Starting phenix.real_space_refine (version: dev) on Tue Dec 20 09:44:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp6_7548/12_2022/6cp6_7548_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp6_7548/12_2022/6cp6_7548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp6_7548/12_2022/6cp6_7548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp6_7548/12_2022/6cp6_7548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp6_7548/12_2022/6cp6_7548_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cp6_7548/12_2022/6cp6_7548_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "Y GLU 127": "OE1" <-> "OE2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "D PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 38853 Number of models: 1 Model: "" Number of chains: 32 Chain: "K" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 535 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 529 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 535 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 523 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 537 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 532 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 533 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1333 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 7, 'TRANS': 180} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3858 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 485} Chain: "B" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3830 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 483} 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: "C" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3861 Classifications: {'peptide': 508} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 486} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3549 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Chain: "E" Number of atoms: 3572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3572 Classifications: {'peptide': 473} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 448} Chain: "F" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3566 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2086 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 1 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 990 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "I" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 392 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 56} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1221 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1357 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "6" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 710 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 8, 'TRANS': 80} Chain: "U" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 639 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 77} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "8" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 364 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "X" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1760 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 292 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.89, per 1000 atoms: 0.54 Number of scatterers: 38853 At special positions: 0 Unit cell: (125.46, 151.29, 244.77, 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 92 16.00 P 13 15.00 O 7364 8.00 N 6557 7.00 C 24827 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.43 Conformation dependent library (CDL) restraints added in 5.9 seconds 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9376 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 198 helices and 24 sheets defined 52.2% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'K' and resid 3 through 39 removed outlier: 4.062A pdb=" N LYS K 8 " --> pdb=" O VAL K 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE K 17 " --> pdb=" O GLY K 13 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLY K 18 " --> pdb=" O ILE K 14 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU K 19 " --> pdb=" O SER K 15 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU K 20 " --> pdb=" O THR K 16 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY K 21 " --> pdb=" O ILE K 17 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA K 22 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA K 27 " --> pdb=" O GLY K 23 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE K 28 " --> pdb=" O ILE K 24 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL K 29 " --> pdb=" O GLY K 25 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU K 33 " --> pdb=" O VAL K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 73 removed outlier: 3.596A pdb=" N LYS K 44 " --> pdb=" O PRO K 41 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASP K 45 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE K 48 " --> pdb=" O ASP K 45 " (cutoff:3.500A) Proline residue: K 49 - end of helix removed outlier: 4.040A pdb=" N PHE K 55 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU K 57 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA K 60 " --> pdb=" O LEU K 57 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR K 61 " --> pdb=" O SER K 58 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU K 71 " --> pdb=" O VAL K 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 14 Processing helix chain 'L' and resid 17 through 23 Processing helix chain 'L' and resid 25 through 38 removed outlier: 3.566A pdb=" N VAL L 29 " --> pdb=" O GLY L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 43 No H-bonds generated for 'chain 'L' and resid 41 through 43' Processing helix chain 'L' and resid 45 through 73 Proline residue: L 49 - end of helix removed outlier: 3.842A pdb=" N LEU L 57 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER L 58 " --> pdb=" O GLY L 54 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY L 62 " --> pdb=" O SER L 58 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS L 65 " --> pdb=" O THR L 61 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU L 66 " --> pdb=" O GLY L 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 14 Processing helix chain 'M' and resid 17 through 23 Processing helix chain 'M' and resid 25 through 37 Processing helix chain 'M' and resid 44 through 73 Proline residue: M 49 - end of helix removed outlier: 3.788A pdb=" N LEU M 57 " --> pdb=" O LEU M 53 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER M 58 " --> pdb=" O GLY M 54 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY M 62 " --> pdb=" O SER M 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS M 65 " --> pdb=" O THR M 61 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU M 66 " --> pdb=" O GLY M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 14 Processing helix chain 'N' and resid 16 through 37 removed outlier: 3.990A pdb=" N LEU N 19 " --> pdb=" O THR N 16 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLY N 21 " --> pdb=" O GLY N 18 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA N 22 " --> pdb=" O LEU N 19 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE N 26 " --> pdb=" O GLY N 23 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL N 37 " --> pdb=" O ILE N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 73 removed outlier: 3.927A pdb=" N LYS N 44 " --> pdb=" O PRO N 41 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASP N 45 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE N 48 " --> pdb=" O ASP N 45 " (cutoff:3.500A) Proline residue: N 49 - end of helix removed outlier: 3.656A pdb=" N LEU N 57 " --> pdb=" O GLY N 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER N 58 " --> pdb=" O PHE N 55 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA N 60 " --> pdb=" O LEU N 57 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR N 61 " --> pdb=" O SER N 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 14 Processing helix chain 'O' and resid 17 through 37 removed outlier: 5.909A pdb=" N GLY O 21 " --> pdb=" O GLY O 18 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE O 26 " --> pdb=" O GLY O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 54 removed outlier: 3.806A pdb=" N LYS O 44 " --> pdb=" O PRO O 41 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASP O 45 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE O 48 " --> pdb=" O ASP O 45 " (cutoff:3.500A) Proline residue: O 49 - end of helix Processing helix chain 'O' and resid 59 through 71 removed outlier: 3.863A pdb=" N CYS O 65 " --> pdb=" O THR O 61 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU O 66 " --> pdb=" O GLY O 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 14 Processing helix chain 'P' and resid 19 through 39 removed outlier: 4.676A pdb=" N ALA P 27 " --> pdb=" O GLY P 23 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE P 30 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 73 removed outlier: 3.781A pdb=" N THR P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY P 62 " --> pdb=" O SER P 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 14 Processing helix chain 'Q' and resid 17 through 39 removed outlier: 3.839A pdb=" N GLY Q 21 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE Q 26 " --> pdb=" O GLY Q 23 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER Q 38 " --> pdb=" O ASN Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 73 removed outlier: 3.999A pdb=" N THR Q 61 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY Q 62 " --> pdb=" O SER Q 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 14 Processing helix chain 'R' and resid 17 through 38 removed outlier: 4.009A pdb=" N GLY R 21 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE R 24 " --> pdb=" O GLY R 21 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE R 26 " --> pdb=" O GLY R 23 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL R 37 " --> pdb=" O ILE R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 74 removed outlier: 3.727A pdb=" N LYS R 44 " --> pdb=" O PRO R 41 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP R 45 " --> pdb=" O SER R 42 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE R 48 " --> pdb=" O ASP R 45 " (cutoff:3.500A) Proline residue: R 49 - end of helix removed outlier: 5.918A pdb=" N LEU R 57 " --> pdb=" O GLY R 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA R 60 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR R 61 " --> pdb=" O SER R 58 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU R 72 " --> pdb=" O SER R 69 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU R 73 " --> pdb=" O PHE R 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 14 Processing helix chain 'S' and resid 16 through 37 removed outlier: 3.580A pdb=" N LEU S 19 " --> pdb=" O THR S 16 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE S 24 " --> pdb=" O GLY S 21 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ILE S 26 " --> pdb=" O GLY S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 43 No H-bonds generated for 'chain 'S' and resid 41 through 43' Processing helix chain 'S' and resid 46 through 64 removed outlier: 4.299A pdb=" N MET S 50 " --> pdb=" O THR S 46 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE S 52 " --> pdb=" O PHE S 48 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY S 54 " --> pdb=" O MET S 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR S 61 " --> pdb=" O LEU S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 73 removed outlier: 3.726A pdb=" N LEU S 72 " --> pdb=" O VAL S 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 14 Processing helix chain 'T' and resid 17 through 37 removed outlier: 4.788A pdb=" N GLY T 21 " --> pdb=" O GLY T 18 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE T 26 " --> pdb=" O GLY T 23 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL T 37 " --> pdb=" O ILE T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 61 removed outlier: 6.378A pdb=" N ASP T 45 " --> pdb=" O SER T 42 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL T 47 " --> pdb=" O LYS T 44 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N PHE T 48 " --> pdb=" O ASP T 45 " (cutoff:3.500A) Proline residue: T 49 - end of helix removed outlier: 3.643A pdb=" N ILE T 52 " --> pdb=" O PRO T 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE T 55 " --> pdb=" O ILE T 52 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU T 57 " --> pdb=" O GLY T 54 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR T 61 " --> pdb=" O SER T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 73 Processing helix chain 'Y' and resid 18 through 30 removed outlier: 4.111A pdb=" N LYS Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN Y 30 " --> pdb=" O ALA Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 49 Processing helix chain 'Y' and resid 65 through 76 Processing helix chain 'Y' and resid 83 through 95 removed outlier: 3.801A pdb=" N VAL Y 86 " --> pdb=" O