Starting phenix.real_space_refine on Sun Mar 17 20:16:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbd_4792/03_2024/6rbd_4792.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbd_4792/03_2024/6rbd_4792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbd_4792/03_2024/6rbd_4792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbd_4792/03_2024/6rbd_4792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbd_4792/03_2024/6rbd_4792.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbd_4792/03_2024/6rbd_4792.pdb" } resolution = 3.47 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= 0.003 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1777 5.49 5 S 115 5.16 5 C 44292 2.51 5 N 14653 2.21 5 O 20211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "G ARG 23": "NH1" <-> "NH2" Residue "G ARG 92": "NH1" <-> "NH2" Residue "G ARG 98": "NH1" <-> "NH2" Residue "G ARG 137": "NH1" <-> "NH2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 47": "NH1" <-> "NH2" Residue "I ARG 164": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "J ARG 3": "NH1" <-> "NH2" Residue "J ARG 53": "NH1" <-> "NH2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ARG 62": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "N ARG 104": "NH1" <-> "NH2" Residue "N ARG 106": "NH1" <-> "NH2" Residue "V ARG 60": "NH1" <-> "NH2" Residue "W TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 19": "NH1" <-> "NH2" Residue "Y PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 264": "NH1" <-> "NH2" Residue "k TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 146": "NH1" <-> "NH2" Residue "y ARG 149": "NH1" <-> "NH2" Residue "y ARG 157": "NH1" <-> "NH2" Residue "y ARG 166": "NH1" <-> "NH2" Residue "y ARG 174": "NH1" <-> "NH2" Residue "y ARG 208": "NH1" <-> "NH2" Residue "y ARG 215": "NH1" <-> "NH2" Residue "y ARG 228": "NH1" <-> "NH2" Residue "y ARG 233": "NH1" <-> "NH2" Residue "y ARG 236": "NH1" <-> "NH2" Residue "y ARG 294": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ARG 219": "NH1" <-> "NH2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "U TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 81048 Number of models: 1 Model: "" Number of chains: 35 Chain: "b" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "e" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 384 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain breaks: 1 Chain: "2" Number of atoms: 37868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1777, 37868 Classifications: {'RNA': 1777} Modifications used: {'rna2p_pur': 136, 'rna2p_pyr': 145, 'rna3p_pur': 800, 'rna3p_pyr': 696} Link IDs: {'rna2p': 281, 'rna3p': 1495} Chain breaks: 4 Chain: "A" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1611 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 189} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1709 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain: "C" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1635 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 13, 'TRANS': 203} Chain: "E" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "G" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1873 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "H" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1481 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 173} Chain: "I" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "J" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "L" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1129 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 8, 'TRANS': 131} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "V" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 684 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "W" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "X" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} Chain: "Y" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "c" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 497 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "d" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 302 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1436 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 9, 'TRANS': 171} Chain: "i" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1116 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "k" Number of atoms: 4860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4860 Classifications: {'peptide': 605} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "l" Number of atoms: 2199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2199 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Chain: "y" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1245 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 1 Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1609 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain: "M" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 941 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "O" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 926 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 902 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "Q" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "R" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1000 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "S" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 840 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "T" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "Z" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 512 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "D" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1442 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Chain: "U" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 674 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Time building chain proxies: 31.29, per 1000 atoms: 0.39 Number of scatterers: 81048 At special positions: 0 Unit cell: (220.869, 288.09, 179.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 115 16.00 P 1777 15.00 O 20211 8.00 N 14653 7.00 C 44292 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: 32.17 Conformation dependent library (CDL) restraints added in 6.2 seconds 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10182 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 56 sheets defined 39.6% alpha, 18.4% beta 494 base pairs and 957 stacking pairs defined. Time for finding SS restraints: 24.34 Creating SS restraints... Processing helix chain 'b' and resid 11 through 18 removed outlier: 3.523A pdb=" N ARG b 17 " --> pdb=" O ALA b 13 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS b 18 " --> pdb=" O SER b 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 44 Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 30 through 34 removed outlier: 3.948A pdb=" N GLN A 33 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU A 34 " --> pdb=" O VAL A 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 30 through 34' Processing helix chain 'A' and resid 49 through 67 removed outlier: 3.644A pdb=" N ILE A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 94 removed outlier: 3.891A pdb=" N ARG A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 166 through 186 Processing helix chain 'B' and resid 22 through 27 removed outlier: 4.220A pdb=" N ARG B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 157 through 179 removed outlier: 3.787A pdb=" N SER B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 65 through 73 removed outlier: 3.991A pdb=" N ILE C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 135 Processing helix chain 'C' and resid 181 through 190 Processing helix chain 'C' and resid 206 through 220 Processing helix chain 'C' and resid 221 through 224 removed outlier: 4.006A pdb=" N PHE C 224 " --> pdb=" O THR C 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 224' Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 238 through 243 removed outlier: 3.908A pdb=" N ILE C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 14 removed outlier: 3.642A pdb=" N ALA E 14 " --> pdb=" O ARG E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 43 through 50 Processing helix chain 