Starting phenix.real_space_refine (version: dev) on Mon May 16 17:18:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohf_12901/05_2022/7ohf_12901.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohf_12901/05_2022/7ohf_12901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohf_12901/05_2022/7ohf_12901.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohf_12901/05_2022/7ohf_12901.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohf_12901/05_2022/7ohf_12901.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ohf_12901/05_2022/7ohf_12901.pdb" } resolution = 3.0 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= 0.105 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 None Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 33576 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "B" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "C" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "D" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "E" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "F" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "G" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "H" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "I" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "J" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "K" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "L" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "M" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "N" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "O" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "P" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "Q" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "R" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "S" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "T" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "U" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "V" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "W" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain: "X" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1399 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Time building chain proxies: 18.19, per 1000 atoms: 0.54 Number of scatterers: 33576 At special positions: 0 Unit cell: (137.346, 137.346, 137.346, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 6312 8.00 N 5328 7.00 C 21816 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: 12.37 Conformation dependent library (CDL) restraints added in 5.3 seconds 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7872 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 0 sheets defined 74.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 57 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE A 123 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'B' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA B 9 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA B 28 " --> pdb=" O TYR B 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 57 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE B 123 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE B 137 " --> pdb=" O SER B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'C' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA C 9 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA C 28 " --> pdb=" O TYR C 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE C 57 " --> pdb=" O HIS C 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 118 Processing helix chain 'C' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE C 123 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C 129 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 157 " --> pdb=" O MET C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'D' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA D 9 " --> pdb=" O ARG D 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA D 28 " --> pdb=" O TYR D 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 57 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER D 98 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE D 123 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU D 129 " --> pdb=" O ASN D 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE D 137 " --> pdb=" O SER D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS D 156 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU D 157 " --> pdb=" O MET D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'E' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA E 9 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA E 21 " --> pdb=" O GLU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE E 57 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA E 90 " --> pdb=" O ALA E 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E 107 " --> pdb=" O GLU E 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU E 109 " --> pdb=" O ALA E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 118 Processing helix chain 'E' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE E 123 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL E 128 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU E 129 " --> pdb=" O ASN E 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE E 137 " --> pdb=" O SER E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS E 156 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU E 157 " --> pdb=" O MET E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 161 No H-bonds generated for 'chain 'E' and resid 159 through 161' Processing helix chain 'F' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA F 9 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA F 28 " --> pdb=" O TYR F 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 29 " --> pdb=" O PHE F 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA F 45 " --> pdb=" O ASN F 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG F 56 " --> pdb=" O GLY F 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE F 57 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 118 Processing helix chain 'F' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE F 123 " --> pdb=" O PHE F 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL F 128 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU F 129 " --> pdb=" O ASN F 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE F 137 " --> pdb=" O SER F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS F 156 " --> pdb=" O PHE F 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU F 157 " --> pdb=" O MET F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'G' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA G 9 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA G 28 " --> pdb=" O TYR G 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA G 29 " --> pdb=" O PHE G 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA G 45 " --> pdb=" O ASN G 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE G 57 " --> pdb=" O HIS G 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER G 98 " --> pdb=" O GLU G 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G 107 " --> pdb=" O GLU G 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU G 109 " --> pdb=" O ALA G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 118 Processing helix chain 'G' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL G 128 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU G 129 " --> pdb=" O ASN G 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE G 137 " --> pdb=" O SER G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS G 156 " --> pdb=" O PHE G 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU G 157 " --> pdb=" O MET G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 161 No H-bonds generated for 'chain 'G' and resid 159 through 161' Processing helix chain 'H' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA H 9 " --> pdb=" O ARG H 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU H 18 " --> pdb=" O LEU H 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA H 28 " --> pdb=" O TYR H 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA H 29 " --> pdb=" O PHE H 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA H 45 " --> pdb=" O ASN H 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG H 56 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE H 57 " --> pdb=" O HIS H 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA H 90 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER H 98 " --> pdb=" O GLU H 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU H 107 " --> pdb=" O GLU H 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 Processing helix chain 'H' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE H 123 " --> pdb=" O PHE H 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL H 128 " --> pdb=" O ILE H 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU H 129 " --> pdb=" O ASN H 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE H 137 " --> pdb=" O SER H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS H 156 " --> pdb=" O PHE H 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU H 157 " --> pdb=" O MET H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 161 No H-bonds generated for 'chain 'H' and resid 159 through 161' Processing helix chain 'I' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA I 9 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU I 18 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA I 21 " --> pdb=" O GLU I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA I 28 " --> pdb=" O TYR I 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA I 29 " --> pdb=" O PHE I 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA I 45 " --> pdb=" O ASN I 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE I 51 " --> pdb=" O ALA I 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG I 56 " --> pdb=" O GLY I 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE I 57 " --> pdb=" O HIS I 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN I 59 " --> pdb=" O LEU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER I 98 " --> pdb=" O GLU I 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU I 107 " --> pdb=" O GLU I 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 118 Processing helix chain 'I' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE I 123 " --> pdb=" O PHE I 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL I 128 " --> pdb=" O ILE I 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU I 129 " --> pdb=" O ASN I 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE I 137 " --> pdb=" O SER I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS I 156 " --> pdb=" O PHE I 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU I 157 " --> pdb=" O MET I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 161 No H-bonds generated for 'chain 'I' and resid 159 through 161' Processing helix chain 'J' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA J 9 " --> pdb=" O ARG J 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA J 21 " --> pdb=" O GLU J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA J 28 " --> pdb=" O TYR J 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA J 29 " --> pdb=" O PHE J 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA J 45 " --> pdb=" O ASN J 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE J 51 " --> pdb=" O ALA J 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE J 57 " --> pdb=" O HIS J 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN J 59 " --> pdb=" O LEU J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER J 98 " --> pdb=" O GLU J 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU J 107 " --> pdb=" O GLU J 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL J 128 " --> pdb=" O ILE J 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU J 129 " --> pdb=" O ASN J 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE J 137 " --> pdb=" O SER J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS J 156 " --> pdb=" O PHE J 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU J 157 " --> pdb=" O MET J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 161 No H-bonds generated for 'chain 'J' and resid 159 through 161' Processing helix chain 'K' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA K 9 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU K 18 " --> pdb=" O LEU K 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA K 21 " --> pdb=" O GLU K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA K 28 " --> pdb=" O TYR K 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA K 29 " --> pdb=" O PHE K 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA K 45 " --> pdb=" O ASN K 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG K 56 " --> pdb=" O GLY K 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE K 57 " --> pdb=" O HIS K 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN K 59 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA K 90 " --> pdb=" O ALA K 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER K 98 " --> pdb=" O GLU K 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU K 107 " --> pdb=" O GLU K 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 118 Processing helix chain 'K' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE K 123 " --> pdb=" O PHE K 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL K 128 " --> pdb=" O ILE K 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU K 129 " --> pdb=" O