GLY Y 83 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU Y 88 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER Y 93 " --> pdb=" O LYS Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 102 through 116 Processing helix chain 'Y' and resid 131 through 143 Processing helix chain 'Y' and resid 181 through 192 removed outlier: 3.694A pdb=" N LEU Y 191 " --> pdb=" O LEU Y 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 17 removed outlier: 3.603A pdb=" N GLU A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 22 No H-bonds generated for 'chain 'A' and resid 19 through 22' Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 177 through 192 removed outlier: 4.248A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 242 through 262 Proline residue: A 249 - end of helix removed outlier: 3.618A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 310 removed outlier: 4.074A pdb=" N PHE A 301 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 305 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU A 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU A 309 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 377 through 380 Processing helix chain 'A' and resid 383 through 407 removed outlier: 3.974A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ALA A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 440 through 451 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 463 through 477 Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 493 through 509 Processing helix chain 'B' and resid 5 through 20 removed outlier: 5.094A pdb=" N GLY B 20 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.983A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 242 through 261 Proline residue: B 249 - end of helix Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 308 removed outlier: 4.014A pdb=" N PHE B 301 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS B 304 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 305 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 307 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 377 through 380 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 390 through 408 removed outlier: 4.514A pdb=" N LEU B 394 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 404 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 405 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N PHE B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 429 Processing helix chain 'B' and resid 440 through 451 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 461 through 476 removed outlier: 3.956A pdb=" N GLY B 464 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 467 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 468 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 475 " --> pdb=" O SER B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 488 Processing helix chain 'B' and resid 493 through 508 removed outlier: 3.739A pdb=" N PHE B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 19 removed outlier: 3.615A pdb=" N GLU C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 17 " --> pdb=" O ILE C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.758A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 225 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 262 Proline residue: C 249 - end of helix Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 298 through 310 removed outlier: 4.294A pdb=" N PHE C 301 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 306 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 308 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU C 309 " --> pdb=" O ARG C 306 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 310 " --> pdb=" O LEU C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 345 Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 377 through 380 Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 392 through 408 removed outlier: 4.001A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 429 Processing helix chain 'C' and resid 440 through 451 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 460 through 476 removed outlier: 4.638A pdb=" N GLY C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 488 Processing helix chain 'C' and resid 493 through 508 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 163 through 174 Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 226 through 245 removed outlier: 5.107A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 269 removed outlier: 3.848A pdb=" N THR D 262 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 323 No H-bonds generated for 'chain 'D' and resid 320 through 323' Processing helix chain 'D' and resid 325 through 328 Processing helix chain 'D' and resid 337 through 342 removed outlier: 3.621A pdb=" N LEU D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 363 No H-bonds generated for 'chain 'D' and resid 360 through 363' Processing helix chain 'D' and resid 365 through 388 removed outlier: 4.754A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D 388 " --> pdb=" O LEU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 395 No H-bonds generated for 'chain 'D' and resid 393 through 395' Processing helix chain 'D' and resid 398 through 414 Processing helix chain 'D' and resid 420 through 425 removed outlier: 4.035A pdb=" N VAL D 423 " --> pdb=" O VAL D 420 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 425 " --> pdb=" O GLU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 445 Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 463 through 474 removed outlier: 3.641A pdb=" N ALA D 474 " --> pdb=" O ALA D 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 163 through 177 Processing helix chain 'E' and resid 191 through 203 Processing helix chain 'E' and resid 226 through 229 No H-bonds generated for 'chain 'E' and resid 226 through 229' Processing helix chain 'E' and resid 232 through 245 Processing helix chain 'E' and resid 258 through 271 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 285 through 293 removed outlier: 3.740A pdb=" N LEU E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 327 removed outlier: 3.838A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 341 Processing helix chain 'E' and resid 360 through 390 removed outlier: 7.450A pdb=" N GLN E 365 " --> pdb=" O ALA E 361 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N GLU E 366 " --> pdb=" O VAL E 362 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N HIS