 214 ASN D 237 GLN F 77 HIS F 134 ASN F 266 GLN G 39 ASN I 31 HIS ** I 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 77 HIS L 237 GLN M 113 GLN N 324 GLN N 484 GLN O 190 ASN O 397 GLN P 300 GLN Q 400 ASN ** Q 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 404 GLN ** R 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 429 GLN ** T 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 429 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 113 GLN U 400 ASN V 396 GLN V 429 GLN W 54 GLN W 107 GLN X 324 GLN ** X 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 72818 Z= 0.159 Angle : 0.561 11.840 98735 Z= 0.305 Chirality : 0.042 0.252 10441 Planarity : 0.004 0.041 12510 Dihedral : 12.229 177.732 10681 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.02 % Allowed : 6.35 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.68 (0.09), residues: 8415 helix: 2.06 (0.09), residues: 3235 sheet: -0.14 (0.13), residues: 1252 loop : 0.91 (0.11), residues: 3928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 239 HIS 0.006 0.001 HIS M 85 PHE 0.021 0.001 PHE W 452 TYR 0.020 0.001 TYR N 271 ARG 0.007 0.001 ARG P 499 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16830 Ramachandran restraints generated. 8415 Oldfield, 0 Emsley, 8415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16830 Ramachandran restraints generated. 8415 Oldfield, 0 Emsley, 8415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 7363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 750 time to evaluate : 6.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 SER cc_start: 0.8535 (m) cc_final: 0.8222 (t) REVERT: C 78 ILE cc_start: 0.9140 (mm) cc_final: 0.8741 (tp) REVERT: D 214 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8589 (p0) REVERT: F 112 SER cc_start: 0.8774 (m) cc_final: 0.8357 (p) REVERT: F 270 TYR cc_start: 0.8478 (m-80) cc_final: 0.8180 (m-80) REVERT: F 302 LEU cc_start: 0.7900 (mt) cc_final: 0.6852 (mt) REVERT: G 260 GLU cc_start: 0.7907 (tp30) cc_final: 0.7492 (tp30) REVERT: G 289 ASP cc_start: 0.8404 (m-30) cc_final: 0.8078 (m-30) REVERT: H 286 GLU cc_start: 0.8101 (tt0) cc_final: 0.7672 (tt0) REVERT: I 36 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7448 (mp0) REVERT: I 39 ASN cc_start: 0.8856 (m-40) cc_final: 0.8501 (m110) REVERT: I 70 MET cc_start: 0.8367 (ttp) cc_final: 0.8110 (ttp) REVERT: I 85 LYS cc_start: 0.9197 (ttmt) cc_final: 0.8937 (ttpp) REVERT: I 230 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8459 (m-80) REVERT: I 292 ARG cc_start: 0.8973 (mtt180) cc_final: 0.8706 (mtt90) REVERT: I 302 LEU cc_start: 0.7781 (mt) cc_final: 0.7326 (mp) REVERT: J 133 PHE cc_start: 0.8731 (t80) cc_final: 0.8527 (t80) REVERT: J 225 GLN cc_start: 0.8418 (tt0) cc_final: 0.8133 (tp-100) REVERT: J 292 ARG cc_start: 0.8669 (mtm-85) cc_final: 0.8400 (ttm110) REVERT: J 300 ILE cc_start: 0.8954 (tt) cc_final: 0.8656 (tt) REVERT: K 97 ASP cc_start: 0.7874 (t0) cc_final: 0.7658 (m-30) REVERT: L 61 VAL cc_start: 0.8850 (t) cc_final: 0.8598 (t) REVERT: L 93 SER cc_start: 0.8722 (t) cc_final: 0.8208 (p) REVERT: L 102 MET cc_start: 0.8534 (tpp) cc_final: 0.8319 (tpp) REVERT: L 219 MET cc_start: 0.8739 (ttp) cc_final: 0.8416 (ttp) REVERT: L 254 GLU cc_start: 0.8022 (tt0) cc_final: 0.7618 (tm-30) REVERT: M 504 MET cc_start: 0.4352 (mmm) cc_final: 0.4074 (mmm) REVERT: N 267 GLU cc_start: 0.9096 (mp0) cc_final: 0.8849 (mp0) REVERT: N 503 MET cc_start: 0.2559 (ttm) cc_final: 0.1961 (tmm) REVERT: N 506 LEU cc_start: 0.6767 (tp) cc_final: 0.6504 (mt) REVERT: O 64 MET cc_start: 0.7156 (mmm) cc_final: 0.6690 (ptt) REVERT: O 129 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.8037 (tmm-80) REVERT: O 465 LYS cc_start: 0.6674 (mmmt) cc_final: 0.6045 (pptt) REVERT: P 329 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6508 (mtp) REVERT: Q 55 GLN cc_start: 0.7328 (mp10) cc_final: 0.6585 (tt0) REVERT: Q 65 MET cc_start: 0.6653 (mmp) cc_final: 0.5811 (mtm) REVERT: Q 345 MET cc_start: 0.8875 (ptm) cc_final: 0.8506 (ptm) REVERT: Q 445 LEU cc_start: 0.8826 (tp) cc_final: 0.8519 (pp) REVERT: Q 478 PHE cc_start: 0.8954 (t80) cc_final: 0.8687 (t80) REVERT: R 502 MET cc_start: 0.7192 (ttt) cc_final: 0.6814 (ppp) REVERT: S 51 TYR cc_start: 0.7893 (m-80) cc_final: 0.7514 (m-80) REVERT: S 132 ASP cc_start: 0.8334 (p0) cc_final: 0.7771 (p0) REVERT: S 143 MET cc_start: 0.9067 (mtm) cc_final: 0.8655 (mtm) REVERT: S 267 GLU cc_start: 0.8960 (mp0) cc_final: 0.8585 (mp0) REVERT: T 64 MET cc_start: 0.6450 (mmt) cc_final: 0.6100 (tpt) REVERT: T 502 MET cc_start: 0.4453 (tmm) cc_final: 0.4251 (tmm) REVERT: U 65 MET cc_start: 0.4863 (mmp) cc_final: 0.3578 (tmm) REVERT: U 300 GLN cc_start: 0.7906 (mt0) cc_final: 0.6733 (mt0) REVERT: U 332 ASP cc_start: 0.7589 (t70) cc_final: 0.6770 (t0) REVERT: U 333 ILE cc_start: 0.9248 (mt) cc_final: 0.8831 (pt) REVERT: U 503 MET cc_start: 0.6437 (ttm) cc_final: 0.6122 (mmm) REVERT: V 332 ASP cc_start: 0.7208 (p0) cc_final: 0.6950 (m-30) REVERT: V 480 GLN cc_start: 0.8725 (tt0) cc_final: 0.8309 (tm-30) REVERT: W 143 MET cc_start: 0.8824 (mtm) cc_final: 0.8107 (ptp) outliers start: 75 outliers final: 30 residues processed: 794 average time/residue: 0.6857 time to fit residues: 912.3702 Evaluate side-chains 588 residues out of total 7363 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 554 time to evaluate : 5.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 230 TYR Chi-restraints excluded: chain L residue 243 ILE Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain M residue 184 GLU Chi-restraints excluded: chain M residue 488 ASP Chi-restraints excluded: chain O residue 129 ARG Chi-restraints excluded: chain O residue 216 ILE Chi-restraints excluded: chain O residue 361 LEU Chi-restraints excluded: chain O residue 452 PHE Chi-restraints excluded: chain P residue 314 SER Chi-restraints excluded: chain P residue 329 MET Chi-restraints excluded: chain P residue 357 ILE Chi-restraints excluded: chain Q residue 452 PHE Chi-restraints excluded: chain R residue 488 ASP Chi-restraints excluded: chain S residue 62 ILE Chi-restraints excluded: chain T residue 495 LYS Chi-restraints excluded: chain U residue 288 THR Chi-restraints excluded: chain U residue 465 LYS Chi-restraints excluded: chain V residue 242 MET Chi-restraints excluded: chain V residue 429 GLN Chi-restraints excluded: chain W residue 291 ILE Chi-restraints excluded: chain W residue 452 PHE Chi-restraints excluded: chain X residue 108 VAL Chi-restraints excluded: chain X residue 294 ILE Chi-restraints excluded: chain X residue 361 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 848 random chunks: chunk 427 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 640 optimal weight: 6.9990 chunk 524 optimal weight: 7.9990 chunk 212 optimal weight: 8.9990 chunk 771 optimal weight: 5.9990 chunk 833 optimal weight: 10.0000 chunk 687 optimal weight: 10.0000 chunk 765 optimal weight: 7.9990 chunk 263 optimal weight: 9.9990 chunk 618 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: