Starting phenix.real_space_refine on Wed Nov 20 15:14:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hee_34689/11_2024/8hee_34689.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hee_34689/11_2024/8hee_34689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hee_34689/11_2024/8hee_34689.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hee_34689/11_2024/8hee_34689.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hee_34689/11_2024/8hee_34689.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hee_34689/11_2024/8hee_34689.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 85 5.16 5 C 14015 2.51 5 N 3785 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21905 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "B" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Chain: "C" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "E" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "F" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1318 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 1 Chain: "L" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Chain: "I" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Chain: "J" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Chain: "K" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 155} Time building chain proxies: 12.42, per 1000 atoms: 0.57 Number of scatterers: 21905 At special positions: 0 Unit cell: (62.4, 178.88, 178.88, 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 85 16.00 O 4020 8.00 N 3785 7.00 C 14015 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.77 Conformation dependent library (CDL) restraints added in 3.2 seconds 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5220 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 50 sheets defined 13.2% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 removed outlier: 4.540A pdb=" N HIS A 29 " --> pdb=" O ARG A 26 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 30 " --> pdb=" O ARG A 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 26 through 30' Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.743A pdb=" N MET A 36 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.838A pdb=" N SER A 99 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.687A pdb=" N HIS B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.772A pdb=" N TYR B 138 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 140 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR B 141 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 143 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 51 removed outlier: 3.764A pdb=" N VAL C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'D' and resid 27 through 30 removed outlier: 3.602A pdb=" N THR D 30 " --> pdb=" O ARG D 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 31 through 36 removed outlier: 3.962A pdb=" N MET D 36 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.669A pdb=" N SER D 99 " --> pdb=" O ALA D 96 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 30 removed outlier: 3.563A pdb=" N THR E 30 " --> pdb=" O ARG E 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 27 through 30' Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.967A pdb=" N MET E 36 " --> pdb=" O VAL E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 94 through 100 removed outlier: 3.764A pdb=" N SER E 99 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 30 Processing helix chain 'F' and resid 31 through 36 removed outlier: 3.944A pdb=" N MET F 36 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 56 removed outlier: 3.741A pdb=" N THR F 56 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 68 Processing helix chain 'F' and resid 94 through 100 removed outlier: 3.778A pdb=" N SER F 99 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 30 removed outlier: 3.823A pdb=" N THR G 30 " --> pdb=" O ARG G 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 27 through 30' Processing helix chain 'G' and resid 31 through 36 Processing helix chain 'G' and resid 52 through 56 removed outlier: 3.520A pdb=" N THR G 56 " --> pdb=" O LEU G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 68 Processing helix chain 'G' and resid 94 through 100 removed outlier: 3.657A pdb=" N SER G 99 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN G 100 " --> pdb=" O ALA G 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 51 removed outlier: 3.773A pdb=" N VAL L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 89 through 96 Processing helix chain 'L' and resid 138 through 143 removed outlier: 3.751A pdb=" N HIS L 142 " --> pdb=" O ARG L 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 51 removed outlier: 3.534A pdb=" N VAL M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 138 through 143 removed outlier: 3.965A pdb=" N HIS M 142 " --> pdb=" O ARG M 139 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS M 143 " --> pdb=" O ALA M 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 51 removed outlier: 3.607A pdb=" N VAL N 47 " --> pdb=" O ASN N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 96 Processing helix chain 'N' and resid 138 through 143 removed outlier: 3.680A pdb=" N HIS N 142 " --> pdb=" O ARG N 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 51 removed outlier: 3.578A pdb=" N VAL O 47 " --> pdb=" O ASN O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 96 Processing helix chain 'O' and resid 138 through 143 removed outlier: 3.761A pdb=" N HIS O 142 " --> pdb=" O ARG O 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 97 removed outlier: 3.686A pdb=" N HIS H 93 " --> pdb=" O GLY H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 143 removed outlier: 3.772A pdb=" N TYR H 138 " --> pdb=" O ARG H 135 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU H 140 " --> pdb=" O