'E' and resid 58 through 66 Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 247 through 258 Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 153 through 157 removed outlier: 3.725A pdb=" N VAL G 157 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 232 removed outlier: 3.531A pdb=" N LEU G 184 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 14 through 30 Processing helix chain 'H' and resid 33 through 39 Processing helix chain 'H' and resid 66 through 72 Processing helix chain 'H' and resid 73 through 85 Processing helix chain 'H' and resid 117 through 130 removed outlier: 3.539A pdb=" N VAL H 121 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL H 130 " --> pdb=" O LEU H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 177 Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 88 through 93 Processing helix chain 'I' and resid 106 through 114 removed outlier: 3.539A pdb=" N ARG I 110 " --> pdb=" O ALA I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 146 Processing helix chain 'I' and resid 147 through 151 removed outlier: 3.725A pdb=" N ALA I 150 " --> pdb=" O ALA I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 163 removed outlier: 3.695A pdb=" N ALA I 162 " --> pdb=" O SER I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 177 Processing helix chain 'I' and resid 185 through 200 Processing helix chain 'J' and resid 20 through 35 Processing helix chain 'J' and resid 39 through 60 removed outlier: 4.049A pdb=" N ILE J 45 " --> pdb=" O GLU J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 83 removed outlier: 3.782A pdb=" N VAL J 83 " --> pdb=" O ARG J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 106 removed outlier: 3.712A pdb=" N PHE J 104 " --> pdb=" O LYS J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 116 removed outlier: 4.044A pdb=" N TYR J 114 " --> pdb=" O GLN J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 131 Processing helix chain 'J' and resid 149 through 154 removed outlier: 4.129A pdb=" N LYS J 154 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 170 through 186 Processing helix chain 'L' and resid 45 through 51 removed outlier: 3.801A pdb=" N ILE L 49 " --> pdb=" O PRO L 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 Processing helix chain 'N' and resid 46 through 57 Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 78 Processing helix chain 'N' and resid 85 through 105 Processing helix chain 'N' and resid 108 through 132 Processing helix chain 'N' and resid 142 through 151 Processing helix chain 'V' and resid 56 through 63 removed outlier: 3.584A pdb=" N GLY V 63 " --> pdb=" O VAL V 59 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 6 through 20 Processing helix chain 'W' and resid 31 through 45 removed outlier: 3.668A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 93 removed outlier: 3.527A pdb=" N ALA W 91 " --> pdb=" O GLU W 87 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 120 Processing helix chain 'X' and resid 11 through 23 Processing helix chain 'X' and resid 24 through 26 No H-bonds generated for 'chain 'X' and resid 24 through 26' Processing helix chain 'X' and resid 27 through 34 Processing helix chain 'X' and resid 132 through 137 Processing helix chain 'Y' and resid 36 through 48 Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 94 Processing helix chain 'Y' and resid 104 through 116 Processing helix chain 'Y' and resid 122 through 135 Processing helix chain 'd' and resid 32 through 36 removed outlier: 3.775A pdb=" N LEU d 36 " --> pdb=" O LYS d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 39 through 44 removed outlier: 3.709A pdb=" N ARG d 44 " --> pdb=" O ARG d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 46 through 51 removed outlier: 3.886A pdb=" N ILE d 50 " --> pdb=" O LYS d 46 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY d 51 " --> pdb=" O ALA d 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 46 through 51' Processing helix chain 'h' and resid 102 through 122 removed outlier: 4.047A pdb=" N THR h 107 " --> pdb=" O PRO h 103 " (cutoff:3.500A) Proline residue: h 108 - end of helix removed outlier: 5.864A pdb=" N THR h 114 " --> pdb=" O ARG h 110 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LYS h 115 " --> pdb=" O ASN h 111 " (cutoff:3.500A) Proline residue: h 118 - end of helix Processing helix chain 'h' and resid 148 through 164 removed outlier: 3.672A pdb=" N LEU h 152 " --> pdb=" O ASP h 148 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN h 153 " --> pdb=" O PRO h 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 167 through 177 removed outlier: 3.547A pdb=" N SER h 171 " --> pdb=" O ASP h 167 " (cutoff:3.500A) Processing helix chain 'h' and resid 195 through 207 Processing helix chain 'h' and resid 210 through 221 removed outlier: 3.529A pdb=" N ALA h 215 " --> pdb=" O LYS h 211 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG h 221 " --> pdb=" O GLU h 217 " (cutoff:3.500A) Processing helix chain 'h' and resid 237 through 252 Processing helix chain 'h' and resid 255 through 272 Processing helix chain 'i' and resid 255 through 269 Processing helix chain 'i' and resid 271 through 293 removed outlier: 4.405A pdb=" N LEU i 284 " --> pdb=" O ASN i 280 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU i 285 " --> pdb=" O LEU i 281 " (cutoff:3.500A) Processing helix chain 'i' and resid 300 through 310 removed outlier: 3.654A pdb=" N TYR i 304 " --> pdb=" O ASN i 300 " (cutoff:3.500A) Processing helix chain 'i' and resid 313 through 321 Processing helix chain 'i' and resid 321 through 326 removed outlier: 3.802A pdb=" N LEU i 325 " --> pdb=" O PHE i 321 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL i 326 " --> pdb=" O LEU i 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 321 through 326' Processing helix chain 'i' and resid 331 through 345 removed outlier: 3.537A pdb=" N VAL i 345 " --> pdb=" O VAL i 341 " (cutoff:3.500A) Processing helix chain 'i' and resid 348 through 360 Processing helix chain 'i' and resid 365 through 376 Processing helix chain 'i' and resid 383 through 390 Processing helix chain 'k' and resid 50 through 72 Processing helix chain 'k' and resid 96 through 106 Processing helix chain 'k' and resid 110 through 117 removed outlier: 3.978A pdb=" N MET k 114 " --> pdb=" O ASP k 110 " (cutoff:3.500A) Processing helix chain 'k' and resid 144 through 153 Processing helix chain 'k' and resid 172 through 184 Processing helix chain 'k' and resid 194 through 198 Processing helix chain 'k' and resid 201 through 220 removed outlier: 4.495A pdb=" N ASP k 207 " --> pdb=" O LYS k 203 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL k 208 " --> pdb=" O PHE k 204 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS k 218 " --> pdb=" O SER k 214 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE k 219 " --> pdb=" O TYR k 215 " (cutoff:3.500A) Processing helix chain 'k' and resid 231 through 245 Processing helix chain 'k' and resid 250 through 255 Processing helix chain 'k' and resid 350 through 355 removed outlier: 3.544A pdb=" N THR k 354 " --> pdb=" O ALA k 350 " (cutoff:3.500A) Processing helix chain 'k' and resid 473 through 478 Processing helix chain 'k' and resid 493 through 498 removed outlier: 3.698A pdb=" N LEU k 498 " --> pdb=" O ALA k 494 " (cutoff:3.500A) Processing helix chain 'k' and resid 533 through 548 Processing helix chain 'k' and resid 566 through 571 removed outlier: 3.712A pdb=" N GLU k 569 " --> pdb=" O PHE k 566 " (cutoff:3.500A) Processing helix chain 'k' and resid 723 through 730 removed outlier: 3.801A pdb=" N VAL k 727 " --> pdb=" O ARG k 723 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE k 730 " --> pdb=" O ASP k 726 " (cutoff:3.500A) Processing helix chain 'l' and resid 14 through 24 Processing helix chain 'l' and resid 33 through 42 removed outlier: 3.679A pdb=" N ILE l 37 " --> pdb=" O PRO l 33 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER l 41 " --> pdb=" O ILE l 37 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY l 42 " --> pdb=" O HIS l 38 " (cutoff:3.500A) Processing helix chain 'l' and resid 45 through 59 removed outlier: 4.201A pdb=" N THR l 49 " --> pdb=" O SER l 45 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 