E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA E 389 " --> pdb=" O GLN E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 413 Processing helix chain 'E' and resid 434 through 446 Processing helix chain 'E' and resid 454 through 457 Processing helix chain 'E' and resid 463 through 476 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 226 through 229 No H-bonds generated for 'chain 'F' and resid 226 through 229' Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 258 through 267 removed outlier: 3.664A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 295 removed outlier: 4.022A pdb=" N ARG F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 328 removed outlier: 4.004A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 365 through 390 removed outlier: 4.803A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 398 through 414 Processing helix chain 'F' and resid 420 through 425 removed outlier: 4.332A pdb=" N VAL F 423 " --> pdb=" O VAL F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 463 through 476 Processing helix chain 'G' and resid 3 through 54 removed outlier: 4.091A pdb=" N LYS G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 101 removed outlier: 3.783A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 121 removed outlier: 3.731A pdb=" N ARG G 120 " --> pdb=" O MET G 116 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR G 121 " --> pdb=" O GLN G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'G' and resid 185 through 189 Processing helix chain 'G' and resid 192 through 194 No H-bonds generated for 'chain 'G' and resid 192 through 194' Processing helix chain 'G' and resid 201 through 203 No H-bonds generated for 'chain 'G' and resid 201 through 203' Processing helix chain 'G' and resid 205 through 275 removed outlier: 4.402A pdb=" N GLU G 211 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE G 253 " --> pdb=" O ASN G 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 114 removed outlier: 3.524A pdb=" N LEU H 104 " --> pdb=" O ASN H 100 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU H 105 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER H 114 " --> pdb=" O LYS H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 137 removed outlier: 3.850A pdb=" N GLU H 122 " --> pdb=" O ARG H 118 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER H 135 " --> pdb=" O GLU H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 23 Processing helix chain 'I' and resid 32 through 37 Processing helix chain 'Z' and resid 56 through 113 removed outlier: 4.881A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) Proline residue: Z 75 - end of helix removed outlier: 3.628A pdb=" N ARG Z 96 " --> pdb=" O LEU Z 92 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU Z 113 " --> pdb=" O SER Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 132 removed outlier: 4.246A pdb=" N VAL Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP Z 125 " --> pdb=" O LYS Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 135 through 184 removed outlier: 3.570A pdb=" N LYS Z 143 " --> pdb=" O GLU Z 139 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 206 removed outlier: 4.252A pdb=" N VAL Z 193 " --> pdb=" O PHE Z 189 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU Z 194 " --> pdb=" O GLN Z 190 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 20 removed outlier: 5.009A pdb=" N ARG 7 20 " --> pdb=" O ILE 7 16 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 47 Processing helix chain '7' and resid 58 through 61 No H-bonds generated for 'chain '7' and resid 58 through 61' Processing helix chain '7' and resid 68 through 77 Processing helix chain '7' and resid 91 through 126 removed outlier: 4.161A pdb=" N LYS 7 115 " --> pdb=" O SER 7 111 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER 7 126 " --> pdb=" O ASP 7 122 " (cutoff:3.500A) Processing helix chain '7' and resid 135 through 141 Processing helix chain '7' and resid 143 through 155 Processing helix chain '6' and resid 5 through 16 Processing helix chain '6' and resid 19 through 22 No H-bonds generated for 'chain '6' and resid 19 through 22' Processing helix chain '6' and resid 43 through 50 Proline residue: 6 47 - end of helix Processing helix chain '6' and resid 78 through 91 Processing helix chain 'U' and resid 18 through 31 removed outlier: 4.050A pdb=" N VAL U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 55 Processing helix chain 'U' and resid 63 through 84 removed outlier: 4.585A pdb=" N GLY U 77 " --> pdb=" O ILE U 74 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N TYR U 78 " --> pdb=" O ALA U 75 " (cutoff:3.500A) Processing helix chain '8' and resid 9 through 30 Processing helix chain '8' and resid 33 through 46 removed outlier: 4.123A pdb=" N LEU 8 38 " --> pdb=" O MET 8 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 43 Processing helix chain 'X' and resid 57 through 76 removed outlier: 3.890A pdb=" N SER X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN X 62 " --> pdb=" O TRP X 58 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET X 72 " --> pdb=" O THR X 68 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY X 75 " --> pdb=" O ASN X 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 99 Proline residue: X 87 - end of helix removed outlier: 4.399A pdb=" N LEU X 92 " --> pdb=" O ILE X 89 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET X 94 " --> pdb=" O THR X 91 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE X 95 " --> pdb=" O LEU X 92 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA X 99 " --> pdb=" O ILE X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 115 through 136 Processing helix chain 'X' and resid 140 through 145 removed outlier: 3.596A pdb=" N PHE X 145 " --> pdb=" O PHE X 142 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 176 Proline residue: X 156 - end of helix removed outlier: 4.027A pdb=" N ILE X 161 " --> pdb=" O LEU X 158 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU X 164 " --> pdb=" O ILE X 161 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE X 167 " --> pdb=" O LEU X 164 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG X 169 " --> pdb=" O TYR X 166 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE X 171 " --> pdb=" O ALA X 168 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER X 172 " --> pdb=" O ARG X 169 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU X 173 " --> pdb=" O ALA X 170 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY X 174 " --> pdb=" O ILE X 171 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG X 176 " --> pdb=" O LEU X 173 " (cutoff:3.500A) Processing helix chain 'X' and resid 178 through 198 removed outlier: 4.032A pdb=" N LEU X 186 " --> pdb=" O LEU X 182 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU X 187 " --> pdb=" O ALA X 183 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA X 192 " --> pdb=" O MET X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 203 through 205 No H-bonds generated for 'chain 'X' and resid 203 through 205' Processing helix chain 'X' and resid 211 through 246 removed outlier: 4.403A pdb=" N GLN X 230 " --> pdb=" O ILE X 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 31 Processing sheet with id= A, first strand: chain 'Y' and resid 122 through 124 Processing sheet with id= B, first strand: chain 'A' and resid 89 through 91 removed outlier: 6.898A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU A 53 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN A 95 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLU A 56 " --> pdb=" O THR A 93 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR A 93 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 98 through 100 Processing sheet with id= D, first strand: chain 'A' and resid 108 through 110 removed outlier: 4.127A pdb=" N ARG A 108 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N SER A 322 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE A 268 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N THR A 324 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR A 270 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU A 326 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 167 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 41 through 43 removed outlier: 6.546A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 53 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN B 95 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLU B 56 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR B 93 " --> pdb=" O GLU B 56 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 98 through 101 Processing sheet with id= G, first strand: chain 'B' and resid 351 through 353 removed outlier: 6.996A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 231 through 236 removed outlier: 6.881A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER B 322 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE B 268 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N THR B 324 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N TYR B 270 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU B 326 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 89 through 91 removed outlier: 6.649A pdb=" N ARG C 42 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL C 36 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN C 67 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 76 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ALA C 65 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU C 53 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN C 95 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N GLU C 56 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR C 93 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 98 through 101 Processing sheet with id= K, first strand: chain 'C' and resid 351 through 354 removed outlier: 6.399A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU C 354 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 231 through 236 removed outlier: 6.761A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER C 322 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE C 268 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR C 324 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N TYR C 270 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU C 326 " --> pdb=" O TYR C 270 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.521A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 331 through 334 removed outlier: 7.719A pdb=" N ILE D 153 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER D 306 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 155 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLN D 308 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLY D 157 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL D 310 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR D 311 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE D 181 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE D 254 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP D 256 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N THR D 185 " --> pdb=" O ASP D 256 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.478A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 87 removed outlier: 4.235A pdb=" N LEU E 113 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 331 through 333 removed outlier: 8.773A pdb=" N ILE E 153 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N SER E 306 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU E 155 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN E 308 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 11 through 17 removed outlier: 6.428A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 331 through 335 removed outlier: 7.623A pdb=" N ILE F 153 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER F 306 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU F 155 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLN F 308 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLY F 157 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL F 310 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE F 181 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N PHE F 254 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 126 through 130 removed outlier: 7.852A pdb=" N ILE G 107 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER G 129 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR G 109 " --> pdb=" O SER G 129 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA G 76 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS G 161 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL G 75 " --> pdb=" O LYS G 161 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER G 163 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ILE G 77 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE G 165 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 49 through 52 removed outlier: 6.132A pdb=" N LYS H 11 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL H 85 " --> pdb=" O LYS H 11 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLN H 13 " --> pdb=" O VAL H 85 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA H 87 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA H 15 " --> pdb=" O ALA H 87 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE H 14 " --> pdb=" O SER H 23 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER H 23 " --> pdb=" O PHE H 14 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 37 through 41 removed outlier: 6.872A pdb=" N VAL H 56 " --> pdb=" O PRO H 33 " (cutoff:3.500A) 1885 hydrogen bonds defined for protein. 