Starting phenix.real_space_refine on Sat Mar 16 15:02:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdr_21644/03_2024/6wdr_21644.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdr_21644/03_2024/6wdr_21644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdr_21644/03_2024/6wdr_21644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdr_21644/03_2024/6wdr_21644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdr_21644/03_2024/6wdr_21644.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wdr_21644/03_2024/6wdr_21644.pdb" } resolution = 3.7 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= 0.000 sd= 0.004 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 1647 5.49 5 S 90 5.16 5 C 40630 2.51 5 N 13443 2.21 5 O 18663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 71": "OE1" <-> "OE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 151": "OD1" <-> "OD2" Residue "E TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 135": "OD1" <-> "OD2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F GLU 181": "OE1" <-> "OE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F ASP 215": "OD1" <-> "OD2" Residue "F ARG 219": "NH1" <-> "NH2" Residue "G ASP 19": "OD1" <-> "OD2" 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 GLU 150": "OE1" <-> "OE2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G ARG 191": "NH1" <-> "NH2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H ASP 87": "OD1" <-> "OD2" Residue "H PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 47": "NH1" <-> "NH2" Residue "I GLU 114": "OE1" <-> "OE2" Residue "I TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 164": "NH1" <-> "NH2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "J ARG 3": "NH1" <-> "NH2" Residue "J PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 53": "NH1" <-> "NH2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ASP 58": "OD1" <-> "OD2" Residue "J ARG 62": "NH1" <-> "NH2" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 186": "OE1" <-> "OE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ASP 55": "OD1" <-> "OD2" Residue "L TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 26": "OD1" <-> "OD2" Residue "M GLU 83": "OE1" <-> "OE2" Residue "M ASP 131": "OD1" <-> "OD2" Residue "N PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 31": "OE1" <-> "OE2" Residue "N TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 104": "NH1" <-> "NH2" Residue "N ARG 106": "NH1" <-> "NH2" Residue "N TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P GLU 31": "OE1" <-> "OE2" Residue "Q GLU 40": "OE1" <-> "OE2" Residue "Q TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 120": "OD1" <-> "OD2" Residue "R ARG 3": "NH1" <-> "NH2" Residue "R TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ASP 103": "OD1" <-> "OD2" Residue "R ASP 108": "OD1" <-> "OD2" Residue "S ASP 23": "OD1" <-> "OD2" Residue "S TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 53": "OD1" <-> "OD2" Residue "T TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 144": "OE1" <-> "OE2" Residue "U GLU 35": "OE1" <-> "OE2" Residue "U GLU 115": "OE1" <-> "OE2" Residue "V GLU 49": "OE1" <-> "OE2" Residue "V TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 60": "NH1" <-> "NH2" Residue "W PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 85": "OD1" <-> "OD2" Residue "W TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 19": "NH1" <-> "NH2" Residue "X TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 98": "OE1" <-> "OE2" Residue "X ASP 116": "OD1" <-> "OD2" Residue "Y ASP 38": "OD1" <-> "OD2" Residue "Y PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 86": "OE1" <-> "OE2" Residue "Y PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 48": "OD1" <-> "OD2" Residue "Z GLU 86": "OE1" <-> "OE2" Residue "b GLU 15": "OE1" <-> "OE2" Residue "b PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 35": "OD1" <-> "OD2" Residue "c GLU 60": "OE1" <-> "OE2" Residue "d PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 109": "OD1" <-> "OD2" Residue "f ARG 119": "NH1" <-> "NH2" Residue "f ASP 137": "OD1" <-> "OD2" Residue "f TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 5": "OE1" <-> "OE2" Residue "g PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 149": "OD1" <-> "OD2" Residue "g GLU 189": "OE1" <-> "OE2" Residue "g PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 239": "OE1" <-> "OE2" Residue "g PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 272": "OD1" <-> "OD2" Residue "g GLU 286": "OE1" <-> "OE2" Residue "g TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 96": "OD1" <-> "OD2" Residue "k PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 265": "OD1" <-> "OD2" Residue "k ASP 275": "OD1" <-> "OD2" Residue "k ASP 297": "OD1" <-> "OD2" Residue "k GLU 338": "OE1" <-> "OE2" Residue "k ASP 356": "OD1" <-> "OD2" Residue "k ASP 361": "OD1" <-> "OD2" Residue "k ASP 363": "OD1" <-> "OD2" Residue "k GLU 365": "OE1" <-> "OE2" Residue "k ASP 367": "OD1" <-> "OD2" Residue "k PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 466": "OE1" <-> "OE2" Residue "k PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 478": "OE1" <-> "OE2" Residue "k GLU 481": "OE1" <-> "OE2" Residue "k GLU 485": "OE1" <-> "OE2" Residue "k GLU 496": "OE1" <-> "OE2" Residue "k ASP 511": "OD1" <-> "OD2" Residue "k ASP 515": "OD1" <-> "OD2" Residue "k TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 767": "OD1" <-> "OD2" 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: 74473 Number of models: 1 Model: "" Number of chains: 32 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: "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: "D" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1734 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 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: "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 breaks: 1 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: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 817 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain breaks: 1 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: "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: "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: "P" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1001 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain breaks: 3 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: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1110 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} 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: "U" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 819 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} 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: {'PTRANS': 6, '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: "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: "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: "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} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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: "f" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 498 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "g" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2431 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 308} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "k" Number of atoms: 5154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5154 Classifications: {'peptide': 638} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 32, 'TRANS': 605} 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: "2" Number of atoms: 35078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1647, 35078 Classifications: {'RNA': 1647} Modifications used: {'rna2p_pur': 142, 'rna2p_pyr': 145, 'rna3p_pur': 717, 'rna3p_pyr': 643} Link IDs: {'rna2p': 286, 'rna3p': 1360} Chain breaks: 34 Time building chain proxies: 29.66, per 1000 atoms: 0.40 Number of scatterers: 74473 At special positions: 0 Unit cell: (266.6, 203.36, 245.52, 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 90 16.00 P 1647 15.00 O 18663 8.00 N 13443 7.00 C 40630 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: 29.44 Conformation dependent library (CDL) restraints added in 6.2 seconds 9794 Ramachandran restraints generated. 4897 Oldfield, 0 Emsley, 4897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9292 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 53 sheets defined 27.9% alpha, 14.8% beta 221 base pairs and 668 stacking pairs defined. Time for finding SS restraints: 20.62 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 10 through 20 removed outlier: 3.526A pdb=" N GLN A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 49 through 56 removed outlier: 3.574A pdb=" N GLU A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.752A pdb=" N ALA A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.799A pdb=" N HIS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 137 removed outlier: 4.010A pdb=" N ILE A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 186 removed outlier: 3.540A pdb=" N GLY A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP A 174 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.560A pdb=" N TYR A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 47 removed outlier: 4.037A pdb=" N LEU C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 removed outlier: 3.927A pdb=" N HIS C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 removed outlier: 3.924A pdb=" N ASP C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR C 71 " --> pdb=" O GLN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 135 removed outlier: 3.744A pdb=" N ARG C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 132 " --> pdb=" O GLY C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 190 removed outlier: 4.004A pdb=" N LEU C 187 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 220 removed outlier: 3.678A pdb=" N LYS C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 removed outlier: 4.334A pdb=" N ALA C 231 " --> pdb=" O ASN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'D' and resid 9 through 28 removed outlier: 3.927A pdb=" N ASP D 14 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLY D 15 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 21 " --> pdb=" O PHE D 17 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN D 22 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLU D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.745A pdb=" N LEU D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 105 removed outlier: 4.143A pdb=" N GLU D 103 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET D 105 " --> pdb=" O GLN D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 120 Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.615A pdb=" N GLU E 40 " --> pdb=" O LYS E 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 37 through 41' Processing helix chain 'E' and resid 43 through 51 removed outlier: 3.558A pdb=" N PHE E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 48 " --> pdb=" O LEU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 66 removed outlier: 3.613A pdb=" N ALA E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) 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 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 249 through 259 removed outlier: 3.900A pdb=" N ASP E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG E 254 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG E 255 " --> pdb=" O GLU E 251 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 removed outlier: 3.854A pdb=" N CYS F 87 " --> pdb=" O LYS F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 96 Processing helix chain 'F' and resid 106 through 116 removed outlier: 3.500A pdb=" N ARG F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 123 Processing helix chain 'F' and resid 130 through 135 removed outlier: 3.851A pdb=" N VAL F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 removed outlier: 3.738A pdb=" N ASN F 139 " --> pdb=" O ASP F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 183 removed outlier: 4.072A pdb=" N ASN F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN F 170 " --> pdb=" O ARG F 166 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 173 " --> pdb=" O ASN F 169 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 174 " --> pdb=" O GLN F 170 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY F 178 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA F 179 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG F 180 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU F 181 " --> pdb=" O ILE F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 203 removed outlier: 3.611A pdb=" N GLU F 196 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS F 203 " --> pdb=" O ILE F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 213 removed outlier: 3.692A pdb=" N LYS F 213 " --> pdb=" O TYR F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 224 removed outlier: 3.709A pdb=" N LEU F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 41 Processing helix chain 'G' and resid 42 through 46 removed outlier: 3.885A pdb=" N LYS G 46 " --> pdb=" O ASP G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 removed outlier: 4.004A pdb=" N PHE G 144 " --> pdb=" O ASN G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 231 removed outlier: 3.658A pdb=" N GLN G 185 " --> pdb=" O PRO G 181 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG G 186 " --> pdb=" O GLN G 182 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS G 187 " --> pdb=" O ARG G 183 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS G 194 " --> pdb=" O GLN G 190 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN G 201 " --> pdb=" O ASN G 197 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA G 224 " --> pdb=" O LYS G 220 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG G 227 " --> pdb=" O LYS G 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 30 removed outlier: 4.152A pdb=" N VAL H 20 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER H 30 " --> pdb=" O GLU H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 66 through 72 removed outlier: 3.739A pdb=" N LYS H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 85 removed outlier: 3.739A pdb=" N THR H 78 " --> pdb=" O GLN H 74 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG H 79 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLU H 80 " --> pdb=" O LYS H 76 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU H 82 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 116 Processing helix chain 'H' and resid 117 through 128 removed outlier: 3.760A pdb=" N HIS H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS H 124 " --> pdb=" O ALA H 120 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 131 No H-bonds generated for 'chain 'H' and resid 129 through 131' Processing helix chain 'H' and resid 158 through 164 removed outlier: 4.392A pdb=" N ASP H 163 " --> pdb=" O GLN H 160 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TYR H 164 " --> pdb=" O GLN H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 177 removed outlier: 3.512A pdb=" N GLN H 170 " --> pdb=" O LEU H 166 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA H 171 " --> pdb=" O GLU H 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 117 removed outlier: 3.631A pdb=" N ALA I 115 " --> pdb=" O GLN I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 144 removed outlier: 4.058A pdb=" N GLU I 140 " --> pdb=" O SER I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 158 removed outlier: 3.672A pdb=" N GLU I 157 " --> pdb=" O GLU I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 177 Processing helix chain 'I' and resid 185 through 197 removed outlier: 3.620A pdb=" N PHE I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 34 removed outlier: 3.614A pdb=" N LEU J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP J 25 " --> pdb=" O SER J 21 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA J 26 " --> pdb=" O SER J 22 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU J 33 " --> pdb=" O LYS J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 60 removed outlier: 3.836A pdb=" N ILE J 45 " --> pdb=" O GLU J 41 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN J 48 " --> pdb=" O ARG J 44 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE J 52 " --> pdb=" O GLN J 48 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP J 58 " --> pdb=" O ARG J 54 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU J 59 " --> pdb=" O ALA J 55 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU J 60 " --> pdb=" O ALA J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 84 removed outlier: 3.808A pdb=" N ASN J 74 " --> pdb=" O LEU J 70 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA J 75 " --> pdb=" O PHE J 71 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU J 76 " --> pdb=" O GLU J 72 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG J 78 " --> pdb=" O ASN J 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL J 83 " --> pdb=" O ARG J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 99 removed outlier: 3.529A pdb=" N VAL J 96 " --> pdb=" O LEU J 93 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA J 98 " --> pdb=" O TYR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 106 removed outlier: 3.524A pdb=" N LEU J 105 " --> pdb=" O VAL J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 113 Processing helix chain 'J' and resid 125 through 131 removed outlier: 3.597A pdb=" N THR J 130 " --> pdb=" O ARG J 126 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN J 131 " --> pdb=" O VAL J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 156 removed outlier: 5.154A pdb=" N LYS J 154 " --> pdb=" O ASP J 151 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS J 155 " --> pdb=" O SER J 152 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE J 156 " --> pdb=" O GLU J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 181 Processing helix chain 'K' and resid 40 through 51 removed outlier: 3.996A pdb=" N SER K 48 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER K 51 " --> pdb=" O GLN K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 71 No H-bonds generated for 'chain 'K' and resid 69 through 71' Processing helix chain 'K' and resid 72 through 80 removed outlier: 3.674A pdb=" N LEU K 76 " --> pdb=" O GLY K 72 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG K 77 " --> pdb=" O VAL K 73 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 50 removed outlier: 4.012A pdb=" N ILE L 49 " --> pdb=" O PRO L 45 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU L 50 " --> pdb=" O LYS L 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 45 through 50' Processing helix chain 'M' and resid 23 through 27 Processing helix chain 'M' and resid 71 through 80 removed outlier: 4.214A pdb=" N GLY M 77 " --> pdb=" O LYS M 73 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU M 78 " --> pdb=" O LEU M 74 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN M 80 " --> pdb=" O GLU M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 134 removed outlier: 3.854A pdb=" N LEU M 133 " --> pdb=" O THR M 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 42 removed outlier: 3.895A pdb=" N GLU N 35 " --> pdb=" O GLU N 31 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLN N 36 " --> pdb=" O SER N 32 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE N 37 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL N 38 " --> pdb=" O ILE N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 59 removed outlier: 3.736A pdb=" N VAL N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) 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 103 removed outlier: 3.586A pdb=" N SER N 97 " --> pdb=" O LYS N 93 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL N 98 " --> pdb=" O LYS N 94 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU N 103 " --> pdb=" O ARG N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 113 removed outlier: 3.642A pdb=" N LYS N 112 " --> pdb=" O ASP N 108 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE N 113 " --> pdb=" O LYS N 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 108 through 113' Processing helix chain 'N' and resid 114 through 132 removed outlier: 3.749A pdb=" N ILE N 118 " --> pdb=" O ARG N 114 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE N 122 " --> pdb=" O ILE N 118 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N HIS N 123 " --> pdb=" O GLU N 119 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG N 124 " --> pdb=" O SER N 120 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR N 128 " --> pdb=" O ARG N 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 36 removed outlier: 3.515A pdb=" N VAL P 34 " --> pdb=" O THR P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 56 through 61 removed outlier: 3.581A pdb=" N ARG P 61 " --> pdb=" O MET P 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'Q' and resid 44 through 53 removed outlier: 4.167A pdb=" N VAL Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR Q 49 " --> pdb=" O ARG Q 45 " (cutoff:3.500A) Proline residue: Q 51 - end of helix Processing helix chain 'Q' and resid 75 through 89 removed outlier: 3.739A pdb=" N TYR Q 79 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG Q 82 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA Q 86 " --> pdb=" O ARG Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 92 No H-bonds generated for 'chain 'Q' and resid 90 through 92' Processing helix chain 'Q' and resid 98 through 113 removed outlier: 3.763A pdb=" N GLU Q 104 " --> pdb=" O GLN Q 100 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU Q 105 " --> pdb=" O SER Q 101 " (cutoff:3.500A) removed outlier: 3.789A 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 removed outlier: 3.855A pdb=" N ALA R 12 " --> pdb=" O THR R 8 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS R 14 " --> pdb=" O LYS R 10 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE R 17 " --> pdb=" O SER R 13 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU R 18 " --> pdb=" O LYS R 14 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG R 19 " --> pdb=" O ALA R 15 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR R 20 " --> pdb=" O LEU R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 24 Processing helix chain 'R' and resid 27 through 33 removed outlier: 3.975A pdb=" N ASN R 31 " --> pdb=" O ASP R 27 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG R 33 " --> pdb=" O GLN R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 38 Processing helix chain 'R' and resid 44 through 62 removed outlier: 3.529A pdb=" N TYR R 53 " --> pdb=" O LYS R 49 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR R 54 " --> pdb=" O ILE R 50 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR R 55 " --> pdb=" O ALA R 51 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS R 56 " --> pdb=" O GLY R 52 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG R 60 " --> pdb=" O HIS R 56 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE R 61 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN R 62 " --> pdb=" O MET R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 75 removed outlier: 3.819A pdb=" N GLN R 74 " --> pdb=" O SER R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 97 Processing helix chain 'R' and resid 105 through 114 removed outlier: 3.676A pdb=" N LEU R 109 " --> pdb=" O GLN R 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL R 110 " --> pdb=" O THR R 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 33 removed outlier: 3.715A pdb=" N THR S 33 " --> pdb=" O VAL S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 51 removed outlier: 4.285A pdb=" N VAL S 46 " --> pdb=" O TYR S 42 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS S 47 " --> pdb=" O SER S 43 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS S 48 " --> pdb=" O ASN S 44 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 61 removed outlier: 3.790A pdb=" N GLU S 60 " --> pdb=" O ARG S 57 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU S 61 " --> pdb=" O ALA S 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 57 through 61' Processing helix chain 'S' and resid 62 through 75 removed outlier: 4.084A pdb=" N LEU S 66 " --> pdb=" O THR S 62 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU S 67 " --> pdb=" O GLN S 63 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL S 70 " --> pdb=" O LEU S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 80 removed outlier: 3.799A pdb=" N TYR S 79 " --> pdb=" O PRO S 76 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS S 80 " --> pdb=" O THR S 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 76 through 80' Processing helix chain 'S' and resid 109 through 118 removed outlier: 3.539A pdb=" N ARG S 115 " --> pdb=" O ASP S 111 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU S 116 " --> pdb=" O ASP S 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 9 removed outlier: 4.241A pdb=" N ASP T 8 " --> pdb=" O SER T 5 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL T 9 " --> pdb=" O VAL T 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 5 through 9' Processing helix chain 'T' and resid 11 through 26 removed outlier: 3.779A pdb=" N ILE T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 35 removed outlier: 3.876A pdb=" N VAL T 34 " --> pdb=" O PRO T 31 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP T 35 " --> pdb=" O GLY T 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 31 through 35' Processing helix chain 'T' and resid 52 through 68 removed outlier: 3.650A pdb=" N ALA T 58 " --> pdb=" O PHE T 54 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA T 62 " --> pdb=" O ALA T 58 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR T 66 " --> pdb=" O ALA T 62 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N MET T 67 " --> pdb=" O ARG T 63 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 78 Processing helix chain 'T' and resid 98 through 107 removed outlier: 3.599A pdb=" N LYS T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL T 104 " --> pdb=" O ILE T 100 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 112 removed outlier: 3.619A pdb=" N GLY T 112 " --> pdb=" O GLU T 109 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 130 Processing helix chain 'T' and resid 131 through 137 Processing helix chain 'T' and resid 138 through 144 removed outlier: 3.604A pdb=" N GLU T 141 " --> pdb=" O GLN T 138 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 35 removed outlier: 3.732A pdb=" N GLU U 35 " --> pdb=" O LYS U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 47 removed outlier: 3.627A pdb=" N VAL U 42 " --> pdb=" O SER U 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN U 44 " --> pdb=" O ASN U 40 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA U 45 " --> pdb=" O ILE U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 104 removed outlier: 4.291A pdb=" N ARG U 102 " --> pdb=" O GLN U 98 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE U 103 " --> pdb=" O ILE U 99 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 62 removed outlier: 3.839A pdb=" N SER V 61 " --> pdb=" O GLY V 57 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG V 62 " --> pdb=" O TYR V 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 57 through 62' Processing helix chain 'V' and resid 64 through 76 removed outlier: 3.747A pdb=" N ASN V 75 " --> pdb=" O ARG V 71 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP V 76 " --> pdb=" O LEU V 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 10 removed outlier: 3.581A pdb=" N ASP W 9 " --> pdb=" O VAL W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 16 removed outlier: 3.807A pdb=" N ASN W 15 " --> pdb=" O LEU W 11 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN W 16 " --> pdb=" O ASN W 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 11 through 16' Processing helix chain 'W' and resid 31 through 39 removed outlier: 3.508A pdb=" N ILE W 35 " --> pdb=" O SER W 31 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS W 36 " --> pdb=" O LYS W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 94 removed outlier: 3.777A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA W 91 " --> pdb=" O GLU W 87 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN W 92 " --> pdb=" O LYS W 88 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU W 93 " --> pdb=" O TRP W 89 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU W 94 " --> pdb=" O THR W 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 20 removed outlier: 3.626A pdb=" N LEU X 15 " --> pdb=" O SER X 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG X 19 " --> pdb=" O LEU X 15 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG X 20 " --> pdb=" O ARG X 16 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 35 removed outlier: 3.585A pdb=" N LYS X 30 " --> pdb=" O GLU X 26 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS X 31 " --> pdb=" O ASN X 27 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG X 32 " --> pdb=" O ASN X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 40 removed outlier: 4.311A pdb=" N LYS X 39 " --> pdb=" O GLY X 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 137 Processing helix chain 'Y' and resid 36 through 49 removed outlier: 3.906A pdb=" N LEU Y 44 " --> pdb=" O LEU Y 40 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA Y 45 " --> pdb=" O ARG Y 41 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU Y 46 " --> pdb=" O GLU Y 42 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL Y 47 " --> pdb=" O LYS Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 86 removed outlier: 3.555A pdb=" N ALA Y 82 " --> pdb=" O SER Y 78 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS Y 84 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU Y 86 " --> pdb=" O ALA Y 82 " (cutoff:3.500A) Processing helix chain 'Y' and resid 87 through 94 removed outlier: 3.524A pdb=" N ARG Y 93 " --> pdb=" O TYR Y 89 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR Y 94 " --> pdb=" O ARG Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 106 through 111 removed outlier: 3.621A pdb=" N GLN Y 110 " --> pdb=" O GLN Y 106 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 133 removed outlier: 3.563A pdb=" N LYS Y 127 " --> pdb=" O LYS Y 123 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS Y 128 " --> pdb=" O ARG Y 124 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 66 removed outlier: 4.194A pdb=" N LEU Z 65 " --> pdb=" O SER Z 61 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL Z 66 " --> pdb=" O VAL Z 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 61 through 66' Processing helix chain 'Z' and resid 72 through 87 removed outlier: 3.840A pdb=" N LEU Z 80 " --> pdb=" O ALA Z 76 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS Z 85 " --> pdb=" O ARG Z 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 11 through 16 removed outlier: 3.671A pdb=" N ALA b 16 " --> pdb=" O ALA b 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 32 through 36 removed outlier: 3.754A pdb=" N GLY d 35 " --> pdb=" O ARG d 32 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU d 36 " --> pdb=" O LYS d 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 32 through 36' Processing helix chain 'd' and resid 39 through 43 Processing helix chain 'd' and resid 46 through 51 removed outlier: 3.656A pdb=" N GLY d 51 " --> pdb=" O ALA d 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 45 removed outlier: 3.803A pdb=" N LYS e 36 " --> pdb=" O GLY e 32 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR e 41 " --> pdb=" O ARG e 37 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG e 43 " --> pdb=" O LEU e 39 " (cutoff:3.500A) Processing helix chain 'k' and resid 52 through 59 Processing helix chain 'k' and resid 96 through 102 Processing helix chain 'k' and resid 103 through 104 No H-bonds generated for 'chain 'k' and resid 103 through 104' Processing helix chain 'k' and resid 105 through 109 removed outlier: 4.461A pdb=" N ASP k 109 " --> pdb=" O LYS k 106 " (cutoff:3.500A) Processing helix chain 'k' and resid 145 through 152 removed outlier: 3.518A pdb=" N LEU k 149 " --> pdb=" O PHE k 145 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP k 150 " --> pdb=" O LEU k 146 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA k 152 " --> pdb=" O ILE k 148 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 184 removed outlier: 3.525A pdb=" N LEU k 180 " --> pdb=" O ILE k 176 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU k 181 " --> pdb=" O ILE k 177 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU k 182 " --> pdb=" O ARG k 178 " (cutoff:3.500A) Processing helix chain 'k' and resid 201 through 212 removed outlier: 3.773A pdb=" N GLN k 205 " --> pdb=" O LYS k 201 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL k 208 " --> pdb=" O PHE k 204 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS k 209 " --> pdb=" O GLN k 205 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN k 210 " --> pdb=" O LEU k 206 " (cutoff:3.500A) Processing helix chain 'k' and resid 213 through 217 Processing helix chain 'k' and resid 236 through 245 removed outlier: 3.688A pdb=" N THR k 241 " --> pdb=" O ASN k 237 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU k 242 " --> pdb=" O VAL k 238 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS k 243 " --> pdb=" O LEU k 239 " (cutoff:3.500A) Processing helix chain 'k' and resid 253 through 257 removed outlier: 4.012A pdb=" N ARG k 256 " --> pdb=" O ARG k 253 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY k 257 " --> pdb=" O ASP k 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 253 through 257' Processing helix chain 'k' and resid 350 through 354 removed outlier: 3.671A pdb=" N GLY k 353 " --> pdb=" O ALA k 350 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR k 354 " --> pdb=" O PRO k 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 350 through 354' Processing helix chain 'k' and resid 472 through 474 No H-bonds generated for 'chain 'k' and resid 472 through 474' Processing helix chain 'k' and resid 475 through 480 Processing helix chain 'k' and resid 522 through 526 removed outlier: 3.737A pdb=" N LYS k 526 " --> pdb=" O ALA k 523 " (cutoff:3.500A) Processing helix chain 'k' and resid 535 through 548 removed outlier: 3.757A pdb=" N ILE k 541 " --> pdb=" O THR k 537 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE k 542 " --> pdb=" O LYS k 538 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS k 543 " --> pdb=" O ASN k 539 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR k 545 " --> pdb=" O ILE k 541 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS k 546 " --> pdb=" O ILE k 542 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN k 547 " --> pdb=" O LYS k 543 " (cutoff:3.500A) Processing helix chain 'k' and resid 725 through 730 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.700A pdb=" N VAL A 47 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 76 removed outlier: 6.118A pdb=" N ALA A 75 " --> pdb=" O ILE A 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 122 removed outlier: 6.449A pdb=" N VAL A 121 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU A 146 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE A 160 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA A 145 " --> pdb=" O ILE A 160 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 90 removed outlier: 5.000A pdb=" N ASP C 78 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY C 105 " --> pdb=" O ASP C 78 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL C 80 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C 103 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 82 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 88 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG C 95 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 90 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA C 118 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 137 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AA6, first strand: chain 'C' and resid 158 through 162 removed outlier: 3.501A pdb=" N VAL C 179 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 42 Processing sheet with id=AA8, first strand: chain 'D' and resid 50 through 51 removed outlier: 6.363A pdb=" N ILE D 50 " --> pdb=" O GLU D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 134 through 135 Processing sheet with id=AB1, first strand: chain 'D' and resid 206 through 208 removed outlier: 3.837A pdb=" N THR D 207 " --> pdb=" O THR R 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.659A pdb=" N LYS E 71 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.471A 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: 6.871A pdb=" N TYR E 138 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL E 129 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL E 140 " --> pdb=" O LYS E 127 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR E 159 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE E 172 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LYS E 161 " --> pdb=" O THR E 170 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.671A pdb=" N LEU E 207 " --> pdb=" O LYS E 198 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS E 198 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N HIS E 209 " --> pdb=" O VAL E 196 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR E 182 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL E 227 " --> pdb=" O TYR E 182 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 161 through 162 removed outlier: 6.331A pdb=" N ASP F 161 " --> pdb=" O LYS c 45 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE c 40 " --> pdb=" O VAL c 30 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL c 25 " --> pdb=" O GLY c 17 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLY c 17 " --> pdb=" O VAL c 25 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLN c 27 " --> pdb=" O VAL c 15 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL c 15 " --> pdb=" O GLN c 27 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG c 29 " --> pdb=" O ILE c 13 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 13 through 17 Processing sheet with id=AB8, first strand: chain 'G' and resid 72 through 76 Processing sheet with id=AB9, first strand: chain 'G' and resid 160 through 164 removed outlier: 3.797A pdb=" N LYS G 164 " --> pdb=" O LYS G 167 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 45 through 50 Processing sheet with id=AC2, first strand: chain 'H' and resid 181 through 184 removed outlier: 9.288A pdb=" N VAL H 182 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLN H 150 " --> pdb=" O VAL H 182 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N GLU H 184 " --> pdb=" O GLN H 150 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL H 152 " --> pdb=" O GLU H 184 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY H 137 " --> pdb=" O LEU H 153 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN W 64 " --> pdb=" O GLY W 48 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE W 50 " --> pdb=" O VAL W 62 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL W 62 " --> pdb=" O PHE W 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.581A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 65 through 67 Processing sheet with id=AC5, first strand: chain 'I' and resid 78 through 83 removed outlier: 6.366A pdb=" N GLN I 103 " --> pdb=" O ALA I 79 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 135 through 136 removed outlier: 3.583A pdb=" N VAL J 136 " --> pdb=" O GLN J 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 70 through 77 removed outlier: 18.223A pdb=" N ILE L 70 " --> pdb=" O LEU L 91 " (cutoff:3.500A) removed outlier: 15.463A pdb=" N LEU L 91 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N THR L 72 " --> pdb=" O ALA L 89 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA L 89 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL L 85 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG L 103 " --> pdb=" O TYR L 90 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG L 99 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 10.542A pdb=" N PHE L 137 " --> pdb=" O ASN L 106 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N VAL L 139 " --> pdb=" O PRO L 108 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N HIS L 110 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N LYS L 141 " --> pdb=" O HIS L 110 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR L 124 " --> pdb=" O VAL L 140 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL L 142 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ILE L 122 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL L 125 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 42 through 43 removed outlier: 4.498A pdb=" N ALA M 42 " --> pdb=" O VAL M 122 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL M 122 " --> pdb=" O ALA M 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'M' and resid 62 through 63 removed outlier: 7.148A pdb=" N LEU M 62 " --> pdb=" O VAL M 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'Q' and resid 7 through 10 removed outlier: 3.540A pdb=" N VAL Q 7 " --> pdb=" O VAL Q 22 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS Q 26 " --> pdb=" O ILE Q 63 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ILE Q 65 " --> pdb=" O LYS Q 26 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU Q 28 " --> pdb=" O ILE Q 65 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL Q 67 " --> pdb=" O LEU Q 28 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LYS Q 30 " --> pdb=" O VAL Q 67 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL Q 69 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 100 through 102 removed outlier: 6.053A pdb=" N LEU R 100 " --> pdb=" O SER R 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'T' and resid 83 through 84 Processing sheet with id=AD4, first strand: chain 'T' and resid 114 through 116 Processing sheet with id=AD5, first strand: chain 'U' and resid 51 through 57 removed outlier: 5.842A pdb=" N LYS U 52 " --> pdb=" O GLU U 94 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLU U 94 " --> pdb=" O LYS U 52 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLY U 54 " --> pdb=" O ASP U 92 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP U 92 " --> pdb=" O GLY U 54 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA U 95 " --> pdb=" O ILE U 20 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'U' and resid 61 through 65 removed outlier: 3.755A pdb=" N ILE U 65 " --> pdb=" O TYR U 82 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR U 82 " --> pdb=" O ILE U 65 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 33 through 39 removed outlier: 3.908A pdb=" N LYS V 38 " --> pdb=" O GLU V 49 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU V 49 " --> pdb=" O LYS V 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 72 through 74 removed outlier: 3.712A pdb=" N PHE W 128 " --> pdb=" O GLY W 73 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY W 127 " --> pdb=" O ILE W 103 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 82 through 84 removed outlier: 4.203A pdb=" N GLU X 55 " --> pdb=" O ARG X 73 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN X 75 " --> pdb=" O VAL X 53 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL X 53 " --> pdb=" O GLN X 75 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA X 49 " --> pdb=" O LEU X 104 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU X 101 " --> pdb=" O VAL X 127 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL X 127 " --> pdb=" O GLU X 101 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU X 103 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA X 105 " --> pdb=" O LYS X 123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Y' and resid 6 through 15 removed outlier: 5.663A pdb=" N ILE Y 7 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 7 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N THR Y 9 " --> pdb=" O ASP Y 26 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP Y 26 " --> pdb=" O THR Y 9 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS Y 11 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL Y 24 " --> pdb=" O LYS Y 11 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE Y 60 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Z' and resid 59 through 60 removed outlier: 3.842A pdb=" N TYR Z 101 " --> pdb=" O VAL Z 60 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE Z 100 " --> pdb=" O ILE Z 92 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'b' and resid 32 through 35 removed outlier: 3.538A pdb=" N THR b 44 " --> pdb=" O VAL b 35 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'b' and resid 64 through 65 Processing sheet with id=AE5, first strand: chain 'g' and resid 5 through 14 removed outlier: 3.674A pdb=" N MET g 316 " --> pdb=" O VAL g 6 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL g 8 " --> pdb=" O GLN g 314 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN g 314 " --> pdb=" O VAL g 8 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL g 312 " --> pdb=" O ARG g 10 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR g 12 " --> pdb=" O ILE g 310 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE g 310 " --> pdb=" O THR g 12 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL g 309 " --> pdb=" O TYR g 305 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER g 291 " --> pdb=" O GLY g 304 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'g' and resid 20 through 24 removed outlier: 3.768A pdb=" N SER g 22 " --> pdb=" O ALA g 36 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'g' and resid 68 through 73 removed outlier: 4.321A pdb=" N ASP g 70 " --> pdb=" O ALA g 83 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA g 83 " --> pdb=" O ASP g 70 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR g 72 " --> pdb=" O LEU g 81 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR g 88 " --> pdb=" O SER g 84 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'g' and resid 110 through 115 removed outlier: 3.791A pdb=" N THR g 130 " --> pdb=" O SER g 126 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL g 133 " --> pdb=" O ALA g 142 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA g 142 " --> pdb=" O VAL g 133 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'g' and resid 153 through 156 removed outlier: 3.756A pdb=" N LYS g 179 " --> pdb=" O SER g 171 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL g 178 " --> pdb=" O ASP g 191 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASP g 191 " --> pdb=" O VAL g 178 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA g 180 " --> pdb=" O GLU g 189 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'g' and resid 199 through 204 removed outlier: 4.146A pdb=" N GLY g 215 " --> pdb=" O GLU g 219 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLU g 219 " --> pdb=" O GLY g 215 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'g' and resid 240 through 245 removed outlier: 3.722A pdb=" N SER g 242 " --> pdb=" O ALA g 255 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'k' and resid 123 through 128 removed outlier: 6.143A pdb=" N LYS k 84 " --> pdb=" O LYS k 136 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE k 138 " --> pdb=" O LYS k 84 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE k 86 " --> pdb=" O ILE k 138 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE k 85 " --> pdb=" O PHE k 157 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N VAL k 159 " --> pdb=" O ILE k 85 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR k 87 " --> pdb=" O VAL k 159 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLY k 161 " --> pdb=" O THR k 87 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL k 89 " --> pdb=" O GLY k 161 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR k 227 " --> pdb=" O GLY k 190 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'k' and resid 258 through 267 removed outlier: 4.144A pdb=" N VAL k 260 " --> pdb=" O THR k 281 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR k 281 " --> pdb=" O VAL k 260 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU k 279 " --> pdb=" O ASP k 262 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL k 264 " --> pdb=" O VAL k 277 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL k 277 " --> pdb=" O VAL k 264 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE k 266 " --> pdb=" O ASP k 275 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP k 275 " --> pdb=" O PHE k 266 