ASN K 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE K 137 " --> pdb=" O SER K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS K 156 " --> pdb=" O PHE K 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU K 157 " --> pdb=" O MET K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 161 No H-bonds generated for 'chain 'K' and resid 159 through 161' Processing helix chain 'L' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA L 9 " --> pdb=" O ARG L 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA L 21 " --> pdb=" O GLU L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA L 29 " --> pdb=" O PHE L 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA L 45 " --> pdb=" O ASN L 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE L 51 " --> pdb=" O ALA L 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG L 56 " --> pdb=" O GLY L 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE L 57 " --> pdb=" O HIS L 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN L 59 " --> pdb=" O LEU L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA L 90 " --> pdb=" O ALA L 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER L 98 " --> pdb=" O GLU L 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU L 107 " --> pdb=" O GLU L 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU L 109 " --> pdb=" O ALA L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 118 Processing helix chain 'L' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL L 128 " --> pdb=" O ILE L 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU L 129 " --> pdb=" O ASN L 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE L 137 " --> pdb=" O SER L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS L 156 " --> pdb=" O PHE L 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU L 157 " --> pdb=" O MET L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 161 No H-bonds generated for 'chain 'L' and resid 159 through 161' Processing helix chain 'M' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA M 9 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU M 18 " --> pdb=" O LEU M 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA M 21 " --> pdb=" O GLU M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA M 28 " --> pdb=" O TYR M 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA M 29 " --> pdb=" O PHE M 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA M 45 " --> pdb=" O ASN M 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE M 51 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG M 56 " --> pdb=" O GLY M 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE M 57 " --> pdb=" O HIS M 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA M 90 " --> pdb=" O ALA M 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU M 107 " --> pdb=" O GLU M 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 118 Processing helix chain 'M' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE M 123 " --> pdb=" O PHE M 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL M 128 " --> pdb=" O ILE M 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU M 129 " --> pdb=" O ASN M 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE M 137 " --> pdb=" O SER M 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS M 156 " --> pdb=" O PHE M 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU M 157 " --> pdb=" O MET M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 161 No H-bonds generated for 'chain 'M' and resid 159 through 161' Processing helix chain 'N' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA N 9 " --> pdb=" O ARG N 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU N 18 " --> pdb=" O LEU N 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA N 21 " --> pdb=" O GLU N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA N 28 " --> pdb=" O TYR N 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA N 29 " --> pdb=" O PHE N 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA N 45 " --> pdb=" O ASN N 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE N 51 " --> pdb=" O ALA N 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG N 56 " --> pdb=" O GLY N 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE N 57 " --> pdb=" O HIS N 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN N 59 " --> pdb=" O LEU N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA N 90 " --> pdb=" O ALA N 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS N 93 " --> pdb=" O ALA N 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER N 98 " --> pdb=" O GLU N 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU N 107 " --> pdb=" O GLU N 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU N 109 " --> pdb=" O ALA N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 118 Processing helix chain 'N' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE N 123 " --> pdb=" O PHE N 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL N 128 " --> pdb=" O ILE N 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU N 129 " --> pdb=" O ASN N 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS N 156 " --> pdb=" O PHE N 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU N 157 " --> pdb=" O MET N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 161 No H-bonds generated for 'chain 'N' and resid 159 through 161' Processing helix chain 'O' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA O 9 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU O 18 " --> pdb=" O LEU O 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA O 21 " --> pdb=" O GLU O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA O 28 " --> pdb=" O TYR O 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA O 29 " --> pdb=" O PHE O 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR O 30 " --> pdb=" O ALA O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA O 45 " --> pdb=" O ASN O 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE O 51 " --> pdb=" O ALA O 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG O 56 " --> pdb=" O GLY O 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE O 57 " --> pdb=" O HIS O 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN O 59 " --> pdb=" O LEU O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS O 93 " --> pdb=" O ALA O 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER O 98 " --> pdb=" O GLU O 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU O 107 " --> pdb=" O GLU O 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU O 109 " --> pdb=" O ALA O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 118 Processing helix chain 'O' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE O 123 " --> pdb=" O PHE O 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL O 128 " --> pdb=" O ILE O 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU O 129 " --> pdb=" O ASN O 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE O 137 " --> pdb=" O SER O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS O 156 " --> pdb=" O PHE O 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU O 157 " --> pdb=" O MET O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 161 No H-bonds generated for 'chain 'O' and resid 159 through 161' Processing helix chain 'P' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA P 9 " --> pdb=" O ARG P 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU P 18 " --> pdb=" O LEU P 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA P 21 " --> pdb=" O GLU P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA P 28 " --> pdb=" O TYR P 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA P 29 " --> pdb=" O PHE P 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA P 45 " --> pdb=" O ASN P 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE P 51 " --> pdb=" O ALA P 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG P 56 " --> pdb=" O GLY P 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE P 57 " --> pdb=" O HIS P 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN P 59 " --> pdb=" O LEU P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA P 90 " --> pdb=" O ALA P 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER P 98 " --> pdb=" O GLU P 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU P 107 " --> pdb=" O GLU P 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU P 109 " --> pdb=" O ALA P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 118 Processing helix chain 'P' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE P 123 " --> pdb=" O PHE P 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL P 128 " --> pdb=" O ILE P 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU P 129 " --> pdb=" O ASN P 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE P 137 " --> pdb=" O SER P 133 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS P 156 " --> pdb=" O PHE P 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU P 157 " --> pdb=" O MET P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 161 No H-bonds generated for 'chain 'P' and resid 159 through 161' Processing helix chain 'Q' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU Q 18 " --> pdb=" O LEU Q 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA Q 21 " --> pdb=" O GLU Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA Q 28 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA Q 29 " --> pdb=" O PHE Q 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR Q 30 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA Q 45 " --> pdb=" O ASN Q 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE Q 51 " --> pdb=" O ALA Q 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG Q 56 " --> pdb=" O GLY Q 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE Q 57 " --> pdb=" O HIS Q 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN Q 59 " --> pdb=" O LEU Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA Q 90 " --> pdb=" O ALA Q 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER Q 98 " --> pdb=" O GLU Q 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU Q 107 " --> pdb=" O GLU Q 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 118 Processing helix chain 'Q' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE Q 123 " --> pdb=" O PHE Q 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL Q 128 " --> pdb=" O ILE Q 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU Q 129 " --> pdb=" O ASN Q 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE Q 137 " --> pdb=" O SER Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS Q 156 " --> pdb=" O PHE Q 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU Q 157 " --> pdb=" O MET Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 161 No H-bonds generated for 'chain 'Q' and resid 159 through 161' Processing helix chain 'R' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA R 9 " --> pdb=" O ARG R 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU R 18 " --> pdb=" O LEU R 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA R 21 " --> pdb=" O GLU R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA R 28 " --> pdb=" O TYR R 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA R 29 " --> pdb=" O PHE R 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA R 45 " --> pdb=" O ASN R 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE R 51 " --> pdb=" O ALA R 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG R 56 " --> pdb=" O GLY R 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE R 57 " --> pdb=" O HIS R 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN R 59 " --> pdb=" O LEU R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER R 98 " --> pdb=" O GLU R 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU R 107 " --> pdb=" O GLU R 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 118 Processing helix chain 'R' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE R 123 " --> pdb=" O PHE R 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU R 129 " --> pdb=" O ASN R 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE R 137 " --> pdb=" O SER R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS R 156 " --> pdb=" O PHE R 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU R 157 " --> pdb=" O MET R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 159 through 161 No H-bonds generated for 'chain 'R' and resid 159 through 161' Processing helix chain 'S' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA S 9 " --> pdb=" O ARG S 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU S 18 " --> pdb=" O LEU S 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA S 21 " --> pdb=" O GLU S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA S 28 " --> pdb=" O TYR S 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA S 29 " --> pdb=" O PHE S 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR S 30 " --> pdb=" O ALA S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA S 45 " --> pdb=" O ASN S 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE S 51 " --> pdb=" O ALA S 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG S 56 " --> pdb=" O GLY S 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE S 57 " --> pdb=" O HIS S 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN S 59 " --> pdb=" O LEU S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA S 90 " --> pdb=" O ALA S 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS S 93 " --> pdb=" O ALA S 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER S 98 " --> pdb=" O GLU S 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU S 107 " --> pdb=" O GLU S 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU S 109 " --> pdb=" O ALA S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 118 Processing helix chain 'S' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE S 123 " --> pdb=" O PHE S 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL S 128 " --> pdb=" O ILE S 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU S 129 " --> pdb=" O ASN S 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE S 137 " --> pdb=" O SER S 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS S 156 " --> pdb=" O PHE S 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU S 157 " --> pdb=" O MET S 153 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 161 No H-bonds generated for 'chain 'S' and resid 159 through 161' Processing helix chain 'T' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA T 9 " --> pdb=" O ARG T 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU T 18 " --> pdb=" O LEU T 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA T 21 " --> pdb=" O GLU T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA T 28 " --> pdb=" O TYR T 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA T 29 " --> pdb=" O PHE T 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR T 30 " --> pdb=" O ALA T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA T 45 " --> pdb=" O ASN T 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE T 51 " --> pdb=" O ALA T 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG T 56 " --> pdb=" O GLY T 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE T 57 " --> pdb=" O HIS T 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN T 59 " --> pdb=" O LEU T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA T 90 " --> pdb=" O ALA T 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS T 93 " --> pdb=" O ALA T 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER T 98 " --> pdb=" O GLU T 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU T 107 " --> pdb=" O GLU T 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU T 109 " --> pdb=" O ALA T 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 113 through 118 Processing helix chain 'T' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE T 123 " --> pdb=" O PHE T 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL T 128 " --> pdb=" O ILE T 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU T 129 " --> pdb=" O ASN T 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE T 137 " --> pdb=" O SER T 133 " (cutoff:3.500A) Processing helix chain 'T' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS T 156 " --> pdb=" O PHE T 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU T 157 " --> pdb=" O MET T 153 " (cutoff:3.500A) Processing helix chain 'T' and resid 159 through 161 No H-bonds generated for 'chain 'T' and resid 159 through 161' Processing helix chain 'U' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA U 9 " --> pdb=" O ARG U 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU U 18 " --> pdb=" O LEU U 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA U 21 " --> pdb=" O GLU U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA U 28 " --> pdb=" O TYR U 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA U 29 " --> pdb=" O PHE U 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR U 30 " --> pdb=" O ALA U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA U 45 " --> pdb=" O ASN U 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE U 51 " --> pdb=" O ALA U 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG U 56 " --> pdb=" O GLY U 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE U 57 " --> pdb=" O HIS U 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN U 59 " --> pdb=" O LEU U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA U 90 " --> pdb=" O ALA U 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS U 93 " --> pdb=" O ALA U 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER U 98 " --> pdb=" O GLU U 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU U 107 " --> pdb=" O GLU U 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU U 109 " --> pdb=" O ALA U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 113 through 118 Processing helix chain 'U' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE U 123 " --> pdb=" O PHE U 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL U 128 " --> pdb=" O ILE U 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU U 129 " --> pdb=" O ASN U 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE U 137 " --> pdb=" O SER U 133 " (cutoff:3.500A) Processing helix chain 'U' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS U 156 " --> pdb=" O PHE U 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU U 157 " --> pdb=" O MET U 153 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 161 No H-bonds generated for 'chain 'U' and resid 159 through 161' Processing helix chain 'V' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA V 9 " --> pdb=" O ARG V 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU V 18 " --> pdb=" O LEU V 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA V 21 " --> pdb=" O GLU V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA V 28 " --> pdb=" O TYR V 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA V 29 " --> pdb=" O PHE V 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR V 30 " --> pdb=" O ALA V 26 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA V 45 " --> pdb=" O ASN V 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE V 51 " --> pdb=" O ALA V 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG V 56 " --> pdb=" O GLY V 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE V 57 " --> pdb=" O HIS V 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN V 59 " --> pdb=" O LEU V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA V 90 " --> pdb=" O ALA V 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS V 93 " --> pdb=" O ALA V 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER V 98 " --> pdb=" O GLU V 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU V 107 " --> pdb=" O GLU V 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU V 109 " --> pdb=" O ALA V 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 118 Processing helix chain 'V' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE V 123 " --> pdb=" O PHE V 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL V 128 " --> pdb=" O ILE V 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU V 129 " --> pdb=" O ASN V 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE V 137 " --> pdb=" O SER V 133 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS V 156 " --> pdb=" O PHE V 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU V 157 " --> pdb=" O MET V 153 " (cutoff:3.500A) Processing helix chain 'V' and resid 159 through 161 No H-bonds generated for 'chain 'V' and resid 159 through 161' Processing helix chain 'W' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA W 9 " --> pdb=" O ARG W 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU W 18 " --> pdb=" O LEU W 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA W 21 " --> pdb=" O GLU W 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA W 28 " --> pdb=" O TYR W 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA W 29 " --> pdb=" O PHE W 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR W 30 " --> pdb=" O ALA W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA W 45 " --> pdb=" O ASN W 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE W 51 " --> pdb=" O ALA W 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG W 56 " --> pdb=" O GLY W 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE W 57 " --> pdb=" O HIS W 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN W 59 " --> pdb=" O LEU W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA W 90 " --> pdb=" O ALA W 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS W 93 " --> pdb=" O ALA W 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER W 98 " --> pdb=" O GLU W 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU W 107 " --> pdb=" O GLU W 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU W 109 " --> pdb=" O ALA W 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 118 Processing helix chain 'W' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE W 123 " --> pdb=" O PHE W 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL W 128 " --> pdb=" O ILE W 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU W 129 " --> pdb=" O ASN W 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE W 137 " --> pdb=" O SER W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS W 156 " --> pdb=" O PHE W 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU W 157 " --> pdb=" O MET W 153 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 161 No H-bonds generated for 'chain 'W' and resid 159 through 161' Processing helix chain 'X' and resid 3 through 22 removed outlier: 3.593A pdb=" N ALA X 9 " --> pdb=" O ARG X 5 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA X 21 " --> pdb=" O GLU X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 23 through 32 removed outlier: 3.520A pdb=" N ALA X 28 " --> pdb=" O TYR X 24 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA X 29 " --> pdb=" O PHE X 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR X 30 " --> pdb=" O ALA X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 38 through 62 removed outlier: 3.624A pdb=" N ALA X 45 " --> pdb=" O ASN X 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE X 51 " --> pdb=" O ALA X 47 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG X 56 " --> pdb=" O GLY X 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE X 57 " --> pdb=" O HIS X 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN X 59 " --> pdb=" O LEU X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 109 removed outlier: 3.801A pdb=" N ALA X 90 " --> pdb=" O ALA X 86 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS X 93 " --> pdb=" O ALA X 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER X 98 " --> pdb=" O GLU X 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU X 107 " --> pdb=" O GLU X 103 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU X 109 " --> pdb=" O ALA X 105 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 118 Processing helix chain 'X' and resid 119 through 142 removed outlier: 4.215A pdb=" N PHE X 123 " --> pdb=" O PHE X 119 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL X 128 " --> pdb=" O ILE X 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU X 129 " --> pdb=" O ASN X 125 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE X 137 " --> pdb=" O SER X 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 158 removed outlier: 3.796A pdb=" N LYS X 156 " --> pdb=" O PHE X 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU X 157 " --> pdb=" O MET X 153 " (cutoff:3.500A) Processing helix chain 'X' and resid 159 through 161 No H-bonds generated for 'chain 'X' and resid 159 through 161' 1752 hydrogen bonds defined for protein. 5256 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: 9.71 Time building geometry restraints manager: 13.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10632 1.34 - 1.45: 5712 1.45 - 1.57: 17808 1.57 - 1.69: 0 1.69 - 1.80: 240 Bond restraints: 34392 Sorted by residual: bond pdb=" CB ILE I 124 " pdb=" CG2 ILE I 124 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" CB ILE J 124 " pdb=" CG2 ILE J 124 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" CB ILE L 124 " pdb=" CG2 ILE L 124 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" CB ILE X 124 " pdb=" CG2 ILE X 124 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" CB ILE F 124 " pdb=" CG2 ILE F 124 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 ... (remaining 34387 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.34: 888 106.34 - 113.27: 17616 113.27 - 120.20: 14592 120.20 - 127.13: 12912 127.13 - 134.06: 312 Bond angle restraints: 46320 Sorted by residual: angle pdb=" CA LEU X 165 " pdb=" C LEU X 165 " pdb=" N PRO X 166 " ideal model delta sigma weight residual 118.44 122.40 -3.96 1.59e+00 3.96e-01 6.19e+00 angle pdb=" CA LEU U 165 " pdb=" C LEU U 165 " pdb=" N PRO U 166 " ideal model delta sigma weight residual 118.44 122.40 -3.96 1.59e+00 3.96e-01 6.19e+00 angle pdb=" CA LEU F 165 " pdb=" C LEU F 165 " pdb=" N PRO F 166 " ideal model delta sigma weight residual 118.44 122.40 -3.96 1.59e+00 3.96e-01 6.19e+00 angle pdb=" CA LEU L 165 " pdb=" C LEU L 165 " pdb=" N PRO L 166 " ideal model delta sigma weight residual 118.44 122.40 -3.96 1.59e+00 3.96e-01 6.19e+00 angle pdb=" CA LEU K 165 " pdb=" C LEU K 165 " pdb=" N PRO K 166 " ideal model delta sigma weight residual 118.44 122.40 -3.96 1.59e+00 3.96e-01 6.19e+00 ... (remaining 46315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.33: 18384 10.33 - 20.65: 1896 20.65 - 30.98: 408 30.98 - 41.31: 168 41.31 - 51.63: 72 Dihedral angle restraints: 20928 sinusoidal: 8784 harmonic: 12144 Sorted by residual: dihedral pdb=" CA GLU N 103 " pdb=" C GLU N 103 " pdb=" N LEU N 104 " pdb=" CA LEU N 104 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU C 103 " pdb=" C GLU C 103 " pdb=" N LEU C 104 " pdb=" CA LEU C 104 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLU J 103 " pdb=" C GLU J 103 " pdb=" N LEU J 104 " pdb=" CA LEU J 104 