4836 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.42 Time building geometry restraints manager: 18.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6560 1.31 - 1.43: 9444 1.43 - 1.56: 23285 1.56 - 1.68: 24 1.68 - 1.81: 168 Bond restraints: 39481 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.93e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.78e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.34e+01 ... (remaining 39476 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.48: 1046 106.48 - 113.94: 23362 113.94 - 121.40: 19695 121.40 - 128.86: 9231 128.86 - 136.31: 173 Bond angle restraints: 53507 Sorted by residual: angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 112.71 24.12 1.00e+00 1.00e+00 5.82e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 113.25 23.58 1.00e+00 1.00e+00 5.56e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 118.01 21.86 1.00e+00 1.00e+00 4.78e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 118.20 21.67 1.00e+00 1.00e+00 4.69e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 118.64 21.23 1.00e+00 1.00e+00 4.51e+02 ... (remaining 53502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 23484 33.93 - 67.87: 246 67.87 - 101.80: 24 101.80 - 135.73: 1 135.73 - 169.67: 1 Dihedral angle restraints: 23756 sinusoidal: 9153 harmonic: 14603 Sorted by residual: dihedral pdb=" C5' ADP F 600 " pdb=" O5' ADP F 600 " pdb=" PA ADP F 600 " pdb=" O2A ADP F 600 " ideal model delta sinusoidal sigma weight residual 300.00 130.34 169.67 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PB ADP D 600 " pdb=" PA ADP D 600 " ideal model delta sinusoidal sigma weight residual 300.00 177.34 122.66 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" CA PHE R 55 " pdb=" C PHE R 55 " pdb=" N ALA R 56 " pdb=" CA ALA R 56 " ideal model delta harmonic sigma weight residual -180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 23753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 5865 0.097 - 0.193: 467 0.193 - 0.290: 15 0.290 - 0.386: 1 0.386 - 0.483: 1 Chirality restraints: 6349 Sorted by residual: chirality pdb=" CB ILE U 5 " pdb=" CA ILE U 5 " pdb=" CG1 ILE U 5 " pdb=" CG2 ILE U 5 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" CB ILE P 43 " pdb=" CA ILE P 43 " pdb=" CG1 ILE P 43 " pdb=" CG2 ILE P 43 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CB ILE Q 14 " pdb=" CA ILE Q 14 " pdb=" CG1 ILE Q 14 " pdb=" CG2 ILE Q 14 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 6346 not shown) Planarity restraints: 6839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA 6 17 " -0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO 6 18 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO 6 18 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO 6 18 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 321 " -0.050 5.00e-02 4.00e+02 7.58e-02 9.19e+00 pdb=" N PRO D 322 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 322 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 322 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 53 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C LEU R 53 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU R 53 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY R 54 " -0.017 2.00e-02 2.50e+03 ... (remaining 6836 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3739 2.74 - 3.28: 41153 3.28 - 3.82: 70053 3.82 - 4.36: 82270 4.36 - 4.90: 133143 Nonbonded interactions: 330358 Sorted by model distance: nonbonded pdb=" O GLY Y 172 " pdb=" OD1 ASP Y 173 " model vdw 2.196 3.040 nonbonded pdb=" OD1 ASP B 172 " pdb=" OG1 THR B 331 " model vdw 2.235 2.440 nonbonded pdb=" O VAL E 87 " pdb=" OG SER E 111 " model vdw 2.239 2.440 nonbonded pdb=" OD1 ASP Y 193 " pdb=" N SER Y 194 " model vdw 2.246 2.520 nonbonded pdb=" CB GLU B 29 " pdb=" CG ARG B 92 " model vdw 2.255 3.840 ... (remaining 330353 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 18 or resid 20 through 22 or (resid 23 and (name \ N or name CA or name C or name O or name CB )) or resid 24 through 28 or (resid \ 29 and (name N or name CA or name C or name O or name CB )) or resid 30 through \ 509 or resid 600)) selection = chain 'B' selection = (chain 'C' and (resid 4 through 18 or resid 20 through 22 or (resid 23 and (name \ N or name CA or name C or name O or name CB )) or resid 24 through 509 or resid \ 600)) } ncs_group { reference = (chain 'D' and resid 7 through 475) selection = (chain 'E' and resid 7 through 475) selection = (chain 'F' and resid 7 through 475) } ncs_group { reference = (chain 'K' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 through \ 74)) selection = (chain 'L' and (resid 1 through 18 or (resid 19 through 20 and (name N or name C \ A or name C or name O or name CB )) or resid 21 through 56 or (resid 57 and (nam \ e N or name CA or name C or name O or name CB )) or resid 58 through 74)) selection = (chain 'M' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 through \ 74)) selection = (chain 'N' and (resid 1 through 18 or (resid 19 through 20 and (name N or name C \ A or name C or name O or name CB )) or resid 21 through 74)) selection = (chain 'O' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 through \ 74)) selection = (chain 'P' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 through \ 74)) selection = chain 'Q' selection = (chain 'R' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 through \ 74)) selection = (chain 'S' and (resid 1 through 18 or (resid 19 through 20 and (name N or name C \ A or name C or name O or name CB )) or resid 21 through 56 or (resid 57 and (nam \ e N or name CA or name C or name O or name CB )) or resid 58 through 74)) selection = (chain 'T' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 18 or (resid 19 through 20 