LYS H 137 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR H 141 " --> pdb=" O TYR H 138 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE H 143 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 97 removed outlier: 3.686A pdb=" N HIS I 93 " --> pdb=" O GLY I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 143 removed outlier: 3.772A pdb=" N TYR I 138 " --> pdb=" O ARG I 135 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU I 140 " --> pdb=" O LYS I 137 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THR I 141 " --> pdb=" O TYR I 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE I 143 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 97 removed outlier: 3.687A pdb=" N HIS J 93 " --> pdb=" O GLY J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 143 removed outlier: 3.773A pdb=" N TYR J 138 " --> pdb=" O ARG J 135 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU J 140 " --> pdb=" O LYS J 137 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR J 141 " --> pdb=" O TYR J 138 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE J 143 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 97 removed outlier: 3.687A pdb=" N HIS K 93 " --> pdb=" O GLY K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 143 removed outlier: 3.772A pdb=" N TYR K 138 " --> pdb=" O ARG K 135 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU K 140 " --> pdb=" O LYS K 137 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR K 141 " --> pdb=" O TYR K 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE K 143 " --> pdb=" O LEU K 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 3.788A pdb=" N ASP A 171 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG A 81 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A 175 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A 79 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 177 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU A 77 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N MET A 179 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP A 75 " --> pdb=" O MET A 179 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG A 181 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE A 73 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLU A 183 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR A 71 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR A 185 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA A 69 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP O 23 " --> pdb=" O ARG A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 127 removed outlier: 3.513A pdb=" N TYR A 72 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ALA A 69 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR A 185 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR A 71 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLU A 183 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE A 73 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG A 181 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP A 75 " --> pdb=" O MET A 179 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N MET A 179 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU A 77 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 177 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A 79 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A 175 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG A 81 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 171 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 184 " --> pdb=" O PHE O 41 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE O 41 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.227A pdb=" N ASP B 106 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS B 207 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY B 104 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU B 213 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE B 98 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 198 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE B 197 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN B 68 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL B 199 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 66 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 203 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.227A pdb=" N ASP B 106 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS B 207 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY B 104 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU B 213 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE B 98 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 82 removed outlier: 6.118A pdb=" N CYS B 120 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLY B 118 " --> pdb=" O PRO B 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 removed outlier: 7.413A pdb=" N VAL L 5 " --> pdb=" O PRO C 4 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA C 6 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS L 7 " --> pdb=" O ALA C 6 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL M 5 " --> pdb=" O PRO L 4 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ALA L 6 " --> pdb=" O VAL M 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS M 7 " --> pdb=" O ALA L 6 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL N 5 " --> pdb=" O PRO M 4 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ALA M 6 " --> pdb=" O VAL N 5 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N CYS N 7 " --> pdb=" O ALA M 6 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL O 5 " --> pdb=" O PRO N 4 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ALA N 6 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N CYS O 7 " --> pdb=" O ALA N 6 