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 20925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1920 0.028 - 0.057: 1704 0.057 - 0.085: 864 0.085 - 0.113: 168 0.113 - 0.141: 96 Chirality restraints: 4752 Sorted by residual: chirality pdb=" CA ILE X 73 " pdb=" N ILE X 73 " pdb=" C ILE X 73 " pdb=" CB ILE X 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE J 73 " pdb=" N ILE J 73 " pdb=" C ILE J 73 " pdb=" CB ILE J 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE O 73 " pdb=" N ILE O 73 " pdb=" C ILE O 73 " pdb=" CB ILE O 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 4749 not shown) Planarity restraints: 5976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 82 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO L 83 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO L 83 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 83 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 82 " 0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO G 83 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO G 83 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 83 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER M 82 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO M 83 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO M 83 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO M 83 " -0.029 5.00e-02 4.00e+02 ... (remaining 5973 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 840 2.70 - 3.25: 30192 3.25 - 3.80: 51036 3.80 - 4.35: 76128 4.35 - 4.90: 119268 Nonbonded interactions: 277464 Sorted by model distance: nonbonded pdb=" OH TYR P 62 " pdb=" O ALA W 29 " model vdw 2.144 2.440 nonbonded pdb=" O ALA C 29 " pdb=" OH TYR M 62 " model vdw 2.144 2.440 nonbonded pdb=" OH TYR A 62 " pdb=" O ALA G 29 " model vdw 2.144 2.440 nonbonded pdb=" O ALA J 29 " pdb=" OH TYR R 62 " model vdw 2.144 2.440 nonbonded pdb=" O ALA N 29 " pdb=" OH TYR S 62 " model vdw 2.144 2.440 ... (remaining 277459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 21816 2.51 5 N 5328 2.21 5 O 6312 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.050 Extract box with map and model: 9.900 Check model and map are aligned: 0.470 Convert atoms to be neutral: 0.290 Process input model: 80.080 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.290 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:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.008 0.051 34392 Z= 0.503 Angle : 0.893 6.368 46320 Z= 0.468 Chirality : 0.047 0.141 4752 Planarity : 0.007 0.052 5976 Dihedral : 9.774 51.631 13056 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.39 (0.06), residues: 4008 helix: -4.96 (0.03), residues: 3312 sheet: None (None), residues: 0 loop : -2.42 (0.18), residues: 696 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 792 time to evaluate : 3.936 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 792 average time/residue: 1.6745 time to fit residues: 1544.3818 Evaluate side-chains 600 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 600 time to evaluate : 4.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.8980 chunk 291 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 155 optimal weight: 0.0870 chunk 300 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 183 optimal weight: 0.0060 chunk 224 optimal weight: 5.9990 chunk 348 optimal weight: 4.9990 overall best weight: 0.4374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 41 ASN B 15 ASN B 41 ASN C 15 ASN C 41 ASN D 15 ASN D 41 ASN E 15 ASN E 41 ASN F 15 ASN F 41 ASN G 15 ASN G 41 ASN H 15 ASN H 41 ASN I 15 ASN I 41 ASN J 15 ASN J 41 ASN K 15 ASN K 41 ASN L 15 ASN L 41 ASN M 15 ASN M 41 ASN N 15 ASN N 41 ASN O 15 ASN O 41 ASN P 15 ASN P 41 ASN Q 15 ASN Q 41 ASN R 15 ASN R 41 ASN S 15 ASN S 41 ASN T 15 ASN T 41 ASN U 15 ASN U 41 ASN V 15 ASN V 41 ASN W 15 ASN W 41 ASN X 15 ASN X 41 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 34392 Z= 0.134 Angle : 0.531 7.116 46320 Z= 0.281 Chirality : 0.035 0.135 4752 Planarity : 0.005 0.036 5976 Dihedral : 5.326 15.155 4440 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.13 (0.09), residues: 4008 helix: -3.25 (0.06), residues: 3456 sheet: None (None), residues: 0 loop : -2.12 (0.21), residues: 552 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 670 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 0 residues processed: 670 average time/residue: 1.6190 time to fit residues: 1268.5125 Evaluate side-chains 549 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 549 time to evaluate : 3.797 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 290 optimal weight: 0.7980 chunk 237 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 6.9990 chunk 377 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN B 127 GLN C 127 GLN D 127 GLN E 127 GLN F 127 GLN G 127 GLN H 127 GLN I 127 GLN J 127 GLN K 127 GLN L 127 GLN M 127 GLN N 127 GLN O 127 GLN P 127 GLN Q 127 GLN R 127 GLN S 127 GLN T 127 GLN U 127 GLN V 127 GLN W 127 GLN X 127 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.021 34392 Z= 0.234 Angle : 0.538 5.089 46320 Z= 0.280 Chirality : 0.039 0.143 4752 Planarity : 0.004 0.033 5976 Dihedral : 5.137 13.336 4440 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.11), residues: 4008 helix: -2.19 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : -1.60 (0.19), residues: 648 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 579 time to evaluate : 3.794 Fit side-chains outliers start: 40 outliers final: 0 residues processed: 603 average time/residue: 1.7010 time to fit residues: 1196.1686 Evaluate side-chains 510 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 3.911 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 350 optimal weight: 0.0980 chunk 371 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 332 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.022 34392 Z= 0.227 Angle : 0.505 5.483 46320 Z= 0.264 Chirality : 0.039 0.138 4752 Planarity : 0.004 0.032 5976 Dihedral : 4.977 12.608 4440 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.12), residues: 4008 helix: -1.63 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : -1.24 (0.19), residues: 648 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 525 time to evaluate : 4.196 Fit side-chains outliers start: 88 outliers final: 0 residues processed: 573 average time/residue: 1.8409 time to fit residues: 1215.7903 Evaluate side-chains 541 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 4.065 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.7980 chunk 210 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 276 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 316 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 333 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 34392 Z= 0.272 Angle : 0.539 5.969 46320 Z= 0.279 Chirality : 0.041 0.143 4752 Planarity : 0.004 0.034 5976 Dihedral : 5.020 13.145 4440 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.12), residues: 4008 helix: -1.34 (0.08), residues: 3360 sheet: None (None), residues: 0 loop : -1.01 (0.20), residues: 648 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 549 time to evaluate : 3.760 Fit side-chains outliers start: 63 outliers final: 0 residues processed: 595 average time/residue: 1.8427 time to fit residues: 1263.8114 Evaluate side-chains 513 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 3.847 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 1.9990 chunk 334 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 0.9990 chunk 308 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 34392 Z= 0.277 Angle : 0.546 5.643 46320 Z= 0.286 Chirality : 0.041 0.141 4752 Planarity : 0.004 0.034 5976 Dihedral : 5.036 13.788 4440 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.12), residues: 4008 helix: -1.19 (0.09), residues: 3360 sheet: None (None), residues: 0 loop : -0.92 (0.21), residues: 648 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 552 time to evaluate : 3.877 Fit side-chains outliers start: 56 outliers final: 0 residues processed: 602 average time/residue: 1.7402 time to fit residues: 1216.6150 Evaluate side-chains 511 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 511 time to evaluate : 4.056 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 312 optimal weight: 0.0770 chunk 207 optimal weight: 1.9990 chunk 370 optimal weight: 6.9990 chunk 231 optimal weight: 0.5980 chunk 225 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 34392 Z= 0.127 Angle : 0.438 4.381 46320 Z= 0.236 Chirality : 0.037 0.158 4752 Planarity : 0.003 0.029 5976 Dihedral : 4.720 11.931 4440 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 4008 helix: -0.58 (0.09), residues: 3360 sheet: None (None), residues: 0 loop : -0.74 (0.21), residues: 648 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 549 time to evaluate : 4.111 Fit side-chains outliers start: 56 outliers final: 0 residues processed: 597 average time/residue: 1.7447 time to fit residues: 1219.7568 Evaluate side-chains 527 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 527 time to evaluate : 3.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 252 optimal weight: 0.9990 chunk 182 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 290 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 34392 Z= 0.233 Angle : 0.515 5.026 46320 Z= 0.271 Chirality : 0.041 0.137 4752 Planarity : 0.004 0.032 5976 Dihedral : 4.843 13.710 4440 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 4008 helix: -0.58 (0.09), residues: 3360 sheet: None (None), residues: 0 loop : -0.66 (0.21), residues: 648 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 501 time to evaluate : 3.962 Fit side-chains outliers start: 36 outliers final: 0 residues processed: 525 average time/residue: 1.7696 time to fit residues: 1081.1774 Evaluate side-chains 498 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 3.944 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 10.0000 chunk 354 optimal weight: 0.9980 chunk 323 optimal weight: 5.9990 chunk 344 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 270 optimal weight: 0.5980 chunk 105 optimal weight: 7.9990 chunk 311 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 343 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 34392 Z= 0.121 Angle : 0.434 5.032 46320 Z= 0.232 Chirality : 0.037 0.141 4752 Planarity : 0.003 0.029 5976 Dihedral : 4.629 11.863 4440 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 4008 helix: -0.08 (0.09), residues: 3360 sheet: None (None), residues: 0 loop : -0.44 (0.21), residues: 648 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 544 time to evaluate : 4.180 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 546 average time/residue: 1.4907 time to fit residues: 969.0965 Evaluate side-chains 499 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 3.784 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 6.9990 chunk 364 optimal weight: 0.7980 chunk 222 optimal weight: 0.1980 chunk 173 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 382 optimal weight: 2.9990 chunk 352 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.004 0.029 34392 Z= 0.238 Angle : 0.528 6.007 46320 Z= 0.274 Chirality : 0.041 0.143 4752 Planarity : 0.004 0.031 5976 Dihedral : 4.824 13.357 4440 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 4008 helix: -0.27 (0.09), residues: 3360 sheet: None (None), residues: 0 loop : -0.36 (0.22), residues: 648 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 569 time to evaluate : 3.864 Fit side-chains outliers start: 9 outliers final: 0 residues processed: 572 average time/residue: 1.5615 time to fit residues: 1051.8778 Evaluate side-chains 550 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 3.848 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 6.9990 chunk 324 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 280 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 305 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 0.0030 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.172421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.155686 restraints weight = 32371.099| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 1.55 r_work: 0.3996 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work: 0.3973 rms_B_bonded: 1.45 restraints_weight: 0.1250 r_work: 0.3961 rms_B_bonded: 1.55 restraints_weight: 0.0625 r_work: 0.3948 rms_B_bonded: 1.69 restraints_weight: 0.0312 r_work: 0.3935 rms_B_bonded: 1.86 restraints_weight: 0.0156 r_work: 0.3920 rms_B_bonded: 2.06 restraints_weight: 0.0078 r_work: 0.3904 rms_B_bonded: 2.30 restraints_weight: 0.0039 r_work: 0.3886 rms_B_bonded: 2.57 restraints_weight: 0.0020 r_work: 0.3866 rms_B_bonded: 2.89 restraints_weight: 0.0010 r_work: 0.3845 rms_B_bonded: 3.26 restraints_weight: 0.0005 r_work: 0.3821 rms_B_bonded: 3.67 restraints_weight: 0.0002 r_work: 0.3795 rms_B_bonded: 4.14 restraints_weight: 0.0001 r_work: 0.3766 rms_B_bonded: 4.68 restraints_weight: 0.0001 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 34392 Z= 0.136 Angle : 0.445 5.151 46320 Z= 0.238 Chirality : 0.037 0.133 4752 Planarity : 0.003 0.030 5976 Dihedral : 4.647 12.513 4440 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 4008 helix: 0.05 (0.09), residues: 3360 sheet: None (None), residues: 0 loop : -0.25 (0.22), residues: 648 =============================================================================== Job complete usr+sys time: 14713.92 seconds wall clock time: 260 minutes 24.46 seconds (15624.46 seconds total)