Starting phenix.real_space_refine on Sun Nov 19 18:33:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbd_4792/11_2023/6rbd_4792.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbd_4792/11_2023/6rbd_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_4792/11_2023/6rbd_4792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbd_4792/11_2023/6rbd_4792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbd_4792/11_2023/6rbd_4792.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rbd_4792/11_2023/6rbd_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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 30.70, per 1000 atoms: 0.38 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: 30.67 Conformation dependent library (CDL) restraints added in 6.3 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: 27.24 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: 62.17 Time building geometry restraints manager: 33.51 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: 46186 35.93 - 71.86: 1908 71.86 - 107.79: 207 107.79 - 143.72: 17 143.72 - 179.65: 38 Dihedral angle restraints: 48356 sinusoidal: 32614 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 48353 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: 4.930 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: 0.090 Extract box with map and model: 14.210 Check model and map are aligned: 0.880 Set scattering table: 0.560 Process input model: 213.580 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.200 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 238.920 ------------------------------------------------------------------------------- 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 : 16.652 179.651 38174 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 *********************** 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 : 4.796 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 outliers start: 13 outliers final: 6 residues processed: 695 average time/residue: 0.8845 time to fit residues: 997.0294 Evaluate side-chains 299 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 293 time to evaluate : 5.002 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.5485 time to fit residues: 12.0000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 642 optimal weight: 0.7980 overall best weight: 2.6584 ------------------------------------------------------------------------------- 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 39 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 ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 h 239 HIS i 269 ASN k 56 ASN k 147 ASN k 228 ASN k 251 ASN k 288 ASN k 513 GLN k 640 HIS k 647 HIS ** k 766 GLN ** 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 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 ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 78 HIS T 43 ASN ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1720 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= 0.197 Angle : 0.645 13.417 125123 Z= 0.328 Chirality : 0.039 0.330 15547 Planarity : 0.005 0.057 9353 Dihedral : 18.248 179.987 27310 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.74 % Favored : 95.24 % Rotamer: Outliers : 1.97 % Allowed : 8.13 % Favored : 89.89 % 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: -1.67 (0.11), residues: 5360 helix: -0.20 (0.11), residues: 1956 sheet: -1.17 (0.16), residues: 946 loop : -1.79 (0.12), residues: 2458 *********************** 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 437 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 345 time to evaluate : 4.862 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 outliers start: 92 outliers final: 41 residues processed: 414 average time/residue: 0.8230 time to fit residues: 574.0716 Evaluate side-chains 314 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 273 time to evaluate : 4.772 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 1 residues processed: 41 average time/residue: 0.6146 time to fit residues: 53.2915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 356 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 chunk 534 optimal weight: 9.9990 chunk 437 optimal weight: 50.0000 chunk 177 optimal weight: 10.0000 chunk 643 optimal weight: 10.0000 chunk 694 optimal weight: 4.9990 chunk 572 optimal weight: 50.0000 chunk 637 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 515 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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** A 46 HIS ** 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** C 87 GLN E 197 HIS E 216 ASN G 56 ASN H 42 GLN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** h 131 ASN k 56 ASN k 255 ASN k 576 GLN ** k 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 766 GLN ** l 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 262 ASN ** y 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 GLN ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 159 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 86276 Z= 0.394 Angle : 0.783 