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ARG k 558 " --> pdb=" O ILE k 306 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE k 306 " --> pdb=" O ARG k 558 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE k 560 " --> pdb=" O ASN k 304 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN k 304 " --> pdb=" O PHE k 560 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN k 302 " --> pdb=" O ARG k 562 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'k' and resid 258 through 267 removed outlier: 4.144A pdb=" N VAL k 260 " --> pdb=" O THR k 281 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR k 281 " --> pdb=" O VAL k 260 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU k 279 " --> pdb=" O ASP k 262 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL k 264 " --> pdb=" O VAL k 277 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL k 277 " --> pdb=" O VAL k 264 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N PHE k 266 " --> pdb=" O ASP k 275 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP k 275 " --> pdb=" O PHE k 266 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ARG k 558 " --> pdb=" O ILE k 306 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE k 306 " --> pdb=" O ARG k 558 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE k 560 " --> pdb=" O ASN k 304 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN k 304 " --> pdb=" O PHE k 560 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN k 302 " --> pdb=" O ARG k 562 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL k 293 " --> pdb=" O PHE k 301 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU k 292 " --> pdb=" O LEU k 584 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'k' and resid 628 through 630 removed outlier: 7.320A pdb=" N ASN k 595 " --> pdb=" O LEU k 689 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU k 689 " --> pdb=" O ASN k 595 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR k 687 " --> pdb=" O SER k 597 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE k 669 " --> pdb=" O ILE k 683 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N HIS k 685 " --> pdb=" O ALA k 667 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA k 667 " --> pdb=" O HIS k 685 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE k 670 " --> pdb=" O VAL k 615 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL k 615 " --> pdb=" O PHE k 670 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR k 623 " --> pdb=" O VAL k 616 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'k' and resid 706 through 710 removed outlier: 3.629A pdb=" N HIS k 706 " --> pdb=" O ARG k 718 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR k 716 " --> pdb=" O PHE k 708 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE k 710 " --> pdb=" O VAL k 714 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL k 714 " --> pdb=" O PHE k 710 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE k 755 " --> pdb=" O VAL k 715 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLU k 747 " --> pdb=" O LYS k 756 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'k' and resid 741 through 742 900 hydrogen bonds defined for protein. 2403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 508 hydrogen bonds 800 hydrogen bond angles 0 basepair planarities 221 basepair parallelities 668 stacking parallelities Total time for adding SS restraints: 45.51 Time building geometry restraints manager: 32.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 8925 1.30 - 1.43: 30526 1.43 - 1.57: 36450 1.57 - 1.70: 3232 1.70 - 1.83: 144 Bond restraints: 79277 Sorted by residual: bond pdb=" P U 21168 " pdb=" O5' U 21168 " ideal model delta sigma weight residual 1.593 1.673 -0.080 1.50e-02 4.44e+03 2.85e+01 bond pdb=" C3' U 21168 " pdb=" O3' U 21168 " ideal model delta sigma weight residual 1.417 1.495 -0.078 1.50e-02 4.44e+03 2.70e+01 bond pdb=" O3' U 21168 " pdb=" P C 21169 " ideal model delta sigma weight residual 1.607 1.672 -0.065 1.50e-02 4.44e+03 1.89e+01 bond pdb=" C4' U 21168 " pdb=" C3' U 21168 " ideal model delta sigma weight residual 1.521 1.581 -0.060 1.50e-02 4.44e+03 1.62e+01 bond pdb=" O5' U 21168 " pdb=" C5' U 21168 " ideal model delta sigma weight residual 1.420 1.472 -0.052 1.50e-02 4.44e+03 1.21e+01 ... (remaining 79272 not shown) Histogram of bond angle deviations from ideal: 93.02 - 102.38: 2546 102.38 - 111.74: 44386 111.74 - 121.10: 45886 121.10 - 130.46: 21274 130.46 - 139.82: 895 Bond angle restraints: 114987 Sorted by residual: angle pdb=" OP1 U 21168 " pdb=" P U 21168 " pdb=" OP2 U 21168 " ideal model delta sigma weight residual 119.60 98.73 20.87 3.00e+00 1.11e-01 4.84e+01 angle pdb=" P U 21168 " pdb=" O5' U 21168 " pdb=" C5' U 21168 " ideal model delta sigma weight residual 120.90 131.25 -10.35 1.50e+00 4.44e-01 4.76e+01 angle pdb=" O3' C 2 835 " pdb=" P C 2 836 " pdb=" O5' C 2 836 " ideal model delta sigma weight residual 104.00 114.02 -10.02 1.50e+00 4.44e-01 4.46e+01 angle pdb=" O3' U 21168 " pdb=" P C 21169 " pdb=" O5' C 21169 " ideal model delta sigma weight residual 104.00 113.83 -9.83 1.50e+00 4.44e-01 4.30e+01 angle pdb=" C3' U 21168 " pdb=" O3' U 21168 " pdb=" P C 21169 " ideal model delta sigma weight residual 120.20 129.56 -9.36 1.50e+00 4.44e-01 3.89e+01 ... (remaining 114982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 44612 35.99 - 71.98: 4705 71.98 - 107.97: 553 107.97 - 143.96: 27 143.96 - 179.95: 31 Dihedral angle restraints: 49928 sinusoidal: 35547 harmonic: 14381 Sorted by residual: dihedral pdb=" CA GLU D 210 " pdb=" C GLU D 210 " pdb=" N PRO D 211 " pdb=" CA PRO D 211 " ideal model delta harmonic sigma weight residual -180.00 -117.44 -62.56 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CA GLN X 63 " pdb=" C GLN X 63 " pdb=" N PRO X 64 " pdb=" CA PRO X 64 " ideal model delta harmonic sigma weight residual -180.00 -121.93 -58.07 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA ARG X 109 " pdb=" C ARG X 109 " pdb=" N LYS X 110 " pdb=" CA LYS X 110 " ideal model delta harmonic sigma weight residual 180.00 128.29 51.71 0 5.00e+00 4.00e-02 1.07e+02 ... (remaining 49925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 13236 0.118 - 0.236: 971 0.236 - 0.354: 76 0.354 - 0.471: 11 0.471 - 0.589: 3 Chirality restraints: 14297 Sorted by residual: chirality pdb=" CA GLU D 210 " pdb=" N GLU D 210 " pdb=" C GLU D 210 " pdb=" CB GLU D 210 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.68e+00 chirality pdb=" CB ILE D 158 " pdb=" CA ILE D 158 " pdb=" CG1 ILE D 158 " pdb=" CG2 ILE D 158 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.80e+00 chirality pdb=" P C 21169 " pdb=" OP1 C 21169 " pdb=" OP2 C 21169 " pdb=" O5' C 21169 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.57e+00 ... (remaining 14294 not shown) Planarity restraints: 8574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 210 " 0.099 5.00e-02 4.00e+02 1.51e-01 3.63e+01 pdb=" N PRO D 211 " -0.260 5.00e-02 4.00e+02 pdb=" CA PRO D 211 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO D 211 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 876 " -0.047 2.00e-02 2.50e+03 2.46e-02 1.81e+01 pdb=" N9 G 2 876 " 0.066 2.00e-02 2.50e+03 pdb=" C8 G 2 876 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G 2 876 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G 2 876 " -0.010 2.00e-02 2.50e+03 pdb=" C6 G 2 876 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G 2 876 " -0.015 2.00e-02 2.50e+03 pdb=" N1 G 2 876 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G 2 876 " 0.009 2.00e-02 2.50e+03 pdb=" N2 G 2 876 " 0.008 2.00e-02 2.50e+03 pdb=" N3 G 2 876 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G 2 876 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN X 63 " 0.064 5.00e-02 4.00e+02 9.71e-02 1.51e+01 pdb=" N PRO X 64 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO X 64 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO X 64 " 0.053 5.00e-02 4.00e+02 ... (remaining 8571 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 9988 2.72 - 3.27: 65586 3.27 - 3.81: 139403 3.81 - 4.36: 163784 4.36 - 4.90: 242175 Nonbonded interactions: 620936 Sorted by model distance: nonbonded pdb=" O SER X 11 " pdb=" OG SER X 11 " model vdw 2.181 2.440 nonbonded pdb=" OH TYR D 34 " pdb=" O ILE D 49 " model vdw 2.181 2.440 nonbonded pdb=" O ILE C 218 " pdb=" OG1 THR C 221 " model vdw 2.192 2.440 nonbonded pdb=" O2' G 21636 " pdb=" O2' C 21758 " model vdw 2.201 2.440 nonbonded pdb=" O GLN H 74 " pdb=" OG1 THR H 78 " model vdw 2.222 2.440 ... (remaining 620931 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 14.180 Check model and map are aligned: 0.830 Set scattering table: 0.560 Process input model: 185.880 Find NCS groups from input model: 1.600 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:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.013 0.152 79277 Z= 0.817 Angle : 1.267 20.867 114987 Z= 0.625 Chirality : 0.067 0.589 14297 Planarity : 0.008 0.151 8574 Dihedral : 23.896 179.952 40636 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.72 % Favored : 88.18 % Rotamer: Outliers : 1.35 % Allowed : 14.44 % Favored : 84.21 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.01 (0.09), residues: 4897 helix: -4.33 (0.07), residues: 1171 sheet: -2.45 (0.17), residues: 781 loop : -3.27 (0.09), residues: 2945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP g 251 HIS 0.015 0.002 HIS L 104 PHE 0.038 0.003 PHE W 99 TYR 0.040 0.003 TYR J 8 ARG 0.027 0.001 ARG Y 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9794 Ramachandran restraints generated. 4897 Oldfield, 0 Emsley, 4897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9794 Ramachandran restraints generated. 4897 Oldfield, 0 Emsley, 4897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 716 time to evaluate : 4.401 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: A 7 PHE cc_start: 0.8870 (m-80) cc_final: 0.8389 (m-80) REVERT: A 55 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7916 (mm-30) REVERT: A 131 GLN cc_start: 0.8060 (tp-100) cc_final: 0.7837 (tp-100) REVERT: A 135 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6906 (mt-10) REVERT: A 180 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7488 (tp30) REVERT: A 184 LEU cc_start: 0.8683 (mp) cc_final: 0.8019 (mt) REVERT: C 245 ASP cc_start: 0.8951 (p0) cc_final: 0.8202 (p0) REVERT: D 87 TYR cc_start: 0.6920 (t80) cc_final: 0.6710 (t80) REVERT: F 66 GLN cc_start: 0.8735 (mp10) cc_final: 0.8219 (mp10) REVERT: F 118 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7980 (mm) REVERT: H 50 ASP cc_start: 0.8775 (p0) cc_final: 0.8565 (p0) REVERT: I 88 ASN cc_start: 0.8663 (p0) cc_final: 0.8257 (p0) REVERT: K 1 MET cc_start: 0.6333 (mmt) cc_final: 0.5868 (mmp) REVERT: K 14 TYR cc_start: 0.6042 (p90) cc_final: 0.5806 (p90) REVERT: N 87 ASP cc_start: 0.8913 (p0) cc_final: 0.8713 (p0) REVERT: N 100 LYS cc_start: 0.9168 (mmtt) cc_final: 0.8711 (mmmm) REVERT: N 104 ARG cc_start: 0.7698 (mtt180) cc_final: 0.7401 (mtt180) REVERT: P 32 ASP cc_start: 0.8408 (t70) cc_final: 0.8106 (t0) REVERT: Q 36 ILE cc_start: 0.8886 (pt) cc_final: 0.8545 (mm) REVERT: Q 58 ASP cc_start: 0.8638 (p0) cc_final: 0.8369 (p0) REVERT: R 17 ILE cc_start: 0.9132 (tt) cc_final: 0.8647 (tt) REVERT: S 72 ILE cc_start: 0.8735 (mm) cc_final: 0.8447 (mm) REVERT: T 23 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8686 (tp-100) REVERT: T 35 ASP cc_start: 0.8746 (p0) cc_final: 0.8225 (p0) REVERT: U 36 ASN cc_start: 0.8628 (p0) cc_final: 0.8304 (p0) REVERT: U 82 TYR cc_start: 0.8612 (m-10) cc_final: 0.8300 (m-80) REVERT: U 102 ARG cc_start: 0.8084 (ptt-90) cc_final: 0.7808 (ptt90) REVERT: X 65 ASN cc_start: 0.9139 (m-40) cc_final: 0.8900 (m-40) REVERT: Y 42 GLU cc_start: 0.7745 (pt0) cc_final: 0.7541 (pt0) REVERT: Z 82 HIS cc_start: 0.7970 (t70) cc_final: 0.7448 (t-170) REVERT: Z 97 LYS cc_start: 0.9066 (tppt) cc_final: 0.8854 (tptt) REVERT: b 34 ASP cc_start: 0.8099 (m-30) cc_final: 0.7764 (p0) REVERT: c 32 PHE cc_start: 0.7429 (t80) cc_final: 0.6409 (t80) REVERT: d 48 ASN cc_start: 0.8572 (t0) cc_final: 0.8356 (t0) REVERT: e 33 ARG cc_start: 0.7215 (ttm170) cc_final: 0.6919 (ttm170) REVERT: e 48 THR cc_start: 0.7419 (OUTLIER) cc_final: 0.6974 (p) REVERT: e 56 MET cc_start: 0.7639 (mpp) cc_final: 0.7395 (mpp) REVERT: g 283 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7607 (mmmt) outliers start: 57 outliers final: 26 residues processed: 767 average time/residue: 0.7385 time to fit residues: 936.1881 Evaluate side-chains 550 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 522 time to evaluate : 4.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain W residue 40 VAL Chi-restraints excluded: chain X residue 53 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain d residue 28 THR Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain g residue 207 ASP Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 282 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 547 optimal weight: 0.7980 chunk 491 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 331 optimal weight: 1.9990 chunk 262 optimal weight: 0.8980 chunk 507 optimal weight: 50.0000 chunk 196 optimal weight: 0.9990 chunk 308 optimal weight: 7.9990 chunk 378 optimal weight: 0.9980 chunk 588 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 140 ASN A 193 GLN ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 GLN D 165 ASN E 57 ASN E 98 ASN E 209 HIS ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 ASN G 185 GLN G 189 HIS I 103 GLN I 116 HIS I 175 GLN J 48 GLN J 112 GLN J 124 HIS ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 ASN N 105 ASN N 123 HIS ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN Q 100 GLN R 48 ASN ** S 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 ASN S 127 HIS ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 77 ASN U 48 HIS V 33 GLN V 35 ASN W 66 ASN W 80 ASN W 92 ASN W 120 HIS X 10 ASN Y 77 ASN Y 110 GLN b 51 GLN d 20 GLN g 66 HIS g 69 GLN g 187 GLN g 237 GLN ** g 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 302 GLN ** k 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 513 GLN k 539 ASN ** k 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 638 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 79277 Z= 0.177 Angle : 0.715 14.215 114987 Z= 0.362 Chirality : 0.041 0.304 14297 Planarity : 0.005 0.125 8574 Dihedral : 24.868 179.773 30850 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.19 % Favored : 92.77 % Rotamer: Outliers : 2.70 % Allowed : 20.30 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.11 % 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: -4.20 (0.10), residues: 4897 helix: -3.18 (0.11), residues: 1198 sheet: -1.86 (0.17), residues: 740 loop : -2.99 (0.10), residues: 2959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 61 HIS 0.012 0.001 HIS K 32 PHE 0.018 0.001 PHE S 85 TYR 0.024 0.002 TYR K 79 ARG 0.012 0.000 ARG c 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9794 Ramachandran restraints generated. 4897 Oldfield, 0 Emsley, 4897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9794 Ramachandran restraints generated. 4897 Oldfield, 0 Emsley, 4897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 654 time to evaluate : 4.465 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: A 7 PHE cc_start: 0.8735 (m-80) cc_final: 0.8373 (m-80) REVERT: A 55 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8028 (mm-30) REVERT: A 120 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9012 (mp) REVERT: A 135 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6750 (mt-10) REVERT: A 180 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7592 (mm-30) REVERT: A 184 LEU cc_start: 0.8628 (mp) cc_final: 0.8388 (mt) REVERT: D 87 TYR cc_start: 0.6819 (t80) cc_final: 0.6608 (t80) REVERT: D 175 VAL cc_start: 0.4895 (OUTLIER) cc_final: 0.4347 (p) REVERT: F 66 GLN cc_start: 0.8746 (mp10) cc_final: 0.8351 (mp10) REVERT: H 50 ASP cc_start: 0.8701 (p0) cc_final: 0.8435 (p0) REVERT: J 180 LYS cc_start: 0.8438 (mptt) cc_final: 0.8117 (mtmm) REVERT: K 2 LEU cc_start: 0.8032 (tp) cc_final: 0.7794 (tt) REVERT: K 14 TYR cc_start: 0.6499 (p90) cc_final: 0.5891 (p90) REVERT: K 34 GLU cc_start: 0.7513 (tp30) cc_final: 0.7096 (tp30) REVERT: K 44 LYS cc_start: 0.5587 (mttp) cc_final: 0.4981 (mttt) REVERT: M 96 GLN cc_start: 0.7326 (mt0) cc_final: 0.6272 (pp30) REVERT: N 40 TYR cc_start: 0.8572 (m-10) cc_final: 0.8186 (m-80) REVERT: N 100 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8652 (mmmm) REVERT: N 104 ARG cc_start: 0.7512 (mtt180) cc_final: 0.7239 (mtt180) REVERT: Q 36 ILE cc_start: 0.8907 (pt) cc_final: 0.8356 (mm) REVERT: Q 40 GLU cc_start: 0.8268 (pm20) cc_final: 0.7992 (pp20) REVERT: Q 45 ARG cc_start: 0.7783 (tpp80) cc_final: 0.7379 (ttm-80) REVERT: Q 58 ASP cc_start: 0.8464 (p0) cc_final: 0.8171 (p0) REVERT: R 79 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8136 (mt-10) REVERT: S 27 LYS cc_start: 0.7225 (mmtm) cc_final: 0.6811 (mmtm) REVERT: S 90 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.6892 (p0) REVERT: S 111 ASP cc_start: 0.8284 (p0) cc_final: 0.7936 (p0) REVERT: T 23 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8231 (tp40) REVERT: T 35 ASP cc_start: 0.8705 (p0) cc_final: 0.8426 (p0) REVERT: T 51 GLU cc_start: 0.7498 (tp30) cc_final: 0.7263 (tm-30) REVERT: T 55 TYR cc_start: 0.7534 (m-80) cc_final: 0.6980 (m-80) REVERT: U 36 ASN cc_start: 0.8809 (p0) cc_final: 0.8331 (p0) REVERT: U 93 LEU cc_start: 0.8372 (tp) cc_final: 0.8098 (tp) REVERT: V 66 ASP cc_start: 0.8842 (p0) cc_final: 0.8490 (p0) REVERT: W 65 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8442 (mt) REVERT: X 65 ASN cc_start: 0.9193 (m-40) cc_final: 0.8850 (m-40) REVERT: X 138 GLU cc_start: 0.6777 (tm-30) cc_final: 0.5583 (tm-30) REVERT: Y 39 GLU cc_start: 0.8324 (mp0) cc_final: 0.7771 (mp0) REVERT: Y 42 GLU cc_start: 0.7512 (pt0) cc_final: 0.7284 (pt0) REVERT: Z 97 LYS cc_start: 0.9120 (tppt) cc_final: 0.8914 (tppt) REVERT: c 32 PHE cc_start: 0.6952 (t80) cc_final: 0.6022 (t80) REVERT: d 46 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8343 (mmmt) REVERT: e 1 MET cc_start: 0.1533 (OUTLIER) cc_final: -0.1028 (tpt) REVERT: e 33 ARG cc_start: 0.6408 (ttm170) cc_final: 0.6205 (ttm170) REVERT: g 79 TYR cc_start: 0.7302 (m-80) cc_final: 0.6965 (m-80) REVERT: k 475 MET cc_start: -0.5387 (ttp) cc_final: -0.5665 (ttp) outliers start: 114 outliers final: 67 residues processed: 724 average time/residue: 0.7205 time to fit residues: 877.9341 Evaluate side-chains 609 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 537 time to evaluate : 4.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 125 TYR Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 115 TYR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 TYR Chi-restraints excluded: chain R residue 35 CYS Chi-restraints excluded: chain R residue 36 ASP Chi-restraints excluded: chain R residue 43 SER Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 111 ILE Chi-restraints excluded: chain T residue 124 ILE Chi-restraints excluded: chain V residue 22 ARG Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 53 VAL Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 57 TYR Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain b residue 11 THR Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain g residue 66 HIS Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 207 ASP Chi-restraints excluded: chain g residue 302 PHE Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 282 VAL Chi-restraints excluded: chain k residue 649 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 327 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 489 optimal weight: 7.9990 chunk 400 optimal weight: 20.0000 chunk 162 optimal weight: 6.9990 chunk 589 optimal weight: 10.0000 chunk 636 optimal weight: 30.0000 chunk 525 optimal weight: 10.0000 chunk 584 optimal weight: 10.0000 chunk 200 optimal weight: 0.0270 chunk 472 optimal weight: 50.0000 overall best weight: 3.