and (name \ N or name CA or name C or name O or name CB )) or resid 21 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB )) or resid 58 through \ 74)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 13 5.49 5 S 92 5.16 5 C 24827 2.51 5 N 6557 2.21 5 O 7364 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.260 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: 0.060 Extract box with map and model: 11.160 Check model and map are aligned: 0.530 Convert atoms to be neutral: 0.290 Process input model: 99.540 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 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 : 0.007 0.090 39481 Z= 0.450 Angle : 1.088 24.118 53507 Z= 0.648 Chirality : 0.054 0.483 6349 Planarity : 0.007 0.086 6839 Dihedral : 10.804 169.666 14380 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.51 % Favored : 94.17 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % 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: -3.06 (0.10), residues: 5060 helix: -2.04 (0.08), residues: 2508 sheet: -1.67 (0.21), residues: 568 loop : -1.88 (0.13), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1168 time to evaluate : 4.479 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 outliers start: 27 outliers final: 6 residues processed: 1190 average time/residue: 0.5247 time to fit residues: 998.8251 Evaluate side-chains 563 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 557 time to evaluate : 4.462 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3403 time to fit residues: 9.8815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 422 optimal weight: 10.0000 chunk 378 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 255 optimal weight: 9.9990 chunk 202 optimal weight: 0.7980 chunk 391 optimal weight: 20.0000 chunk 151 optimal weight: 0.0980 chunk 238 optimal weight: 4.9990 chunk 291 optimal weight: 0.9990 chunk 454 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 2 GLN K 35 ASN ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 ASN Y 95 ASN Y 112 ASN A 26 ASN A 145 HIS A 193 ASN A 332 GLN A 428 GLN A 432 GLN B 145 HIS B 192 ASN B 217 GLN B 304 HIS B 332 GLN B 351 GLN C 187 ASN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 173 ASN D 385 GLN E 293 GLN F 52 GLN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN F 455 HIS G 217 GLN H 51 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** Z 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 171 GLN Z 203 GLN 7 123 ASN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 27 ASN 6 38 ASN U 14 ASN ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 HIS 8 11 ASN X 76 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 39481 Z= 0.225 Angle : 0.692 11.725 53507 Z= 0.349 Chirality : 0.044 0.226 6349 Planarity : 0.005 0.064 6839 Dihedral : 7.210 170.420 5469 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.89 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.11), residues: 5060 helix: -0.77 (0.09), residues: 2637 sheet: -1.27 (0.21), residues: 579 loop : -1.37 (0.15), residues: 1844 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 661 time to evaluate : 4.497 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 outliers start: 117 outliers final: 61 residues processed: 731 average time/residue: 0.4840 time to fit residues: 591.1733 Evaluate side-chains 552 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 491 time to evaluate : 4.727 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.3623 time to fit residues: 47.3960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 252 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 377 optimal weight: 5.9990 chunk 309 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 454 optimal weight: 20.0000 chunk 491 optimal weight: 6.9990 chunk 405 optimal weight: 20.0000 chunk 451 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 364 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 35 ASN ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 ASN B 145 HIS B 217 GLN B 343 ASN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN F 249 GLN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 203 GLN 7 47 GLN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 39481 Z= 0.279 Angle : 0.686 13.366 53507 Z= 0.344 Chirality : 0.044 0.308 6349 Planarity : 0.004 0.066 6839 Dihedral : 6.800 165.681 5469 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % 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: -0.96 (0.12), residues: 5060 helix: -0.08 (0.10), residues: 2671 sheet: -1.02 (0.21), residues: 579 loop : -1.16 (0.15), residues: 1810 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 569 time to evaluate : 4.868 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 outliers start: 81 outliers final: 39 residues processed: 619 average time/residue: 0.4771 time to fit residues: 499.3997 Evaluate side-chains 512 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 473 time to evaluate : 4.631 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.3501 time to fit residues: 31.9499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 449 optimal weight: 6.9990 chunk 341 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 305 optimal weight: 4.9990 chunk 456 optimal weight: 10.0000 chunk 483 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 432 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 35 ASN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 112 ASN A 48 ASN B 217 GLN ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN F 52 GLN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 203 GLN 7 98 HIS 7 123 ASN 7 125 GLN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 71 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 39481 Z= 0.320 Angle : 0.693 14.732 53507 Z= 0.345 Chirality : 0.044 0.238 6349 Planarity : 0.004 0.063 6839 Dihedral : 6.740 163.162 5469 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.62 % Favored : 95.32 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % 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: -0.71 (0.12), residues: 5060 helix: 0.16 (0.10), residues: 2671 sheet: -0.86 (0.22), residues: 571 loop : -1.13 (0.15), residues: 1818 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 514 time to evaluate : 4.706 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 outliers start: 94 outliers final: 43 residues processed: 583 average time/residue: 0.4912 time to fit residues: 481.3683 Evaluate side-chains 491 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 