79 No H-bonds generated for 'chain 'l' and resid 77 through 79' Processing helix chain 'l' and resid 80 through 91 Processing helix chain 'l' and resid 149 through 173 Processing helix chain 'l' and resid 198 through 200 No H-bonds generated for 'chain 'l' and resid 198 through 200' Processing helix chain 'l' and resid 205 through 224 removed outlier: 4.340A pdb=" N ILE l 217 " --> pdb=" O LEU l 213 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 283 removed outlier: 3.561A pdb=" N TYR l 268 " --> pdb=" O ASP l 264 " (cutoff:3.500A) Processing helix chain 'l' and resid 294 through 299 Processing helix chain 'y' and resid 138 through 142 removed outlier: 3.590A pdb=" N ILE y 142 " --> pdb=" O PHE y 139 " (cutoff:3.500A) Processing helix chain 'y' and resid 157 through 164 Processing helix chain 'y' and resid 173 through 182 removed outlier: 3.924A pdb=" N ALA y 177 " --> pdb=" O CYS y 173 " (cutoff:3.500A) Processing helix chain 'y' and resid 219 through 233 removed outlier: 3.669A pdb=" N ARG y 233 " --> pdb=" O ILE y 229 " (cutoff:3.500A) Processing helix chain 'y' and resid 237 through 243 removed outlier: 3.810A pdb=" N PHE y 242 " --> pdb=" O ILE y 238 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS y 243 " --> pdb=" O SER y 239 " (cutoff:3.500A) Processing helix chain 'y' and resid 246 through 258 removed outlier: 4.290A pdb=" N GLU y 252 " --> pdb=" O MET y 248 " (cutoff:3.500A) Processing helix chain 'y' and resid 278 through 288 removed outlier: 3.632A pdb=" N ASP y 282 " --> pdb=" O LYS y 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 39 Processing helix chain 'F' and resid 58 through 63 removed outlier: 3.581A pdb=" N VAL F 62 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 58 through 63' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 88 through 98 Processing helix chain 'F' and resid 106 through 124 removed outlier: 3.931A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 140 Processing helix chain 'F' and resid 163 through 184 Processing helix chain 'F' and resid 189 through 203 removed outlier: 3.925A pdb=" N LYS F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 224 Processing helix chain 'M' and resid 21 through 38 removed outlier: 4.359A pdb=" N VAL M 37 " --> pdb=" O ARG M 33 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS M 38 " --> pdb=" O THR M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 54 Processing helix chain 'M' and resid 69 through 76 Processing helix chain 'M' and resid 93 through 100 Processing helix chain 'M' and resid 126 through 128 No H-bonds generated for 'chain 'M' and resid 126 through 128' Processing helix chain 'M' and resid 129 through 142 Processing helix chain 'O' and resid 33 through 36 Processing helix chain 'O' and resid 44 through 48 Processing helix chain 'O' and resid 56 through 75 Processing helix chain 'O' and resid 95 through 108 Processing helix chain 'P' and resid 21 through 27 removed outlier: 3.580A pdb=" N GLU P 27 " --> pdb=" O GLU P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 36 Processing helix chain 'P' and resid 38 through 48 removed outlier: 3.672A pdb=" N ARG P 47 " --> pdb=" O ARG P 43 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY P 48 " --> pdb=" O ARG P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 65 removed outlier: 3.863A pdb=" N GLY P 55 " --> pdb=" O SER P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.696A pdb=" N ILE P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.807A pdb=" N LEU P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 120 removed outlier: 3.583A pdb=" N GLU P 118 " --> pdb=" O TYR P 115 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE P 119 " --> pdb=" O LEU P 116 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER P 120 " --> pdb=" O GLY P 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 115 through 120' Processing helix chain 'Q' and resid 44 through 49 removed outlier: 3.535A pdb=" N VAL Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 54 removed outlier: 3.687A pdb=" N LEU Q 54 " --> pdb=" O GLU Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 96 Processing helix chain 'Q' and resid 98 through 113 removed outlier: 3.567A pdb=" N LYS Q 102 " --> pdb=" O ASP Q 98 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 117 Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 27 through 39 removed outlier: 3.633A pdb=" N ARG R 33 " --> pdb=" O GLN R 29 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA R 39 " --> pdb=" O CYS R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 62 Processing helix chain 'R' and resid 73 through 84 removed outlier: 4.145A pdb=" N ASP R 82 " --> pdb=" O ARG R 78 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR R 84 " --> pdb=" O ARG R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 97 removed outlier: 3.615A pdb=" N ASN R 97 " --> pdb=" O SER R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 114 Processing helix chain 'S' and resid 27 through 33 Processing helix chain 'S' and resid 39 through 50 removed outlier: 3.574A pdb=" N SER S 43 " --> pdb=" O GLY S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 75 Processing helix chain 'S' and resid 82 through 86 removed outlier: 3.662A pdb=" N LEU S 86 " --> pdb=" O ALA S 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 9 removed outlier: 3.648A pdb=" N ASP T 8 " --> pdb=" O SER T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 26 Processing helix chain 'T' and resid 52 through 67 removed outlier: 3.581A pdb=" N LYS T 56 " --> pdb=" O GLY T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 81 removed outlier: 3.781A pdb=" N LEU T 76 " --> pdb=" O GLY T 72 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY T 81 " --> pdb=" O ASN T 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 111 removed outlier: 4.043A pdb=" N ASN T 101 " --> pdb=" O SER T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 142 Processing helix chain 'Z' and resid 47 through 57 removed outlier: 3.909A pdb=" N LEU Z 51 " --> pdb=" O TYR Z 47 " (cutoff:3.500A) Proline residue: Z 55 - end of helix Processing helix chain 'Z' and resid 65 through 69 removed outlier: 3.997A pdb=" N ARG Z 68 " --> pdb=" O LEU Z 65 " (cutoff:3.500A) Processing helix chain 'Z' and resid 74 through 87 removed outlier: 3.946A pdb=" N ILE Z 78 " --> pdb=" O SER Z 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 29 removed outlier: 3.508A pdb=" N ARG D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 97 through 111 removed outlier: 3.631A pdb=" N GLN D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 130 Processing helix chain 'D' and resid 161 through 167 removed outlier: 4.005A pdb=" N ASN D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 195 Processing helix chain 'U' and resid 30 through 48 removed outlier: 3.658A pdb=" N LEU U 34 " --> pdb=" O LYS U 30 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS U 48 " --> pdb=" O ASN U 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 107 Processing sheet with id=AA1, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AA2, first strand: chain 'b' and resid 54 through 55 removed outlier: 6.796A pdb=" N VAL b 54 " --> pdb=" O LEU b 63 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR b 67 " --> pdb=" O LYS b 70 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS b 70 " --> pdb=" O THR b 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'e' and resid 49 through 50 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.370A pdb=" N VAL A 47 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 99 removed outlier: 6.576A pdb=" N VAL A 73 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA A 75 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 74 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 48 removed outlier: 3.934A pdb=" N THR B 98 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL B 91 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU B 97 " --> pdb=" O ASP B 89 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 45 through 48 removed outlier: 3.934A pdb=" N THR B 98 " --> pdb=" O LYS B 33 " (cutoff:3.500A) removed outlier: 13.802A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.310A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N