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL C 3 " --> pdb=" O PRO O 4 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 40 through 41 removed outlier: 4.453A pdb=" N LEU D 184 " --> pdb=" O PHE C 41 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA D 69 " --> pdb=" O PRO D 187 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 72 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 78 removed outlier: 6.994A pdb=" N LEU C 73 " --> pdb=" O GLN C 189 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLN C 189 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 75 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG C 120 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 121 " --> pdb=" O TRP C 148 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP C 148 " --> pdb=" O TYR C 121 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 123 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE C 144 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'D' and resid 40 through 41 removed outlier: 3.930A pdb=" N ASP D 171 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG D 81 " --> pdb=" O SER D 173 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU D 175 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL D 79 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL D 177 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU D 77 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 48 through 51 removed outlier: 4.158A pdb=" N GLY D 165 " --> pdb=" O ILE D 51 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 40 through 41 removed outlier: 4.003A pdb=" N ASP E 171 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG E 81 " --> pdb=" O SER E 173 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU E 175 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL E 79 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL E 177 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU E 77 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP L 23 " --> pdb=" O ARG E 114 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA E 116 " --> pdb=" O ASP L 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 48 through 50 Processing sheet with id=AB8, first strand: chain 'E' and resid 126 through 127 removed outlier: 6.202A pdb=" N ALA E 69 " --> pdb=" O PRO E 187 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU E 184 " --> pdb=" O PHE L 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 40 through 41 removed outlier: 3.872A pdb=" N ASP F 171 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG F 81 " --> pdb=" O SER F 173 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU F 175 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL F 79 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL F 177 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU F 77 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP M 23 " --> pdb=" O ARG F 114 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 116 " --> pdb=" O ASP M 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 48 through 50 Processing sheet with id=AC2, first strand: chain 'F' and resid 126 through 127 removed outlier: 6.274A pdb=" N ALA F 69 " --> pdb=" O PRO F 187 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU F 184 " --> pdb=" O PHE M 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 39 through 41 removed outlier: 6.029A pdb=" N ILE G 172 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU G 83 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU G 174 " --> pdb=" O ARG G 81 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP N 23 " --> pdb=" O ARG G 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 48 through 50 Processing sheet with id=AC5, first strand: chain 'G' and resid 126 through 127 removed outlier: 6.224A pdb=" N ALA G 69 " --> pdb=" O PRO G 187 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU G 184 " --> pdb=" O PHE N 41 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'L' and resid 73 through 78 removed outlier: 6.695A pdb=" N LEU L 73 " --> pdb=" O GLN L 189 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLN L 189 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA L 75 " --> pdb=" O ILE L 187 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP L 184 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG L 120 " --> pdb=" O ILE L 190 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR L 121 " --> pdb=" O TRP L 148 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP L 148 " --> pdb=" O TYR L 121 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE L 144 " --> pdb=" O TYR L 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 169 through 170 Processing sheet with id=AD1, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AD2, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AD3, first strand: chain 'M' and resid 73 through 79 removed outlier: 7.004A pdb=" N LEU M 73 " --> pdb=" O GLN M 189 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLN M 189 " --> pdb=" O LEU M 73 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA M 75 " --> pdb=" O ILE M 187 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY M 183 " --> pdb=" O VAL M 79 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP M 184 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG M 120 " --> pdb=" O ILE M 190 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE M 144 " --> pdb=" O TYR M 125 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 169 through 170 Processing sheet with id=AD5, first strand: chain 'N' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'N' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'N' and resid 73 through 78 removed outlier: 6.717A pdb=" N LEU N 73 " --> pdb=" O GLN N 189 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLN N 