21.590 125123 Z= 0.394 Chirality : 0.044 0.339 15547 Planarity : 0.006 0.061 9353 Dihedral : 18.620 179.741 27310 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.46 % Favored : 93.53 % Rotamer: Outliers : 1.85 % Allowed : 9.46 % Favored : 88.69 % 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: -1.55 (0.11), residues: 5360 helix: 0.01 (0.11), residues: 1950 sheet: -1.28 (0.16), residues: 914 loop : -1.74 (0.12), residues: 2496 *********************** 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 367 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 281 time to evaluate : 6.052 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 outliers start: 86 outliers final: 39 residues processed: 353 average time/residue: 0.8437 time to fit residues: 517.6580 Evaluate side-chains 270 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 231 time to evaluate : 4.715 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 1 residues processed: 39 average time/residue: 0.6872 time to fit residues: 55.7622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 707 random chunks: chunk 635 optimal weight: 7.9990 chunk 483 optimal weight: 3.9990 chunk 333 optimal weight: 0.3980 chunk 71 optimal weight: 8.9990 chunk 306 optimal weight: 2.9990 chunk 431 optimal weight: 20.0000 chunk 645 optimal weight: 4.9990 chunk 683 optimal weight: 30.0000 chunk 337 optimal weight: 1.9990 chunk 611 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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 40 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN ** 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** ** Y 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 ASN h 111 ASN ** k 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 GLN ** l 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 180 GLN 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 95 ASN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN ** S 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS ** U 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 86276 Z= 0.198 Angle : 0.620 14.474 125123 Z= 0.315 Chirality : 0.038 0.314 15547 Planarity : 0.004 0.054 9353 Dihedral : 18.300 179.083 27310 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.34 % Favored : 94.65 % Rotamer: Outliers : 1.20 % Allowed : 11.01 % Favored : 87.79 % 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: -1.07 (0.11), residues: 5360 helix: 0.51 (0.12), residues: 1960 sheet: -1.04 (0.16), residues: 936 loop : -1.57 (0.12), residues: 2464 *********************** 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 321 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 265 time to evaluate : 4.689 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 outliers start: 56 outliers final: 24 residues processed: 312 average time/residue: 0.7629 time to fit residues: 414.6443 Evaluate side-chains 252 residues out of total 4688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 228 time to evaluate : 4.693 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.5904 time to fit residues: 32.6862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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: 67.5498 > 50: distance: 8 - 11: 25.903 distance: 12 - 13: 14.868 distance: 12 - 15: 22.671 distance: 13 - 14: 31.167 distance: 13 - 22: 21.533 distance: 15 - 16: 13.979 distance: 16 - 17: 14.499 distance: 17 - 18: 4.395 distance: 22 - 23: 13.025 distance: 23 - 24: 21.248 distance: 23 - 26: 18.685 distance: 24 - 25: 6.695 distance: 27 - 28: 5.887 distance: 28 - 29: 11.480 distance: 28 - 31: 4.331 distance: 29 - 30: 27.409 distance: 29 - 36: 18.747 distance: 31 - 32: 6.398 distance: 32 - 33: 3.990 distance: 36 - 37: 11.853 distance: 37 - 38: 38.691 distance: 37 - 40: 33.456 distance: 38 - 39: 34.311 distance: 38 - 45: 44.576 distance: 40 - 41: 6.693 distance: 41 - 42: 6.744 distance: 42 - 43: 3.996 distance: 45 - 46: 50.196 distance: 45 - 51: 29.966 distance: 46 - 47: 22.939 distance: 46 - 49: 42.387 distance: 47 - 48: 14.273 distance: 47 - 52: 37.068 distance: 49 - 50: 39.139 distance: 50 - 51: 23.970 distance: 52 - 53: 31.832 distance: 53 - 54: 42.978 distance: 53 - 56: 21.345 distance: 54 - 55: 26.968 distance: 54 - 61: 37.905 distance: 56 - 57: 8.322 distance: 57 - 58: 16.156 distance: 58 - 59: 12.024 distance: 62 - 63: 29.924 distance: 62 - 65: 66.981 distance: 63 - 64: 22.586 distance: 63 - 70: 21.479 distance: 65 - 66: 35.083 distance: 66 - 67: 40.849 distance: 67 - 68: 17.863 distance: 68 - 69: 8.844 distance: 70 - 71: 24.627 distance: 70 - 76: 22.706 distance: 71 - 72: 22.833 distance: 71 - 74: 16.192 distance: 72 - 73: 39.193 distance: 72 - 77: 47.445 distance: 74 - 75: 19.996 distance: 75 - 76: 25.723 distance: 77 - 78: 16.850 distance: 78 - 79: 14.744 distance: 78 - 81: 32.977 distance: 79 - 80: 33.939 distance: 79 - 86: 35.087 distance: 81 - 82: 18.359 distance: 82 - 83: 10.401 distance: 83 - 84: 5.689 distance: 86 - 87: 25.961 distance: 87 - 88: 39.615 distance: 88 - 89: 3.676 distance: 88 - 90: 28.174 distance: 89 - 113: 26.570