HIS B 101 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 105 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N ARG B 213 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 210 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE B 142 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL B 212 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE B 140 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 214 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 90 removed outlier: 4.999A pdb=" N ASP C 78 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY C 105 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL C 80 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL C 103 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB1, first strand: chain 'C' and resid 158 through 162 Processing sheet with id=AB2, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AB3, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.707A pdb=" N VAL E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 5.670A pdb=" N VAL E 136 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU E 131 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR E 138 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL E 129 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL E 140 " --> pdb=" O LYS E 127 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP E 171 " --> pdb=" O LYS E 161 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.846A pdb=" N LEU E 207 " --> pdb=" O LYS E 198 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS E 198 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N HIS E 209 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.964A pdb=" N LEU G 106 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP G 57 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL G 108 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY G 55 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA G 110 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AB8, first strand: chain 'G' and resid 160 through 164 Processing sheet with id=AB9, first strand: chain 'H' and resid 45 through 50 Processing sheet with id=AC1, first strand: chain 'H' and resid 180 through 184 removed outlier: 4.128A pdb=" N GLN H 180 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY H 137 " --> pdb=" O LEU H 153 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.970A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 37 through 38 removed outlier: 4.272A pdb=" N ASN I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 62 through 67 removed outlier: 3.622A pdb=" N GLY I 80 " --> pdb=" O GLN I 103 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE I 101 " --> pdb=" O VAL I 82 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 139 through 140 Processing sheet with id=AC6, first strand: chain 'L' and resid 70 through 80 removed outlier: 18.480A pdb=" N ILE L 70 " --> pdb=" O LEU L 91 " (cutoff:3.500A) removed outlier: 15.729A pdb=" N LEU L 91 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N THR L 72 " --> pdb=" O ALA L 89 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ALA L 89 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR L 74 " --> pdb=" O ARG L 87 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL L 85 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N THR L 78 " --> pdb=" O THR L 83 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR L 83 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 10.290A pdb=" N PHE L 137 " --> pdb=" O ASN L 106 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N VAL L 139 " --> pdb=" O PRO L 108 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N HIS L 110 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LYS L 141 " --> pdb=" O HIS L 110 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL L 139 " --> pdb=" O GLY L 126 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY L 126 " --> pdb=" O VAL L 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V' and resid 15 through 16 removed outlier: 4.026A pdb=" N ARG V 15 " --> pdb=" O ILE V 24 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'V' and resid 32 through 39 removed outlier: 11.487A pdb=" N VAL V 32 " --> pdb=" O THR V 52 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N THR V 52 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 10.288A pdb=" N ILE V 34 " --> pdb=" O TYR V 50 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N TYR V 50 " --> pdb=" O ILE V 34 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N VAL V 36 " --> pdb=" O GLY V 48 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N GLY V 48 " --> pdb=" O VAL V 36 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS V 38 " --> pdb=" O ILE V 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 72 through 74 removed outlier: 5.314A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY W 127 " --> pdb=" O ILE W 103 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 130 through 131 removed outlier: 6.449A pdb=" N LEU X 103 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL X 127 " --> pdb=" O GLU X 101 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU X 101 " --> pdb=" O VAL X 127 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG X 73 " --> pdb=" O LEU X 54 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS X 56 " --> pdb=" O CYS X 71 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS X 71 " --> pdb=" O LYS X 56 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY X 58 " --> pdb=" O ARG X 69 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG X 69 " --> pdb=" O GLY X 58 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU X 60 " --> pdb=" O ALA X 67 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA X 67 " --> pdb=" O GLU X 60 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE X 122 " --> pdb=" O THR X 84 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Y' and resid 6 through 15 removed outlier: 4.566A pdb=" N VAL Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLN Y 22 " --> pdb=" O VAL Y 12 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N SER Y 14 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG Y 20 " --> pdb=" O SER Y 14 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N PHE Y 60 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 39 through 45 removed outlier: 6.671A pdb=" N VAL c 25 " --> pdb=" O ARG c 18 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG c 18 " --> pdb=" O VAL c 25 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLN c 27 " --> pdb=" O LEU c 16 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU c 31 " --> pdb=" O VAL c 12 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL c 12 " --> pdb=" O GLU c 31 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'h' and resid 95 through 100 Processing sheet with id=AD5, first strand: chain 'h' and resid 180 through 186 Processing sheet with id=AD6, first strand: chain 'k' and resid 123 through 128 removed outlier: 6.306A pdb=" N LYS k 84 " --> pdb=" O LYS k 136 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE k 138 " --> pdb=" O LYS k 84 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE k 86 " --> pdb=" O ILE k 138 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'k' and resid 299 through 301 removed outlier: 5.246A pdb=" N VAL k 259 " --> pdb=" O ARG k 283 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG k 283 " --> pdb=" O VAL k 259 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA k 261 " --> pdb=" O THR k 281 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR k 281 " --> pdb=" O ALA k 261 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE k 263 " --> pdb=" O GLU k 279 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE k 563 " --> pdb=" O GLY k 274 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU k 276 " --> pdb=" O ILE k 561 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE k 561 " --> pdb=" O LEU k 276 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ARG k 562 " --> pdb=" O LEU k 303 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU k 303 " --> pdb=" O ARG k 562 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'k' and resid 628 through 631 removed outlier: 6.604A pdb=" N ASN k 595 " --> pdb=" O LEU k 689 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR k 687 " --> pdb=" O SER k 597 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU k 682 " --> pdb=" O LYS k 671 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS k 671 " --> pdb=" O LEU k 682 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'k' and resid 639 through 641 removed outlier: 4.118A pdb=" N LEU k 697 " --> pdb=" O MET k 777 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE k 745 " --> pdb=" O THR k 758 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N THR k 758 " --> pdb=" O ILE k 745 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU k 747 " --> pdb=" O LYS k 756 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL k 714 " --> pdb=" O PHE k 710 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N PHE k 710 " --> pdb=" O VAL k 714 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR k 716 " --> pdb=" O PHE k 708 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'l' and resid 63 through 67 Processing sheet with id=AE2, first strand: chain 'l' and resid 100 through 103 removed outlier: 5.690A pdb=" N THR l 100 " --> pdb=" O LYS l 111 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS l 111 " --> pdb=" O THR l 100 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY l 102 " --> pdb=" O ILE l 109 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU l 190 " --> pdb=" O PRO l 179 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'l' and resid 194 through 196 removed outlier: 4.000A pdb=" N TYR l 195 " --> pdb=" O ILE l 237 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE l 237 " --> pdb=" O TYR l 195 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS l 238 " --> pdb=" O GLY l 248 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY l 248 " --> pdb=" O LYS l 238 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'l' and resid 225 through 227 Processing sheet with id=AE5, first strand: chain 'y' and resid 151 through 156 removed outlier: 3.861A pdb=" N VAL y 206 " --> pdb=" O ILE y 188 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 145 through 148 Processing sheet with id=AE7, first strand: chain 'M' and resid 41 through 43 removed outlier: 4.007A pdb=" N LEU M 59 " --> pdb=" O VAL M 123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 105 through 108 Processing sheet with id=AE9, first strand: chain 'O' and resid 38 through 43 removed outlier: 6.703A pdb=" N VAL O 30 " --> pdb=" O ILE O 39 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG O 41 " --> pdb=" O VAL O 28 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL O 28 " --> pdb=" O ARG O 41 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N THR O 43 " --> pdb=" O THR O 26 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR O 26 " --> pdb=" O THR O 43 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY O 15 " --> pdb=" O HIS O 80 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LYS O 82 " --> pdb=" O GLY O 15 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA O 17 " --> pdb=" O LYS O 82 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ARG O 84 " --> pdb=" O ALA O 17 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE O 19 " --> pdb=" O ARG O 84 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL O 79 " --> pdb=" O GLY O 113 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE O 115 " --> pdb=" O VAL O 79 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL O 81 " --> pdb=" O ILE O 115 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP O 117 " --> pdb=" O VAL O 81 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE O 83 " --> pdb=" O ASP O 117 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 76 through 78 Processing sheet with id=AF2, first strand: chain 'Q' and resid 6 through 9 Processing sheet with id=AF3, first strand: chain 'R' and resid 100 through 102 removed outlier: 6.262A pdb=" N LEU R 100 " --> pdb=" O SER R 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'S' and resid 14 through 17 Processing sheet with id=AF5, first strand: chain 'T' and resid 82 through 86 removed outlier: 4.042A pdb=" N ARG T 86 " --> pdb=" O PRO T 90 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'T' and resid 114 through 117 Processing sheet with id=AF7, first strand: chain 'Z' and resid 90 through 94 removed outlier: 6.798A pdb=" N ILE Z 100 " --> pdb=" O ILE Z 92 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 36 through 42 removed outlier: 3.719A pdb=" N VAL D 85 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL D 48 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR D 87 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 50 " --> pdb=" O TYR D 87 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU D 89 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 148 through 155 Processing sheet with id=AG1, first strand: chain 'U' and resid 20 through 28 removed outlier: 5.545A pdb=" N ILE U 86 " --> pdb=" O THR U 60 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR U 60 " --> pdb=" O ILE U 86 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS U 88 " --> pdb=" O LEU U 58 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 65 through 67 1863 hydrogen bonds defined for protein. 5283 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1214 hydrogen bonds 1976 hydrogen bond angles 0 basepair planarities 494 basepair parallelities 957 stacking parallelities Total time for adding SS restraints: 64.19 Time building geometry restraints manager: 34.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11755 1.33 - 1.45: 31686 1.45 - 1.57: 39097 1.57 - 1.69: 3549 1.69 - 1.81: 189 Bond restraints: 86276 Sorted by residual: bond pdb=" C SER T 117 " pdb=" N PRO T 118 " ideal model delta sigma weight residual 1.337 1.367 -0.031 9.80e-03 1.04e+04 9.78e+00 bond pdb=" C GLU Z 45 " pdb=" N LYS Z 46 " ideal model delta sigma weight residual 1.329 1.377 -0.048 1.79e-02 3.12e+03 7.11e+00 bond pdb=" CD LYS Z 46 " pdb=" CE LYS Z 46 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.21e+00 bond pdb=" C LEU W 26 " pdb=" N ILE W 27 " ideal model delta sigma weight residual 1.330 1.297 0.034 1.48e-02 4.57e+03 5.17e+00 bond pdb=" C THR D 42 " pdb=" N PRO D 43 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.63e+00 ... (remaining 86271 not shown) Histogram of bond angle deviations from ideal: 97.65 - 105.55: 9579 105.55 - 113.45: 51542 113.45 - 121.35: 41937 121.35 - 129.25: 20613 129.25 - 137.15: 1452 Bond angle restraints: 125123 Sorted by residual: angle pdb=" C SER l 183 " pdb=" N ARG l 184 " pdb=" CA ARG l 184 " ideal model delta sigma weight residual 121.54 133.23 -11.69 1.91e+00 2.74e-01 3.75e+01 angle pdb=" C3' U 21343 " pdb=" O3' U 21343 " pdb=" P A 21344 " ideal model delta sigma weight residual 120.20 128.39 -8.19 1.50e+00 4.44e-01 2.98e+01 angle pdb=" C3' C 21156 " pdb=" O3' C 21156 " pdb=" P A 21157 " ideal model delta sigma weight residual 120.20 128.04 -7.84 1.50e+00 4.44e-01 2.73e+01 angle pdb=" C THR l 93 " pdb=" N VAL l 94 " pdb=" CA VAL l 94 " ideal model delta sigma weight residual 121.97 131.18 -9.21 1.80e+00 3.09e-01 2.62e+01 angle pdb=" N ILE H 162 " pdb=" CA ILE H 162 " pdb=" C ILE H 162 " ideal model delta sigma weight residual 113.71 108.93 4.78 9.50e-01 1.11e+00 2.53e+01 ... (remaining 125118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 49230 35.93 - 71.86: 4658 71.86 - 107.79: 513 107.79 - 143.72: 17 143.72 - 179.65: 38 Dihedral angle restraints: 54456 sinusoidal: 38714 harmonic: 15742 Sorted by residual: dihedral pdb=" O4' U 21307 " pdb=" C1' U 21307 " pdb=" N1 U 21307 " pdb=" C2 U 21307 " ideal model delta sinusoidal sigma weight residual 200.00 26.86 173.14 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U 21560 " pdb=" C1' U 21560 " pdb=" N1 U 21560 " pdb=" C2 U 21560 " ideal model delta sinusoidal sigma weight residual -160.00 11.68 -171.68 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U 2 830 " pdb=" C1' U 2 830 " pdb=" N1 U 2 830 " pdb=" C2 U 2 830 " ideal model delta sinusoidal sigma weight residual 200.00 29.30 170.70 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 54453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 