189 " --> pdb=" O LEU N 73 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA N 75 " --> pdb=" O ILE N 187 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG N 120 " --> pdb=" O ILE N 190 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR N 121 " --> pdb=" O TRP N 148 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP N 148 " --> pdb=" O TYR N 121 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE N 144 " --> pdb=" O TYR N 125 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 169 through 170 Processing sheet with id=AD9, first strand: chain 'O' and resid 53 through 54 Processing sheet with id=AE1, first strand: chain 'O' and resid 73 through 79 removed outlier: 7.021A pdb=" N LEU O 73 " --> pdb=" O GLN O 189 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N GLN O 189 " --> pdb=" O LEU O 73 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA O 75 " --> pdb=" O ILE O 187 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY O 183 " --> pdb=" O VAL O 79 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG O 120 " --> pdb=" O ILE O 190 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR O 121 " --> pdb=" O TRP O 148 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TRP O 148 " --> pdb=" O TYR O 121 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE O 144 " --> pdb=" O TYR O 125 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 100 through 101 Processing sheet with id=AE3, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.226A pdb=" N ASP H 106 " --> pdb=" O PRO H 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS H 207 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLY H 104 " --> pdb=" O HIS H 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU H 213 " --> pdb=" O PHE H 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE H 98 " --> pdb=" O GLU H 213 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS H 198 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE H 197 " --> pdb=" O ASN H 68 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ASN H 68 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL H 199 " --> pdb=" O LEU H 66 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 66 " --> pdb=" O VAL H 199 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE H 203 " --> pdb=" O PHE H 62 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.226A pdb=" N ASP H 106 " --> pdb=" O PRO H 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS H 207 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLY H 104 " --> pdb=" O HIS H 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU H 213 " --> pdb=" O PHE H 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE H 98 " --> pdb=" O GLU H 213 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 78 through 82 removed outlier: 6.117A pdb=" N CYS H 120 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLY H 118 " --> pdb=" O PRO H 186 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.226A pdb=" N ASP I 106 " --> pdb=" O PRO I 205 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS I 207 " --> pdb=" O GLY I 104 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY I 104 " --> pdb=" O HIS I 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU I 213 " --> pdb=" O PHE I 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE I 98 " --> pdb=" O GLU I 213 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS I 198 " --> pdb=" O VAL I 112 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE I 197 " --> pdb=" O ASN I 68 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN I 68 " --> pdb=" O ILE I 197 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL I 199 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU I 66 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE I 203 " --> pdb=" O PHE I 62 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.226A pdb=" N ASP I 106 " --> pdb=" O PRO I 205 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS I 207 " --> pdb=" O GLY I 104 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY I 104 " --> pdb=" O HIS I 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU I 213 " --> pdb=" O PHE I 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE I 98 " --> pdb=" O GLU I 213 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 78 through 82 removed outlier: 6.118A pdb=" N CYS I 120 " --> pdb=" O VAL I 184 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLY I 118 " --> pdb=" O PRO I 186 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.227A pdb=" N ASP J 106 " --> pdb=" O PRO J 205 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS J 207 " --> pdb=" O GLY J 104 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLY J 104 " --> pdb=" O HIS J 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU J 213 " --> pdb=" O PHE J 98 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE J 98 " --> pdb=" O GLU J 213 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS J 198 " --> pdb=" O VAL J 112 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE J 197 " --> pdb=" O ASN J 68 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN J 68 " --> pdb=" O ILE J 197 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL J 199 " --> pdb=" O LEU J 66 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU J 66 " --> pdb=" O VAL J 199 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE J 203 " --> pdb=" O PHE J 62 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.227A pdb=" N ASP J 106 " --> pdb=" O PRO J 205 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N HIS J 207 " --> pdb=" O GLY J 104 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLY J 104 " --> pdb=" O HIS J 207 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU J 213 " --> pdb=" O PHE J 98 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE J 98 " --> pdb=" O GLU J 213 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 78 through 82 removed outlier: 6.118A pdb=" N CYS J 120 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLY J 118 " --> pdb=" O PRO J 186 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.227A pdb=" N ASP K 106 " --> pdb=" O PRO K 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS K 207 " --> pdb=" O GLY K 104 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLY K 104 " --> pdb=" O HIS K 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU K 213 " --> pdb=" O PHE K 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE K 98 " --> pdb=" O GLU K 213 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS K 198 " --> pdb=" O VAL K 112 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE K 197 " --> pdb=" O ASN K 68 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN K 68 " --> pdb=" O ILE K 197 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N VAL K 199 " --> pdb=" O LEU K 66 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU K 66 " --> pdb=" O VAL K 199 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE K 203 " --> pdb=" O PHE K 62 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.227A pdb=" N ASP K 106 " --> pdb=" O PRO K 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N HIS K 207 " --> pdb=" O GLY K 104 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLY K 104 " --> pdb=" O HIS K 207 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLU K 213 " --> pdb=" O PHE K 98 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N PHE K 98 " --> pdb=" O GLU K 213 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 78 through 82 removed outlier: 6.118A pdb=" N CYS K 120 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLY K 118 " --> pdb=" O PRO K 186 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1569 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: 8.00 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.08: 1 1.08 - 1.27: 3500 1.27 - 1.45: 6519 1.45 - 1.63: 12365 1.63 - 1.82: 135 Bond restraints: 22520 Sorted by residual: bond pdb=" CB PRO D 208 " pdb=" CG PRO D 208 " ideal model delta sigma weight residual 1.492 0.899 0.593 5.00e-02 4.00e+02 1.41e+02 bond pdb=" CG PRO D 208 " pdb=" CD PRO D 208 " ideal model delta sigma weight residual 1.503 1.341 0.162 3.40e-02 8.65e+02 2.28e+01 bond pdb=" CA PRO D 208 " pdb=" CB PRO D 208 " ideal model delta sigma weight residual 1.533 1.578 -0.045 1.42e-02 4.96e+03 9.92e+00 bond pdb=" CB VAL B 210 " pdb=" CG1 VAL B 210 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 6.03e+00 bond pdb=" CB VAL H 210 " pdb=" CG1 VAL H 210 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.99e+00 ... (remaining 22515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.77: 30717 14.77 - 29.53: 0 29.53 - 44.30: 2 44.30 - 59.07: 0 59.07 - 73.83: 1 Bond angle restraints: 30720 Sorted by residual: angle pdb=" CB PRO D 208 " pdb=" CG PRO D 208 " pdb=" CD PRO D 208 " ideal model delta sigma weight residual 106.10 179.93 -73.83 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO D 208 " pdb=" CD PRO D 208 " pdb=" CG PRO D 208 " ideal model delta sigma weight residual 103.20 71.81 31.39 1.50e+00 4.44e-01 4.38e+02 angle pdb=" CA PRO D 208 " pdb=" CB PRO D 208 " pdb=" CG PRO D 208 " ideal model delta sigma weight residual 104.50 69.76 34.74 1.90e+00 2.77e-01 3.34e+02 angle pdb=" CA PRO D 208 " pdb=" N PRO D 208 " pdb=" CD PRO D 208 " ideal model delta sigma weight residual 112.00 98.37 13.63 1.40e+00 5.10e-01 9.48e+01 angle pdb=" N PRO D 208 " pdb=" CA PRO D 208 " pdb=" CB PRO D 208 " ideal model delta sigma weight residual 103.25 95.15 8.10 1.05e+00 9.07e-01 5.94e+01 ... (remaining 30715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11614 17.94 - 35.88: 1380 35.88 - 53.82: 281 53.82 - 71.76: 31 71.76 - 89.71: 24 Dihedral angle restraints: 13330 sinusoidal: 5210 harmonic: 8120 Sorted by residual: dihedral pdb=" CA LEU C 212 " pdb=" C LEU C 212 " pdb=" N ARG C 213 " pdb=" CA ARG C 213 " ideal model delta harmonic sigma weight residual 180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU L 212 " pdb=" C LEU L 212 " pdb=" N ARG L 213 " pdb=" CA ARG L 213 " ideal model delta harmonic sigma weight residual 180.00 -159.70 -20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA SER A 74 " pdb=" C SER A 74 " pdb=" N ASP A 75 " pdb=" CA ASP A 75 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 13327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2379 0.042 - 0.083: 734 0.083 - 0.125: 273 0.125 - 0.167: 19 0.167 - 0.208: 5 Chirality restraints: 3410 Sorted by residual: chirality pdb=" CB VAL M 123 " pdb=" CA VAL M 123 " pdb=" CG1 VAL M 123 " pdb=" CG2 VAL M 123 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA VAL M 123 " pdb=" N VAL M 123 " pdb=" C VAL M 123 " pdb=" CB VAL M 123 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE M 187 " pdb=" CA ILE M 187 " pdb=" CG1 ILE M 187 " pdb=" CG2 ILE M 187 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 3407 not shown) Planarity restraints: 3960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 207 " 0.078 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO D 208 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO D 208 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 208 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 200 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C TYR H 200 " 0.062 2.00e-02 2.50e+03 pdb=" O TYR H 200 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA H 201 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR K 200 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C TYR K 200 " 0.062 2.00e-02 2.50e+03 pdb=" O TYR K 200 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA K 201 " -0.021 2.00e-02 2.50e+03 ... (remaining 3957 