448 time to evaluate : 4.516 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4306 time to fit residues: 39.9074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 402 optimal weight: 5.9990 chunk 274 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 359 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 412 optimal weight: 0.5980 chunk 334 optimal weight: 0.5980 chunk 0 optimal weight: 40.0000 chunk 246 optimal weight: 5.9990 chunk 433 optimal weight: 7.9990 chunk 121 optimal weight: 0.4980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 2 GLN N 35 ASN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 112 ASN A 47 ASN A 304 HIS B 217 GLN B 332 GLN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 HIS G 260 GLN H 31 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 142 GLN 7 125 GLN 6 4 GLN ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 62 GLN ** X 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 39481 Z= 0.182 Angle : 0.630 11.078 53507 Z= 0.309 Chirality : 0.042 0.231 6349 Planarity : 0.004 0.060 6839 Dihedral : 6.492 163.280 5469 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.89 % Favored : 96.05 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % 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: -0.37 (0.12), residues: 5060 helix: 0.46 (0.10), residues: 2652 sheet: -0.72 (0.22), residues: 570 loop : -0.98 (0.15), residues: 1838 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 540 time to evaluate : 5.085 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 outliers start: 51 outliers final: 23 residues processed: 567 average time/residue: 0.4766 time to fit residues: 458.8004 Evaluate side-chains 480 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 457 time to evaluate : 4.683 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3718 time to fit residues: 22.8715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 162 optimal weight: 0.9990 chunk 435 optimal weight: 10.0000 chunk 95 optimal weight: 0.0970 chunk 283 optimal weight: 3.9990 chunk 119 optimal weight: 0.0970 chunk 483 optimal weight: 0.7980 chunk 401 optimal weight: 1.9990 chunk 223 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 112 ASN B 217 GLN B 332 GLN B 454 HIS C 165 GLN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 ASN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 39481 Z= 0.159 Angle : 0.623 14.162 53507 Z= 0.302 Chirality : 0.042 0.249 6349 Planarity : 0.004 0.056 6839 Dihedral : 6.256 159.012 5469 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % 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: -0.18 (0.12), residues: 5060 helix: 0.60 (0.10), residues: 2688 sheet: -0.64 (0.22), residues: 571 loop : -0.91 (0.15), residues: 1801 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 512 time to evaluate : 4.599 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 outliers start: 41 outliers final: 18 residues processed: 542 average time/residue: 0.4767 time to fit residues: 438.2522 Evaluate side-chains 467 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 449 time to evaluate : 4.577 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3690 time to fit residues: 18.3538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 500 random chunks: chunk 466 optimal weight: 0.0570 chunk 54 optimal weight: 5.9990 chunk 275 optimal weight: 0.9980 chunk 353 optimal weight: 3.9990 chunk 273 optimal weight: 0.0020 chunk 407 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 481 optimal weight: 1.9990 chunk 301 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 overall best weight: 1.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 35 ASN ** T 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 112 ASN B 217 GLN D 173 ASN ** F 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 71 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 39481 Z= 0.194 Angle : 0.633 13.999 53507 Z= 0.306 Chirality : 0.042 0.226 6349 Planarity : 0.004 0.058 6839 Dihedral : 6.173 157.995 5469 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.91 % Cis-general : 0.12 % 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: -0.04 (0.12), residues: 5060 helix: 0.67 (0.10), residues: 2700 sheet: -0.54 (0.22), residues: 571 loop : -0.78 (0.15), residues: 1789 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10120 Ramachandran restraints generated. 5060 Oldfield, 0 Emsley, 5060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 483 time to evaluate : 4.591 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 outliers start: 45 outliers final: 24 residues processed: 509 average time/residue: 0.4839 time to fit residues: 419.8110 Evaluate side-chains 473 residues out of total 4165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 449 time to evaluate : 4.573 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3450 time to fit residues: 20.5571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.5813 > 50: distance: 93 - 185: 35.372 distance: 102 - 188: 33.614 distance: 105 - 198: 31.924 distance: 118 - 201: 31.150 distance: 121 - 216: 35.861 distance: 126 - 219: 36.864 distance: 174 - 178: 29.465 distance: 178 - 179: 15.336 distance: 179 - 182: 53.835 distance: 180 - 181: 29.036 distance: 180 - 185: 40.601 distance: 182 - 183: 54.974 distance: 186 - 187: 38.877 distance: 187 - 188: 40.495 distance: 192 - 198: 13.475 distance: 195 - 196: 40.026 distance: 195 - 197: 40.397 distance: 198 - 199: 34.641 distance: 199 - 200: 26.511 distance: 199 - 202: 44.514 distance: 200 - 201: 40.901 distance: 200 - 205: 20.772 distance: 202 - 203: 40.804 distance: 205 - 206: 39.740 distance: 206 - 207: 39.019 distance: 206 - 209: 69.418 distance: 207 - 216: 41.123 distance: 209 - 210: 11.528 distance: 210 - 211: 11.589 distance: 210 - 212: 26.803 distance: 212 - 214: 37.986 distance: 216 - 217: 40.099 distance: 218 - 220: 39.992 distance: 220 - 221: 39.239 distance: 222 - 229: 54.433 distance: 224 - 225: 40.946 distance: 226 - 227: 40.002 distance: 226 - 228: 55.668 distance: 229 - 230: 39.025 distance: 231 - 237: 38.815 distance: 233 - 234: 39.831 distance: 234 - 235: 19.084 distance: 235 - 236: 41.800 distance: 237 - 238: 40.505 distance: 238 - 239: 41.763 distance: 238 - 241: 16.050 distance: 239 - 240: 41.038 distance: 239 - 245: 50.761 distance: 241 - 242: 42.372 distance: 245 - 246: 55.882 distance: 246 - 249: 41.243 distance: 247 - 254: 33.780 distance: 250 - 251: 36.830 distance: 251 - 252: 55.128 distance: 251 - 253: 40.004