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS E 197 HIS F 86 GLN ** F 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 GLN ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 ASN N 78 ASN ** P 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 HIS S 122 HIS ** T 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 92 ASN W 120 HIS ** Z 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 66 HIS g 69 GLN g 147 HIS ** g 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 79277 Z= 0.295 Angle : 0.713 12.894 114987 Z= 0.360 Chirality : 0.043 0.306 14297 Planarity : 0.005 0.121 8574 Dihedral : 24.743 179.746 30841 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.82 % Favored : 91.16 % Rotamer: Outliers : 4.43 % Allowed : 21.94 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 1.46 % Twisted General : 0.06 % 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: -3.75 (0.10), residues: 4897 helix: -2.50 (0.12), residues: 1198 sheet: -1.67 (0.18), residues: 748 loop : -2.84 (0.10), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 25 HIS 0.020 0.001 HIS g 66 PHE 0.016 0.002 PHE Q 60 TYR 0.021 0.002 TYR T 66 ARG 0.009 0.001 ARG T 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9794 Ramachandran restraints generated. 4897 Oldfield, 0 Emsley, 4897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9794 Ramachandran restraints generated. 4897 Oldfield, 0 Emsley, 4897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 597 time to evaluate : 4.633 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: A 7 PHE cc_start: 0.8743 (m-80) cc_final: 0.8258 (m-80) REVERT: A 120 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9048 (tt) REVERT: A 135 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7005 (mt-10) REVERT: A 180 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7755 (mm-30) REVERT: A 184 LEU cc_start: 0.8859 (mp) cc_final: 0.8574 (mt) REVERT: D 87 TYR cc_start: 0.6929 (t80) cc_final: 0.6676 (t80) REVERT: D 127 MET cc_start: 0.3223 (tpt) cc_final: 0.2654 (tpt) REVERT: E 216 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8353 (p0) REVERT: F 66 GLN cc_start: 0.8838 (mp10) cc_final: 0.8413 (mp10) REVERT: H 50 ASP cc_start: 0.8676 (p0) cc_final: 0.8429 (p0) REVERT: H 155 ASP cc_start: 0.7414 (t0) cc_final: 0.7047 (t0) REVERT: I 88 ASN cc_start: 0.8496 (p0) cc_final: 0.8235 (p0) REVERT: J 180 LYS cc_start: 0.8528 (mptt) cc_final: 0.8059 (mtmm) REVERT: K 14 TYR cc_start: 0.6997 (p90) cc_final: 0.6204 (p90) REVERT: K 20 VAL cc_start: 0.7613 (OUTLIER) cc_final: 0.7375 (m) REVERT: K 34 GLU cc_start: 0.7535 (tp30) cc_final: 0.7134 (tp30) REVERT: L 10 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6949 (pt0) REVERT: M 96 GLN cc_start: 0.7460 (mt0) cc_final: 0.6473 (pp30) REVERT: N 40 TYR cc_start: 0.8516 (m-10) cc_final: 0.7928 (m-80) REVERT: Q 40 GLU cc_start: 0.8371 (pm20) cc_final: 0.8111 (pp20) REVERT: Q 45 ARG cc_start: 0.7776 (tpp80) cc_final: 0.7561 (ttm-80) REVERT: Q 58 ASP cc_start: 0.8425 (p0) cc_final: 0.8140 (p0) REVERT: R 5 ARG cc_start: 0.6753 (ptt180) cc_final: 0.6451 (ptt90) REVERT: R 79 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8374 (mt-10) REVERT: S 112 ASP cc_start: 0.8450 (m-30) cc_final: 0.8228 (m-30) REVERT: S 126 ARG cc_start: 0.5431 (OUTLIER) cc_final: 0.3343 (mmm160) REVERT: T 23 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8459 (tp-100) REVERT: T 55 TYR cc_start: 0.7364 (m-80) cc_final: 0.7005 (m-80) REVERT: U 36 ASN cc_start: 0.8650 (p0) cc_final: 0.8107 (p0) REVERT: U 63 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8815 (mm) REVERT: V 66 ASP cc_start: 0.8898 (p0) cc_final: 0.8657 (p0) REVERT: Y 39 GLU cc_start: 0.8557 (mp0) cc_final: 0.8123 (mp0) REVERT: Y 42 GLU cc_start: 0.7518 (pt0) cc_final: 0.7294 (pt0) REVERT: Z 81 ARG cc_start: 0.8550 (mmt180) cc_final: 0.8338 (mmt180) REVERT: Z 97 LYS cc_start: 0.9067 (tppt) cc_final: 0.8854 (tppt) REVERT: c 32 PHE cc_start: 0.7052 (t80) cc_final: 0.6019 (t80) REVERT: c 50 GLU cc_start: 0.7260 (tp30) cc_final: 0.7057 (tp30) REVERT: e 1 MET cc_start: 0.1766 (tmm) cc_final: 0.1106 (tmm) REVERT: f 103 LEU cc_start: 0.2052 (OUTLIER) cc_final: 0.1597 (tt) REVERT: g 307 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7365 (t0) REVERT: k 720 MET cc_start: 0.4511 (mmm) cc_final: 0.4262 (mmt) outliers start: 187 outliers final: 125 residues processed: 722 average time/residue: 0.7265 time to fit residues: 890.5438 Evaluate side-chains 653 residues out of total 4260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 520 time to evaluate : 4.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 162 CYS Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 TYR Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 125 TYR Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 126 ASP Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 151 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 85 PHE Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 158 ASP Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 63 TYR Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 82 ASN Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 115 TYR Chi-restraints excluded: chain P residue 119 PHE Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 61 SER Chi-restraints excluded: chain Q residue 62 ASN Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 92 TYR Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain R residue 35 CYS Chi-restraints excluded: chain R residue 36 ASP Chi-restraints excluded: chain R residue 40 THR Chi-restraints excluded: chain R residue 43 SER Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 77 THR Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 126 ARG Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 13 ASP Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 111 ILE Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 22 ARG Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 76 SER Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 52 ILE Chi-restraints excluded: chain X residue 53 VAL Chi-restraints excluded: chain X residue 68 ILE Chi-restraints excluded: chain X residue 72 VAL Chi-restraints excluded: chain X residue 97 ASP Chi-restraints excluded: chain X residue 100 ASP Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 125 VAL Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 125 LEU Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 57 TYR Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 64 VAL Chi-restraints excluded: chain b residue 11 THR Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain b residue 64 CYS Chi-restraints excluded: chain c residue 7 VAL Chi-restraints excluded: chain c residue 15 VAL Chi-restraints excluded: chain c residue 26 THR Chi-restraints excluded: chain c residue 41 VAL Chi-restraints excluded: chain c residue 48 VAL Chi-restraints excluded: chain c residue 53 ILE Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 207 ASP Chi-restraints excluded: chain g residue 302 PHE Chi-restraints excluded: chain g residue 307 ASP Chi-restraints excluded: chain k residue 89 VAL Chi-restraints excluded: chain k residue 237 ASN Chi-restraints excluded: chain k residue 282 VAL Chi-restraints excluded: chain k residue 345 THR Chi-restraints excluded: chain k residue 649 ASP Chi-restraints excluded: chain k residue 716 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 70.6706 > 50: distance: 49 - 54: 24.298 distance: 54 - 55: 25.940 distance: 55 - 56: 26.486 distance: 55 - 58: 17.361 distance: 56 - 57: 33.225 distance: 56 - 62: 18.170 distance: 58 - 59: 35.737 distance: 59 - 60: 29.096 distance: 59 - 61: 28.924 distance: 62 - 63: 18.927 distance: 63 - 64: 39.719 distance: 63 - 66: 20.316 distance: 64 - 65: 51.075 distance: 64 - 71: 49.189 distance: 66 - 67: 38.070 distance: 67 - 68: 38.989 distance: 68 - 69: 39.817 distance: 69 - 70: 15.993 distance: 71 - 72: 41.851 distance: 72 - 73: 8.457 distance: 72 - 75: 56.733 distance: 73 - 74: 37.677 distance: 75 - 76: 41.443 distance: 76 - 77: 56.738 distance: 76 - 78: 42.029 distance: 79 - 80: 20.779 distance: 80 - 81: 44.698 distance: 80 - 83: 57.338 distance: 81 - 82: 12.889 distance: 81 - 85: 5.533 distance: 83 - 84: 52.994 distance: 85 - 86: 57.216 distance: 86 - 87: 27.521 distance: 87 - 88: 34.193 distance: 87 - 89: 39.829 distance: 89 - 90: 21.044 distance: 90 - 91: 25.203 distance: 90 - 93: 40.487 distance: 91 - 92: 36.473 distance: 91 - 95: 21.281 distance: 93 - 94: 49.065 distance: 95 - 96: 26.564 distance: 96 - 97: 44.330 distance: 96 - 99: 20.988 distance: 97 - 98: 39.909 distance: 97 - 107: 19.791 distance: 99 - 100: 24.689 distance: 100 - 101: 19.550 distance: 100 - 102: 30.026 distance: 101 - 103: 53.683 distance: 102 - 104: 31.708 distance: 103 - 105: 25.658 distance: 104 - 105: 16.663 distance: 105 - 106: 40.705 distance: 107 - 108: 27.798 distance: 108 - 109: 16.533 distance: 109 - 110: 24.607 distance: 109 - 112: 53.351 distance: 112 - 113: 31.587 distance: 112 - 118: 56.488 distance: 113 - 114: 42.255 distance: 113 - 116: 45.992 distance: 114 - 115: 43.700 distance: 114 - 119: 28.266 distance: 116 - 117: 61.715 distance: 117 - 118: 30.125 distance: 120 - 121: 9.640 distance: 120 - 123: 56.387 distance: 121 - 122: 31.820 distance: 121 - 130: 30.841 distance: 123 - 124: 50.273 distance: 124 - 125: 32.483 distance: 125 - 126: 12.129 distance: 126 - 127: 20.884 distance: 127 - 128: 24.344 distance: 127 - 129: 9.153