13980 0.081 - 0.162: 1414 0.162 - 0.243: 122 0.243 - 0.324: 27 0.324 - 0.405: 4 Chirality restraints: 15547 Sorted by residual: chirality pdb=" C3' G 2 418 " pdb=" C4' G 2 418 " pdb=" O3' G 2 418 " pdb=" C2' G 2 418 " both_signs ideal model delta sigma weight residual False -2.48 -2.07 -0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CB ILE M 89 " pdb=" CA ILE M 89 " pdb=" CG1 ILE M 89 " pdb=" CG2 ILE M 89 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" C1' A 2 215 " pdb=" O4' A 2 215 " pdb=" C2' A 2 215 " pdb=" N9 A 2 215 " both_signs ideal model delta sigma weight residual False 2.46 2.11 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 15544 not shown) Planarity restraints: 9353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG l 184 " -0.016 2.00e-02 2.50e+03 3.31e-02 1.09e+01 pdb=" C ARG l 184 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG l 184 " -0.021 2.00e-02 2.50e+03 pdb=" N HIS l 185 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 62 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C VAL F 62 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL F 62 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN F 63 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 447 " 0.042 2.00e-02 2.50e+03 2.08e-02 9.73e+00 pdb=" N1 U 2 447 " -0.040 2.00e-02 2.50e+03 pdb=" C2 U 2 447 " -0.007 2.00e-02 2.50e+03 pdb=" O2 U 2 447 " -0.006 2.00e-02 2.50e+03 pdb=" N3 U 2 447 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U 2 447 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U 2 447 " 0.018 2.00e-02 2.50e+03 pdb=" C5 U 2 447 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U 2 447 " -0.005 2.00e-02 2.50e+03 ... (remaining 9350 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 12450 2.76 - 3.29: 70566 3.29 - 3.83: 161025 3.83 - 4.36: 185554 4.36 - 4.90: 268440 Nonbonded interactions: 698035 Sorted by model distance: nonbonded pdb=" O2' C 21537 " pdb=" O6 G 21540 " model vdw 2.223 2.440 nonbonded pdb=" O2' G 2 610 " pdb=" O2' G 2 613 " model vdw 2.224 2.440 nonbonded pdb=" O2' U 2 861 " pdb=" O HIS W 56 " model vdw 2.228 2.440 nonbonded pdb=" O6 G 21273 " pdb=" O4 U 21437 " model vdw 2.248 2.432 nonbonded pdb=" O6 G 21295 " pdb=" O4 U 21302 " model vdw 2.252 3.040 ... (remaining 698030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 13.840 Check model and map are aligned: 0.880 Set scattering table: 0.560 Process input model: 214.580 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 237.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 0.073 86276 Z= 0.348 Angle : 0.969 15.829 125123 Z= 0.491 Chirality : 0.051 0.405 15547 Planarity : 0.006 0.072 9353 Dihedral : 22.062 179.651 44274 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 0.28 % Allowed : 3.18 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.01 (0.10), residues: 5360 helix: -1.88 (0.09), residues: 1877 sheet: -1.54 (0.16), residues: 942 loop : -2.19 (0.11), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP N 139 HIS 0.017 0.003 HIS P 79 PHE 0.030 0.003 PHE l 254 TYR 0.036 0.003 TYR A 202 ARG 0.040 0.001 ARG Z 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 682 time to evaluate : 4.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 29 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8346 (mtmt) REVERT: B 228 LEU cc_start: 0.7941 (mt) cc_final: 0.7691 (tp) REVERT: C 201 ASN cc_start: 0.8053 (t0) cc_final: 0.7793 (t0) REVERT: G 73 ILE cc_start: 0.9292 (tp) cc_final: 0.9061 (mm) REVERT: H 87 ASP cc_start: 0.8299 (m-30) cc_final: 0.7782 (m-30) REVERT: I 120 THR cc_start: 0.8508 (m) cc_final: 0.8210 (t) REVERT: W 111 MET cc_start: 0.8845 (pmt) cc_final: 0.8193 (pmt) REVERT: X 14 LYS cc_start: 0.8961 (tptp) cc_final: 0.8760 (tppt) REVERT: c 38 ARG cc_start: 0.6046 (mtt180) cc_final: 0.5716 (tpt-90) REVERT: h 211 LYS cc_start: 0.9147 (mttt) cc_final: 0.8607 (tttt) REVERT: k 474 ASP cc_start: 0.8746 (m-30) cc_final: 0.8381 (p0) REVERT: k 600 ARG cc_start: 0.7119 (ttm-80) cc_final: 0.6618 (ttt-90) REVERT: k 690 ASN cc_start: 0.9131 (m-40) cc_final: 0.8603 (t0) REVERT: l 122 MET cc_start: 0.9144 (ttp) cc_final: 0.8790 (ptm) REVERT: l 195 TYR cc_start: 0.7736 (m-80) cc_final: 0.7445 (m-80) REVERT: y 169 ASP cc_start: 0.7041 (m-30) cc_final: 0.6065 (m-30) REVERT: y 189 MET cc_start: 0.0454 (tpp) cc_final: 0.0252 (ttt) REVERT: y 249 ASP cc_start: 0.8249 (m-30) cc_final: 0.7944 (m-30) REVERT: y 254 ASN cc_start: 0.8967 (m-40) cc_final: 0.8347 (t0) REVERT: y 272 SER cc_start: 0.2600 (m) cc_final: 0.2045 (p) REVERT: F 31 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8535 (tp30) REVERT: F 43 PHE cc_start: 0.4358 (OUTLIER) cc_final: 0.2453 (m-10) REVERT: P 57 MET cc_start: 0.6450 (mmp) cc_final: 0.4693 (mtt) REVERT: P 123 TYR cc_start: 0.7924 (p90) cc_final: 0.7397 (p90) REVERT: Q 49 TYR cc_start: 0.7987 (m-80) cc_final: 0.7515 (m-80) REVERT: Q 118 ILE cc_start: 0.8903 (mt) cc_final: 0.8629 (pt) REVERT: R 27 ASP cc_start: 0.8696 (t70) cc_final: 0.8490 (p0) REVERT: S 74 GLN cc_start: 0.7746 (mp10) cc_final: 0.7321 (mm-40) REVERT: S 75 ASN cc_start: 0.9322 (m-40) cc_final: 0.9006 (t0) REVERT: T 67 MET cc_start: 0.5974 (mtm) cc_final: 0.5747 (mmt) REVERT: Z 68 ARG cc_start: 0.8437 (mmp-170) cc_final: 0.7900 (ptt180) REVERT: Z 70 LYS cc_start: 0.7304 (mttp) cc_final: 0.6846 (mtpt) REVERT: Z 71 ILE cc_start: 0.2908 (pt) cc_final: 0.1774 (pt) REVERT: D 38 GLU cc_start: 0.8072 (tt0) cc_final: 0.7687 (tp30) REVERT: D 70 THR cc_start: 0.5632 (m) cc_final: 0.5273 (p) REVERT: D 105 MET cc_start: 0.5452 (tpp) cc_final: 0.4987 (mmm) REVERT: D 127 MET cc_start: 0.3512 (mmm) cc_final: 0.3178 (mmm) REVERT: D 177 MET cc_start: 0.0179 (mtp) cc_final: -0.0292 (ppp) outliers start: 13 outliers final: 6 residues processed: 695 average time/residue: 0.8629 time to fit residues: 967.1103 Evaluate side-chains 315 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 308 time to evaluate : 4.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain M residue 115 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 597 optimal weight: 10.0000 chunk 535 optimal weight: 4.9990 chunk 297 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 361 optimal weight: 0.6980 chunk 286 optimal weight: 5.9990 chunk 554 optimal weight: 0.7980 chunk 214 optimal weight: 8.9990 chunk 336 optimal weight: 6.9990 chunk 412 optimal weight: 2.9990 chunk 642 optimal weight: 8.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 51 ASN A 46 HIS A 69 ASN A 163 ASN B 160 HIS ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 87 GLN C 108 ASN C 147 ASN E 50 ASN E 98 ASN E 112 HIS E 157 ASN E 197 HIS G 190 GLN G 201 GLN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN I 32 GLN I 84 HIS I 87 ASN I 138 ASN J 139 GLN L 8 GLN L 104 HIS N 105 ASN N 138 ASN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 ASN ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS W 80 ASN W 98 GLN X 10 ASN X 22 ASN X 48 HIS ** X 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 99 ASN Y 29 HIS Y 31 ASN c 27 GLN c 43 ASN d 27 HIS ** h 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 239 HIS i 269 ASN k 147 ASN k 228 ASN k 251 ASN k 288 ASN k 513 GLN k 640 HIS ** k 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 29 HIS l 39 GLN ** l 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 ASN l 99 ASN l 125 HIS l 262 HIS ** y 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 262 ASN ** y 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 ASN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 HIS ** F 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN R 101 ASN R 123 ASN T 43 ASN ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 86276 Z= 0.207 Angle : 0.648 13.226 125123 Z= 0.330 Chirality : 0.039 0.332 15547 Planarity : 0.005 0.056 9353 Dihedral : 24.364 179.792 33419 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.70 % Favored : 95.28 % Rotamer: Outliers : 2.02 % Allowed : 7.70 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.11), residues: 5360 helix: -0.20 (0.11), residues: 1962 sheet: -1.21 (0.16), residues: 946 loop : -1.79 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP l 151 HIS 0.008 0.001 HIS W 56 PHE 0.025 0.002 PHE F 82 TYR 0.023 0.001 TYR S 30 ARG 0.010 0.001 ARG Y 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 350 time to evaluate : 4.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 51 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6631 (p0) REVERT: B 194 ASN cc_start: 0.8620 (p0) cc_final: 0.7752 (m-40) REVERT: C 201 ASN cc_start: 0.8024 (t0) cc_final: 0.7791 (t0) REVERT: C 205 ARG cc_start: 0.6649 (mtp85) cc_final: 0.6276 (mmm-85) REVERT: E 40 GLU cc_start: 0.7317 (pp20) cc_final: 0.7062 (pp20) REVERT: G 73 ILE cc_start: 0.9259 (tp) cc_final: 0.9044 (mm) REVERT: H 87 ASP cc_start: 0.8058 (m-30) cc_final: 0.7793 (m-30) REVERT: J 143 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8801 (mt) REVERT: W 111 MET cc_start: 0.8856 (pmt) cc_final: 0.8313 (pmt) REVERT: c 38 ARG cc_start: 0.5865 (mtt180) cc_final: 0.5623 (tpt170) REVERT: d 55 PHE cc_start: 0.7940 (m-80) cc_final: 0.7600 (p90) REVERT: h 211 LYS cc_start: 0.9298 (mttt) cc_final: 0.8733 (tmmt) REVERT: h 242 MET cc_start: 0.7934 (mmm) cc_final: 0.7162 (ptt) REVERT: k 474 ASP cc_start: 0.8690 (m-30) cc_final: 0.8390 (p0) REVERT: k 600 ARG cc_start: 0.7331 (ttm-80) cc_final: 0.6709 (ttp-170) REVERT: k 690 ASN cc_start: 0.9088 (m-40) cc_final: 0.8721 (t0) REVERT: l 122 MET cc_start: 0.9052 (ttp) cc_final: 0.8671 (ptm) REVERT: l 236 MET cc_start: 0.7973 (tmm) cc_final: 0.7454 (tmm) REVERT: y 181 MET cc_start: 0.7984 (ttm) cc_final: 0.7599 (ttm) REVERT: y 254 ASN cc_start: 0.8941 (m-40) cc_final: 0.8344 (t0) REVERT: F 31 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8568 (tp30) REVERT: F 43 PHE cc_start: 0.4258 (OUTLIER) cc_final: 0.3763 (m-10) REVERT: F 98 MET cc_start: 0.6122 (tmm) cc_final: 0.5705 (tmm) REVERT: M 137 MET cc_start: 0.0552 (mtp) cc_final: 0.0212 (mtp) REVERT: P 57 MET cc_start: 0.6073 (mmp) cc_final: 0.4891 (mtt) REVERT: P 123 TYR cc_start: 0.8115 (p90) cc_final: 0.7537 (p90) REVERT: R 27 ASP cc_start: 0.8435 (t70) cc_final: 0.8108 (p0) REVERT: R 78 ARG cc_start: 0.5751 (mtt180) cc_final: 0.4990 (ttp80) REVERT: S 23 ASP cc_start: 0.9446 (m-30) cc_final: 0.9222 (t0) REVERT: Z 68 ARG cc_start: 0.8146 (mmp-170) cc_final: 0.7940 (ptt180) REVERT: Z 71 ILE cc_start: 0.3060 (pt) cc_final: 0.1745 (pt) REVERT: D 127 MET cc_start: 0.3353 (mmm) cc_final: 0.3095 (mmm) REVERT: D 177 MET cc_start: 0.0094 (mtp) cc_final: -0.0401 (ppp) outliers start: 94 outliers final: 46 residues processed: 422 average time/residue: 0.8214 time to fit residues: 579.5837 Evaluate side-chains 325 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 276 time to evaluate : 4.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 102 VAL Chi-restraints excluded: chain X residue 27 ASN Chi-restraints excluded: chain X residue 71 CYS Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain d residue 43 PHE Chi-restraints excluded: chain h residue 99 ILE Chi-restraints excluded: chain h residue 238 THR Chi-restraints excluded: chain i residue 265 LEU Chi-restraints excluded: chain i residue 293 THR Chi-restraints excluded: chain k residue 157 PHE Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain l residue 197 MET Chi-restraints excluded: chain l residue 227 HIS Chi-restraints excluded: chain y residue 151 SER Chi-restraints excluded: chain y residue 221 ASN Chi-restraints excluded: chain y residue 238 ILE Chi-restraints excluded: chain y residue 247 VAL Chi-restraints excluded: chain y residue 299 ASP Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain T residue 23 GLN Chi-restraints excluded: chain Z residue 48 ASP Chi-restraints excluded: chain Z residue 56 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 141 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 356 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 534 optimal weight: 8.9990 chunk 437 optimal weight: 50.0000 chunk 177 optimal weight: 10.0000 chunk 643 optimal weight: 5.9990 chunk 694 optimal weight: 0.8980 chunk 572 optimal weight: 50.0000 chunk 637 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 515 optimal weight: 50.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN H 42 GLN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 37 ASN ** k 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 262 ASN ** y 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 HIS T 48 GLN ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 86276 Z= 0.333 Angle : 0.722 17.099 125123 Z= 0.364 Chirality : 0.042 0.345 15547 Planarity : 0.006 0.055 9353 Dihedral : 24.389 179.698 33419 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.14 % Favored : 93.82 % Rotamer: Outliers : 2.36 % Allowed : 8.86 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % 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: -1.41 (0.11), residues: 5360 helix: 0.18 (0.11), residues: 1946 sheet: -1.21 (0.16), residues: 931 loop : -1.71 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 67 HIS 0.015 0.002 HIS W 56 PHE 0.023 0.002 PHE I 27 TYR 0.023 0.002 TYR I 55 ARG 0.007 0.001 ARG l 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 285 time to evaluate : 4.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 ASN cc_start: 0.8676 (p0) cc_final: 0.7908 (m-40) REVERT: E 87 MET cc_start: 0.8449 (mmm) cc_final: 0.7914 (mmm) REVERT: H 87 ASP cc_start: 0.8128 (m-30) cc_final: 0.7912 (m-30) REVERT: J 143 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8899 (mt) REVERT: c 38 ARG cc_start: 0.6052 (mtt180) cc_final: 0.5658 (tpt170) REVERT: c 40 ILE cc_start: 0.0110 (OUTLIER) cc_final: -0.1853 (mt) REVERT: d 55 PHE cc_start: 0.8207 (m-80) cc_final: 0.7784 (p90) REVERT: h 211 LYS cc_start: 0.9461 (mttt) cc_final: 0.9082 (ptmt) REVERT: k 474 ASP cc_start: 0.8777 (m-30) cc_final: 0.8496 (p0) REVERT: k 559 MET cc_start: 0.8104 (ptp) cc_final: 0.7175 (ttt) REVERT: k 600 ARG cc_start: 0.7309 (ttm-80) cc_final: 0.6752 (ttt-90) REVERT: k 690 ASN cc_start: 0.9046 (m-40) cc_final: 0.8723 (t0) REVERT: l 122 MET cc_start: 0.9069 (ttp) cc_final: 0.8680 (ptm) REVERT: l 201 ARG cc_start: 0.4215 (mmt180) cc_final: 0.3714 (mmp-170) REVERT: l 236 MET cc_start: 0.8147 (tmm) cc_final: 0.7648 (tmm) REVERT: y 254 ASN cc_start: 0.8977 (m-40) cc_final: 0.8454 (t0) REVERT: y 262 ASN cc_start: 0.8900 (m-40) cc_final: 0.8093 (t0) REVERT: F 31 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8510 (tp30) REVERT: F 43 PHE cc_start: 0.5062 (OUTLIER) cc_final: 0.4361 (m-10) REVERT: M 96 GLN cc_start: 0.8530 (mp10) cc_final: 0.8226 (mp10) REVERT: M 122 VAL cc_start: 0.0480 (OUTLIER) cc_final: 0.0231 (t) REVERT: P 57 MET cc_start: 0.6435 (mmp) cc_final: 0.5965 (mtt) REVERT: P 89 MET cc_start: 0.0690 (ppp) cc_final: -0.1703 (tpt) REVERT: P 123 TYR cc_start: 0.8258 (p90) cc_final: 0.7704 (p90) REVERT: R 78 ARG cc_start: 0.5486 (mtt180) cc_final: 0.4867 (ttp80) REVERT: S 104 ASN cc_start: 0.7071 (t0) cc_final: 0.6734 (p0) REVERT: T 67 MET cc_start: 0.3460 (mmt) cc_final: 0.2058 (mpp) REVERT: Z 70 LYS cc_start: 0.7655 (mttp) cc_final: 0.7131 (mtpt) REVERT: Z 71 ILE cc_start: 0.3239 (pt) cc_final: 0.2069 (pt) REVERT: D 105 MET cc_start: 0.4193 (tpp) cc_final: 0.3003 (mmm) REVERT: D 127 MET cc_start: 0.3138 (mmm) cc_final: 0.2899 (mmm) REVERT: D 177 MET cc_start: 0.0663 (mtp) cc_final: 0.0350 (ttp) outliers start: 110 outliers final: 63 residues processed: 379 average time/residue: 0.8410 time to fit residues: 548.2981 Evaluate side-chains 310 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 243 time to evaluate : 4.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 55 THR Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 174 LYS Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 66 ASN Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain W residue 102 VAL Chi-restraints excluded: chain X residue 27 ASN Chi-restraints excluded: chain X residue 71 CYS Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain Y residue 38 ASP Chi-restraints excluded: chain c residue 40 ILE Chi-restraints excluded: chain h residue 99 ILE Chi-restraints excluded: chain h residue 199 SER Chi-restraints excluded: chain h residue 238 THR Chi-restraints excluded: chain i residue 265 LEU Chi-restraints excluded: chain i residue 293 THR Chi-restraints excluded: chain i residue 311 LEU Chi-restraints excluded: chain k residue 75 LEU Chi-restraints excluded: chain k residue 536 ASN Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain l residue 152 MET Chi-restraints excluded: chain l residue 235 ILE Chi-restraints excluded: chain y residue 151 SER Chi-restraints excluded: chain y residue 169 ASP Chi-restraints excluded: chain y residue 221 ASN Chi-restraints excluded: chain y residue 238 ILE Chi-restraints excluded: chain y residue 247 VAL Chi-restraints excluded: chain y residue 249 ASP Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain R residue 32 LYS Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 75 ASN Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain Z residue 56 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain U residue 62 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 635 optimal weight: 30.0000 chunk 483 optimal weight: 1.9990 chunk 333 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 chunk 431 optimal weight: 4.9990 chunk 645 optimal weight: 10.0000 chunk 683 optimal weight: 6.9990 chunk 337 optimal weight: 6.9990 chunk 611 optimal weight: 1.9990 chunk 184 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 ASN h 111 ASN k 255 ASN ** k 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 647 HIS ** l 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 GLN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 75 ASN S 78 HIS ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 86276 Z= 0.196 Angle : 0.608 13.924 125123 Z= 0.308 Chirality : 0.038 0.320 15547 Planarity : 0.004 0.053 9353 Dihedral : 24.241 179.793 33418 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.06 % Favored : 94.93 % Rotamer: Outliers : 2.02 % Allowed : 10.06 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.11), residues: 5360 helix: 0.59 (0.12), residues: 1956 sheet: -0.98 (0.16), residues: 950 loop : -1.54 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 126 HIS 0.008 0.001 HIS W 56 PHE 0.028 0.001 PHE C 66 TYR 0.021 0.001 TYR O 58 ARG 0.006 0.000 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10720 Ramachandran restraints generated. 5360 Oldfield, 0 Emsley, 5360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 283 time to evaluate : 4.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 ASN cc_start: 0.6915 (t0) cc_final: 0.6674 (t0) REVERT: B 194 ASN cc_start: 0.8668 (p0) cc_final: 0.8011 (m-40) REVERT: C 205 ARG cc_start: 0.7081 (mmm-85) cc_final: 0.6507 (mmm-85) REVERT: E 87 MET cc_start: 0.8329 (mmm) cc_final: 0.7872 (mmm) REVERT: H 87 ASP cc_start: 0.8158 (m-30) cc_final: 0.7956 (m-30) REVERT: J 143 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8961 (mt) REVERT: c 38 ARG cc_start: 0.6061 (mtt180) cc_final: 0.5735 (tpt170) REVERT: c 40 ILE cc_start: 0.0449 (OUTLIER) cc_final: -0.1714 (mt) REVERT: d 55 PHE cc_start: 0.8147 (m-80) cc_final: 0.7252 (m-80) REVERT: h 112 SER cc_start: 0.8572 (m) cc_final: 0.8244 (p) REVERT: h 211 LYS cc_start: 0.9493 (mttt) cc_final: 0.9111 (ptmt) REVERT: h 242 MET cc_start: 0.7978 (mmm) cc_final: 0.7710 (mmm) REVERT: k 474 ASP cc_start: 0.8775 (m-30) cc_final: 0.8373 (p0) REVERT: k 475 MET cc_start: 0.5673 (tpt) cc_final: 0.5469 (tpt) REVERT: k 600 ARG cc_start: 0.7464 (ttm-80) cc_final: 0.6689 (ttt-90) REVERT: k 690 ASN cc_start: 0.8959 (m-40) cc_final: 0.8676 (t0) REVERT: k 783 LEU cc_start: 0.9221 (pp) cc_final: 0.8931 (tp) REVERT: l 122 MET cc_start: 0.9099 (ttp) cc_final: 0.8807 (ptm) REVERT: l 236 MET cc_start: 0.8055 (tmm) cc_final: 0.7633 (tmm) REVERT: y 262 ASN cc_start: 0.8969 (m-40) cc_final: 0.8200 (t0) REVERT: F 31 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8455 (tp30) REVERT: F 43 PHE cc_start: 0.5284 (OUTLIER) cc_final: 0.4472 (m-10) REVERT: M 96 GLN cc_start: 0.8648 (mp10) cc_final: 0.8445 (mp10) REVERT: M 137 MET cc_start: -0.1754 (mtt) cc_final: -0.2541 (mtt) REVERT: O 115 ILE cc_start: 0.9040 (tp) cc_final: 0.8838 (mm) REVERT: P 57 MET cc_start: 0.5810 (mmp) cc_final: 0.5299 (mtt) REVERT: P 80 MET cc_start: 0.7266 (tpt) cc_final: 0.6666 (tpt) REVERT: P 89 MET cc_start: 0.0488 (ppp) cc_final: -0.1867 (tpt) REVERT: P 111 MET cc_start: 0.1214 (mtp) cc_final: 0.0682 (ptp) REVERT: P 123 TYR cc_start: 0.8238 (p90) cc_final: 0.7655 (p90) REVERT: R 78 ARG cc_start: 0.5417 (mtt180) cc_final: 0.4813 (ttp80) REVERT: S 67 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8349 (pp20) REVERT: Z 69 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5877 (mm) REVERT: D 105 MET cc_start: 0.3718 (tpp) cc_final: 0.2447 (mmm) REVERT: D 127 MET cc_start: 0.3088 (mmm) cc_final: 0.2773 (mmm) outliers start: 94 outliers final: 53 residues processed: 365 average time/residue: 0.7689 time to fit residues: 483.3317 Evaluate side-chains 308 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 251 time to evaluate : 4.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 9 HIS Chi-restraints excluded: chain e residue 5 HIS Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 8 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 216 LYS Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 174 LYS Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 102 VAL Chi-restraints excluded: chain X residue 27 ASN Chi-restraints excluded: chain X residue 71 CYS Chi-restraints excluded: chain X residue 87 VAL Chi-restraints excluded: chain c residue 40 ILE Chi-restraints excluded: chain h residue 99 ILE Chi-restraints excluded: chain i residue 293 THR Chi-restraints excluded: chain i residue 311 LEU Chi-restraints excluded: chain k residue 75 LEU Chi-restraints excluded: chain k residue 157 PHE Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain l residue 152 MET Chi-restraints excluded: chain l residue 176 VAL Chi-restraints excluded: chain y residue 151 SER Chi-restraints excluded: chain y residue 169 ASP Chi-restraints excluded: chain y residue 221 ASN Chi-restraints excluded: chain y residue 244 SER Chi-restraints excluded: chain y residue 247 VAL Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 74 LEU Chi-restraints excluded: chain M residue 115 VAL Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 32 LYS Chi-restraints excluded: chain S residue 75 ASN Chi-restraints excluded: chain Z residue 49 ARG Chi-restraints excluded: chain Z residue 69 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain U residue 62 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.1273 > 50: distance: 8 - 11: 31.218 distance: 11 - 12: 37.915 distance: 12 - 13: 39.976 distance: 12 - 15: 21.173 distance: 13 - 22: 56.401 distance: 15 - 16: 48.794 distance: 16 - 17: 17.363 distance: 17 - 18: 28.679 distance: 18 - 19: 7.789 distance: 19 - 21: 7.138 distance: 22 - 23: 39.539 distance: 23 - 24: 55.788 distance: 24 - 25: 35.950 distance: 27 - 28: 32.150 distance: 28 - 29: 22.300 distance: 28 - 31: 18.459 distance: 29 - 30: 39.652 distance: 29 - 36: 38.035 distance: 31 - 32: 18.297 distance: 32 - 33: 13.765 distance: 33 - 34: 12.177 distance: 33 - 35: 12.885 distance: 36 - 37: 38.166 distance: 37 - 38: 59.633 distance: 37 - 40: 39.128 distance: 38 - 39: 45.712 distance: 38 - 45: 59.245 distance: 40 - 41: 27.721 distance: 41 - 42: 20.366 distance: 42 - 43: 27.822 distance: 43 - 44: 16.052 distance: 45 - 46: 56.998 distance: 45 - 51: 52.817 distance: 46 - 47: 41.209 distance: 46 - 49: 58.316 distance: 47 - 48: 51.055 distance: 47 - 52: 56.161 distance: 49 - 50: 18.461 distance: 50 - 51: 42.792 distance: 52 - 53: 39.799 distance: 53 - 54: 56.127 distance: 54 - 55: 39.853 distance: 56 - 57: 38.858 distance: 58 - 59: 33.048 distance: 59 - 60: 21.405 distance: 62 - 63: 40.345 distance: 62 - 65: 41.085 distance: 63 - 64: 39.154 distance: 63 - 70: 36.090 distance: 65 - 66: 40.134 distance: 66 - 67: 56.371 distance: 67 - 68: 46.384 distance: 68 - 69: 8.066 distance: 70 - 71: 41.491 distance: 70 - 76: 47.572 distance: 71 - 72: 53.532 distance: 71 - 74: 56.933 distance: 72 - 73: 6.249 distance: 72 - 77: 39.538 distance: 74 - 75: 39.917 distance: 75 - 76: 44.723 distance: 77 - 78: 54.931 distance: 78 - 79: 40.951 distance: 78 - 81: 54.262 distance: 79 - 80: 39.283 distance: 79 - 86: 57.025 distance: 81 - 82: 69.572 distance: 82 - 83: 37.260 distance: 83 - 84: 23.759 distance: 84 - 85: 15.988 distance: 86 - 87: 40.808 distance: 87 - 88: 40.460 distance: 88 - 90: 34.360 distance: 89 - 111: 35.580