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 122 2.42 - 3.04: 12917 3.04 - 3.66: 32458 3.66 - 4.28: 49285 4.28 - 4.90: 85783 Nonbonded interactions: 180565 Sorted by model distance: nonbonded pdb=" OD1 ASN M 88 " pdb=" NH1 ARG J 135 " model vdw 1.796 3.120 nonbonded pdb=" OH TYR E 71 " pdb=" OE2 GLU I 128 " model vdw 2.047 3.040 nonbonded pdb=" OD1 ASN L 88 " pdb=" NH1 ARG I 135 " model vdw 2.055 3.120 nonbonded pdb=" O ARG C 213 " pdb=" ND1 HIS D 29 " model vdw 2.072 3.120 nonbonded pdb=" ND1 HIS A 29 " pdb=" O ARG O 213 " model vdw 2.088 3.120 ... (remaining 180560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 50.810 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.006 0.593 22520 Z= 0.270 Angle : 0.881 73.834 30720 Z= 0.461 Chirality : 0.046 0.208 3410 Planarity : 0.006 0.108 3960 Dihedral : 15.875 89.705 8110 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 0.64 % Allowed : 23.95 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -1.31 (0.16), residues: 2735 helix: -2.34 (0.31), residues: 245 sheet: -0.24 (0.20), residues: 750 loop : -0.92 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP O 148 HIS 0.005 0.001 HIS G 201 PHE 0.029 0.002 PHE H 98 TYR 0.057 0.002 TYR L 168 ARG 0.007 0.001 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 415 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ARG cc_start: 0.7300 (ptm160) cc_final: 0.6872 (mtt-85) REVERT: F 81 ARG cc_start: 0.8119 (ttp-170) cc_final: 0.7866 (ttp-170) REVERT: H 61 PHE cc_start: 0.6431 (OUTLIER) cc_final: 0.5717 (m-10) REVERT: H 65 HIS cc_start: 0.6520 (t70) cc_final: 0.6300 (t70) REVERT: H 167 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7512 (mtp180) REVERT: H 170 GLN cc_start: 0.7316 (mt0) cc_final: 0.7090 (mt0) REVERT: I 63 LYS cc_start: 0.6074 (OUTLIER) cc_final: 0.5824 (mmtm) REVERT: I 168 TYR cc_start: 0.7517 (m-80) cc_final: 0.7302 (m-80) REVERT: J 107 VAL cc_start: 0.8085 (m) cc_final: 0.7836 (t) REVERT: J 170 GLN cc_start: 0.7976 (mt0) cc_final: 0.7527 (mt0) outliers start: 15 outliers final: 5 residues processed: 421 average time/residue: 0.3730 time to fit residues: 237.0697 Evaluate side-chains 346 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 339 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain F residue 75 ASP Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain I residue 63 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 227 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 245 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 HIS B 157 HIS ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN ** G 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN M 106 ASN M 189 GLN H 166 ASN ** H 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 HIS I 166 ASN J 139 GLN K 77 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 22520 Z= 0.256 Angle : 0.615 7.395 30720 Z= 0.323 Chirality : 0.046 0.171 3410 Planarity : 0.005 0.059 3960 Dihedral : 5.309 53.824 3058 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.52 % Allowed : 21.78 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -1.29 (0.16), residues: 2735 helix: -1.10 (0.45), residues: 155 sheet: -0.38 (0.19), residues: 765 loop : -1.07 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 69 HIS 0.008 0.001 HIS I 93 PHE 0.016 0.002 PHE C 77 TYR 0.015 0.002 TYR H 91 ARG 0.005 0.001 ARG I 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5470 Ramachandran restraints generated. 2735 Oldfield, 0 Emsley, 2735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 355 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ARG cc_start: 0.7357 (ptm160) cc_final: 0.7005 (mtt-85) REVERT: C 80 SER cc_start: 0.5283 (OUTLIER) cc_final: 0.4920 (p) REVERT: D 130 TYR cc_start: 0.9192 (t80) cc_final: 0.8835 (t80) REVERT: M 106 ASN cc_start: 0.8062 (m-40) cc_final: 0.7831 (m110) REVERT: N 122 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6510 (ttp) REVERT: N 216 ILE cc_start: 0.8781 (pt) cc_final: 0.8544 (pt) REVERT: H 65 HIS cc_start: 0.6355 (t70) cc_final: 0.6139 (t70) REVERT: H 103 ASN cc_start: 0.7915 (p0) cc_final: 0.7678 (p0) REVERT: H 152 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7964 (p) REVERT: H 167 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7634 (mtp180) REVERT: H 168 TYR cc_start: 0.8331 (m-80) cc_final: 0.8081 (m-80) REVERT: I 168 TYR cc_start: 0.7506 (m-80) cc_final: 0.7241 (m-80) REVERT: J 213 GLU cc_start: -0.1004 (OUTLIER) cc_final: -0.1777 (tt0) REVERT: K 100 TYR cc_start: 0.6851 (m-80) cc_final: 0.6083 (m-80) outliers start: 83 outliers final: 49 residues processed: 408 average time/residue: 0.3460 time to fit residues: 217.2595 Evaluate side-chains 377 residues out of total 2360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 324 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain C residue 7 CYS Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 203 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain L residue 77 PHE Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 143 CYS Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 122 MET Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain N residue 199 THR Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 80 SER Chi-restraints excluded: chain H residue 61 PHE Chi-restraints excluded: chain H residue 80 LYS Chi-restraints excluded: chain H residue 101 MET Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain H residue 213 GLU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 213 GLU Chi-restraints excluded: chain K residue 86 ASP Chi-restraints excluded: chain K residue 90 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 204 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 218 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 197 optimal weight: 40.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: