Starting phenix.real_space_refine on Fri Mar 15 20:25:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swc_10322/03_2024/6swc_10322_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swc_10322/03_2024/6swc_10322.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swc_10322/03_2024/6swc_10322_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swc_10322/03_2024/6swc_10322_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swc_10322/03_2024/6swc_10322_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swc_10322/03_2024/6swc_10322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swc_10322/03_2024/6swc_10322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swc_10322/03_2024/6swc_10322_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6swc_10322/03_2024/6swc_10322_updated.pdb" } resolution = 3.3 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= 0.003 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 1596 5.49 5 Mg 34 5.21 5 S 133 5.16 5 C 38423 2.51 5 N 13016 2.21 5 O 17536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "H GLU 112": "OE1" <-> "OE2" Residue "H GLU 186": "OE1" <-> "OE2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K GLU 54": "OE1" <-> "OE2" Residue "K ARG 135": "NH1" <-> "NH2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "M GLU 37": "OE1" <-> "OE2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N GLU 143": "OE1" <-> "OE2" Residue "O TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 23": "OE1" <-> "OE2" Residue "T GLU 88": "OE1" <-> "OE2" Residue "T ARG 124": "NH1" <-> "NH2" Residue "U TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 22": "OE1" <-> "OE2" Residue "V GLU 2": "OE1" <-> "OE2" Residue "V TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 59": "OE1" <-> "OE2" Residue "Y ARG 42": "NH1" <-> "NH2" Residue "Z GLU 139": "OE1" <-> "OE2" Residue "3 GLU 14": "OE1" <-> "OE2" Residue "3 GLU 120": "OE1" <-> "OE2" Residue "6 GLU 29": "OE1" <-> "OE2" Residue "6 GLU 103": "OE1" <-> "OE2" Residue "7 GLU 9": "OE1" <-> "OE2" Residue "7 GLU 39": "OE1" <-> "OE2" Residue "7 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 53": "OE1" <-> "OE2" Residue "7 GLU 66": "OE1" <-> "OE2" Residue "7 GLU 71": "OE1" <-> "OE2" Residue "7 ARG 87": "NH1" <-> "NH2" Residue "7 ARG 88": "NH1" <-> "NH2" Residue "7 GLU 122": "OE1" <-> "OE2" Residue "7 GLU 131": "OE1" <-> "OE2" Residue "7 GLU 157": "OE1" <-> "OE2" Residue "7 GLU 158": "OE1" <-> "OE2" Residue "7 GLU 176": "OE1" <-> "OE2" Residue "7 GLU 196": "OE1" <-> "OE2" Residue "7 ARG 207": "NH1" <-> "NH2" Residue "7 GLU 232": "OE1" <-> "OE2" Residue "7 GLU 262": "OE1" <-> "OE2" Residue "7 GLU 355": "OE1" <-> "OE2" Residue "7 GLU 379": "OE1" <-> "OE2" Residue "7 GLU 381": "OE1" <-> "OE2" Residue "7 ARG 384": "NH1" <-> "NH2" Residue "7 ARG 394": "NH1" <-> "NH2" Residue "7 GLU 414": "OE1" <-> "OE2" Residue "8 GLU 4": "OE1" <-> "OE2" Residue "8 GLU 6": "OE1" <-> "OE2" Residue "8 GLU 57": "OE1" <-> "OE2" Residue "8 GLU 68": "OE1" <-> "OE2" Residue "8 GLU 80": "OE1" <-> "OE2" Residue "8 GLU 105": "OE1" <-> "OE2" Residue "8 GLU 119": "OE1" <-> "OE2" Residue "9 GLU 11": "OE1" <-> "OE2" Residue "9 GLU 13": "OE1" <-> "OE2" Residue "9 GLU 141": "OE1" <-> "OE2" Residue "9 GLU 146": "OE1" <-> "OE2" Residue "9 GLU 189": "OE1" <-> "OE2" Residue "9 GLU 198": "OE1" <-> "OE2" Residue "9 GLU 208": "OE1" <-> "OE2" Residue "9 GLU 241": "OE1" <-> "OE2" Residue "9 GLU 257": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 70744 Number of models: 1 Model: "" Number of chains: 48 Chain: "2" Number of atoms: 32291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1497, 32291 Classifications: {'RNA': 1497} Modifications used: {'rna2p': 1, 'rna2p_pur': 115, 'rna2p_pyr': 81, 'rna3p': 41, 'rna3p_pur': 723, 'rna3p_pyr': 535} Link IDs: {'rna2p': 197, 'rna3p': 1299} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 5 Chain: "A" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1533 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "B" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1571 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "C" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 482 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 6, 'TRANS': 54} Chain: "D" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1470 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "E" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1983 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 18, 'TRANS': 223} Chain: "F" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1808 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "G" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 977 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "H" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1720 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "I" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "J" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "K" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1065 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 817 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "M" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 119} Chain: "N" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1148 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain: "O" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1151 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "P" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 51} Chain: "Q" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1262 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 12, 'TRANS': 139} Chain: "R" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 900 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "S" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 558 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "T" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1057 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 8, 'TRANS': 121} Chain: "U" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1223 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 11, 'TRANS': 137} Chain: "V" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 790 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "W" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 481 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "X" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 536 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "Y" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 408 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Z" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1550 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "0" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 343 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "3" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 114} Chain: "5" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 430 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 16} Chain: "4" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1622 Classifications: {'RNA': 76} Modifications used: {'rna2p': 1, 'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p': 4, 'rna3p_pur': 30, 'rna3p_pyr': 28} Link IDs: {'rna2p': 13, 'rna3p': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "6" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "7" Number of atoms: 3213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3213 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 392} Chain: "8" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1033 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "9" Number of atoms: 2033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2033 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "2" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Unusual residues: {' MG': 30} Classifications: {'undetermined': 30} Link IDs: {None: 29} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 35634 SG CYS C 32 66.156 174.802 138.056 1.00 42.93 S ATOM 35655 SG CYS C 35 64.306 177.113 139.644 1.00 52.67 S ATOM 35817 SG CYS C 55 66.299 174.593 141.536 1.00 58.29 S ATOM 35839 SG CYS C 58 63.685 176.877 140.464 1.00 63.39 S ATOM 35493 SG CYS C 14 72.450 162.374 140.112 1.00 41.44 S ATOM 35512 SG CYS C 17 72.279 158.632 141.350 1.00 44.16 S ATOM 35720 SG CYS C 43 73.749 158.931 137.811 1.00 32.61 S ATOM 35742 SG CYS C 46 71.436 158.711 138.401 1.00 33.69 S ATOM 40352 SG CYS F 128 96.419 150.660 157.309 1.00 23.20 S ATOM 40391 SG CYS F 133 98.829 149.705 159.315 1.00 24.29 S ATOM 40408 SG CYS F 135 99.045 152.464 159.332 1.00 27.74 S ATOM 51174 SG CYS P 21 136.941 150.209 80.208 1.00 25.76 S ATOM 51199 SG CYS P 24 135.172 148.958 83.632 1.00 30.38 S ATOM 51314 SG CYS P 39 134.729 147.448 80.052 1.00 20.55 S ATOM 51341 SG CYS P 42 133.500 150.108 82.918 1.00 22.82 S ATOM 52844 SG CYS R 16 59.139 92.333 187.721 1.00 70.47 S ATOM 52882 SG CYS R 21 62.055 93.503 188.539 1.00 52.33 S ATOM 53370 SG CYS R 77 58.359 94.483 186.238 1.00 52.59 S ATOM 57411 SG CYS W 20 10.198 138.786 138.570 1.00 69.15 S ATOM 57433 SG CYS W 23 7.847 136.668 139.663 1.00 79.15 S ATOM 57559 SG CYS W 39 10.744 134.986 141.247 1.00 68.61 S ATOM 57580 SG CYS W 42 9.208 135.073 139.100 1.00 73.35 S Time building chain proxies: 27.51, per 1000 atoms: 0.39 Number of scatterers: 70744 At special positions: 0 Unit cell: (219.09, 209.28, 247.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 133 16.00 P 1596 15.00 Mg 34 11.99 O 17536 8.00 N 13016 7.00 C 38423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 7 59 " - pdb=" SG CYS 7 74 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 62 " - pdb=" SG CYS 7 77 " distance=2.04 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: 24.29 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 101 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 55 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 35 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 58 " pdb="ZN ZN C 101 " - pdb=" SG CYS C 32 " pdb=" ZN C 102 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 46 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 17 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 14 " pdb="ZN ZN C 102 " - pdb=" SG CYS C 43 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 139 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 133 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 135 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 128 " pdb=" ZN P 101 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 39 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 24 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 21 " pdb="ZN ZN P 101 " - pdb=" SG CYS P 42 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 24 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 16 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 77 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 21 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 23 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 42 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 39 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 20 " Number of angles added : 30 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8348 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 143 helices and 52 sheets defined 25.3% alpha, 13.8% beta 383 base pairs and 839 stacking pairs defined. Time for finding SS restraints: 25.26 Creating SS restraints... Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 60 through 62 No H-bonds generated for 'chain 'A' and resid 60 through 62' Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.864A pdb=" N SER A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 150 removed outlier: 3.637A pdb=" N LYS A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 168 through 174 removed outlier: 4.255A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 15 removed outlier: 3.665A pdb=" N ALA B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 removed outlier: 3.728A pdb=" N LYS B 53 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 78 through 86 removed outlier: 3.777A pdb=" N PHE B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 161 through 179 removed outlier: 3.780A pdb=" N ALA B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 187 No H-bonds generated for 'chain 'B' and resid 185 through 187' Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'D' and resid 20 through 33 removed outlier: 3.907A pdb=" N ARG D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL D 28 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU D 29 " --> pdb=" O ARG D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 55 removed outlier: 4.075A pdb=" N TRP D 42 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS D 43 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN D 50 " --> pdb=" O GLN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 79 removed outlier: 3.629A pdb=" N GLU D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN D 72 " --> pdb=" O ILE D 68 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 74 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 97 through 100 No H-bonds generated for 'chain 'D' and resid 97 through 100' Processing helix chain 'D' and resid 105 through 110 Processing helix chain 'D' and resid 118 through 126 removed outlier: 3.550A pdb=" N ARG D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLN D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 4.466A pdb=" N GLU D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 168 through 172' Processing helix chain 'E' and resid 45 through 50 removed outlier: 3.622A pdb=" N VAL E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 62 No H-bonds generated for 'chain 'E' and resid 59 through 62' Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'F' and resid 4 through 12 removed outlier: 5.281A pdb=" N ALA F 9 " --> pdb=" O TRP F 5 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS F 10 " --> pdb=" O LYS F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 27 Processing helix chain 'F' and resid 34 through 36 No H-bonds generated for 'chain 'F' and resid 34 through 36' Processing helix chain 'F' and resid 48 through 53 Processing helix chain 'F' and resid 106 through 116 Processing helix chain 'F' and resid 169 through 177 removed outlier: 4.059A pdb=" N LYS F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE F 174 " --> pdb=" O VAL F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 210 removed outlier: 4.783A pdb=" N ASN F 209 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYS F 210 " --> pdb=" O TYR F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 221 No H-bonds generated for 'chain 'F' and resid 218 through 221' Processing helix chain 'G' and resid 25 through 27 No H-bonds generated for 'chain 'G' and resid 25 through 27' Processing helix chain 'G' and resid 40 through 43 No H-bonds generated for 'chain 'G' and resid 40 through 43' Processing helix chain 'H' and resid 5 through 8 No H-bonds generated for 'chain 'H' and resid 5 through 8' Processing helix chain 'H' and resid 34 through 36 No H-bonds generated for 'chain 'H' and resid 34 through 36' Processing helix chain 'H' and resid 63 through 71 removed outlier: 3.523A pdb=" N LYS H 70 " --> pdb=" O ARG H 66 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 114 removed outlier: 3.827A pdb=" N LYS H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 126 Processing helix chain 'H' and resid 154 through 171 removed outlier: 3.680A pdb=" N ALA H 171 " --> pdb=" O LEU H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 193 removed outlier: 4.556A pdb=" N LEU H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN H 193 " --> pdb=" O ILE H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 214 removed outlier: 4.215A pdb=" N ILE H 210 " --> pdb=" O GLU H 206 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER H 214 " --> pdb=" O ILE H 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 18 Processing helix chain 'I' and resid 32 through 43 removed outlier: 3.882A pdb=" N VAL I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS I 43 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 93 removed outlier: 4.126A pdb=" N ARG I 92 " --> pdb=" O ARG I 88 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE I 93 " --> pdb=" O TRP I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 119 removed outlier: 4.057A pdb=" N GLU I 118 " --> pdb=" O LYS I 114 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS I 119 " --> pdb=" O GLU I 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 27 No H-bonds generated for 'chain 'J' and resid 25 through 27' Processing helix chain 'J' and resid 114 through 117 No H-bonds generated for 'chain 'J' and resid 114 through 117' Processing helix chain 'K' and resid 39 through 42 No H-bonds generated for 'chain 'K' and resid 39 through 42' Processing helix chain 'K' and resid 47 through 51 Processing helix chain 'K' and resid 56 through 58 No H-bonds generated for 'chain 'K' and resid 56 through 58' Processing helix chain 'K' and resid 75 through 89 removed outlier: 4.019A pdb=" N GLU K 88 " --> pdb=" O ARG K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 101 No H-bonds generated for 'chain 'K' and resid 98 through 101' Processing helix chain 'K' and resid 104 through 108 removed outlier: 3.589A pdb=" N LEU K 107 " --> pdb=" O ARG K 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 29 removed outlier: 3.631A pdb=" N GLU L 18 " --> pdb=" O ARG L 14 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL L 19 " --> pdb=" O SER L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 82 No H-bonds generated for 'chain 'L' and resid 79 through 82' Processing helix chain 'M' and resid 53 through 55 No H-bonds generated for 'chain 'M' and resid 53 through 55' Processing helix chain 'M' and resid 57 through 73 removed outlier: 3.642A pdb=" N ARG M 65 " --> pdb=" O MET M 61 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA M 68 " --> pdb=" O ALA M 64 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU M 70 " --> pdb=" O ARG M 66 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU M 73 " --> pdb=" O GLU M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 103 Processing helix chain 'N' and resid 13 through 23 Processing helix chain 'N' and resid 31 through 34 No H-bonds generated for 'chain 'N' and resid 31 through 34' Processing helix chain 'N' and resid 93 through 95 No H-bonds generated for 'chain 'N' and resid 93 through 95' Processing helix chain 'N' and resid 111 through 113 No H-bonds generated for 'chain 'N' and resid 111 through 113' Processing helix chain 'N' and resid 134 through 139 removed outlier: 3.611A pdb=" N LYS N 139 " --> pdb=" O LYS N 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 27 removed outlier: 3.944A pdb=" N THR O 26 " --> pdb=" O ARG O 22 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA O 27 " --> pdb=" O TRP O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 43 removed outlier: 3.874A pdb=" N MET O 38 " --> pdb=" O ASN O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 53 No H-bonds generated for 'chain 'O' and resid 51 through 53' Processing helix chain 'O' and resid 56 through 67 Processing helix chain 'O' and resid 69 through 72 Processing helix chain 'O' and resid 95 through 111 removed outlier: 3.854A pdb=" N ASP O 99 " --> pdb=" O THR O 95 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET O 100 " --> pdb=" O ALA O 96 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU O 109 " --> pdb=" O ASP O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 122 removed outlier: 3.731A pdb=" N ARG O 119 " --> pdb=" O TYR O 115 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N HIS O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 18 No H-bonds generated for 'chain 'P' and resid 16 through 18' Processing helix chain 'P' and resid 33 through 35 No H-bonds generated for 'chain 'P' and resid 33 through 35' Processing helix chain 'P' and resid 47 through 50 No H-bonds generated for 'chain 'P' and resid 47 through 50' Processing helix chain 'Q' and resid 31 through 43 removed outlier: 3.774A pdb=" N LEU Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG Q 41 " --> pdb=" O VAL Q 37 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS Q 42 " --> pdb=" O VAL Q 38 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU Q 43 " --> pdb=" O LYS Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 57 removed outlier: 3.758A pdb=" N ILE Q 53 " --> pdb=" O MET Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 85 removed outlier: 4.066A pdb=" N GLU Q 83 " --> pdb=" O THR Q 79 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS Q 84 " --> pdb=" O ARG Q 80 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS Q 85 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 102 removed outlier: 3.659A pdb=" N ALA Q 102 " --> pdb=" O LEU Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 108 No H-bonds generated for 'chain 'Q' and resid 105 through 108' Processing helix chain 'Q' and resid 119 through 138 removed outlier: 3.731A pdb=" N GLN Q 123 " --> pdb=" O MET Q 119 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR Q 135 " --> pdb=" O ARG Q 131 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 16 removed outlier: 3.701A pdb=" N ARG S 11 " --> pdb=" O GLY S 7 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL S 12 " --> pdb=" O PHE S 8 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU S 15 " --> pdb=" O ARG S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.734A pdb=" N LYS S 33 " --> pdb=" O GLU S 29 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU S 36 " --> pdb=" O LYS S 32 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU S 37 " --> pdb=" O LYS S 33 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU S 38 " --> pdb=" O LYS S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 62 removed outlier: 3.725A pdb=" N ARG S 49 " --> pdb=" O LYS S 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 17 Processing helix chain 'T' and resid 25 through 27 No H-bonds generated for 'chain 'T' and resid 25 through 27' Processing helix chain 'T' and resid 30 through 35 Processing helix chain 'T' and resid 42 through 56 removed outlier: 3.693A pdb=" N LYS T 50 " --> pdb=" O LYS T 46 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA T 54 " --> pdb=" O LYS T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 106 Processing helix chain 'U' and resid 4 through 6 No H-bonds generated for 'chain 'U' and resid 4 through 6' Processing helix chain 'U' and resid 9 through 22 removed outlier: 3.665A pdb=" N GLN U 18 " --> pdb=" O GLU U 14 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG U 19 " --> pdb=" O ARG U 15 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS U 21 " --> pdb=" O ALA U 17 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLU U 22 " --> pdb=" O GLN U 18 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 34 No H-bonds generated for 'chain 'U' and resid 32 through 34' Processing helix chain 'U' and resid 50 through 63 removed outlier: 3.569A pdb=" N ARG U 54 " --> pdb=" O TRP U 50 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG U 60 " --> pdb=" O ALA U 56 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG U 61 " --> pdb=" O SER U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 76 removed outlier: 4.622A pdb=" N THR U 75 " --> pdb=" O GLU U 71 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR U 76 " --> pdb=" O ARG U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 108 removed outlier: 3.633A pdb=" N ALA U 101 " --> pdb=" O ILE U 97 " (cutoff:3.500A) Processing helix chain 'U' and resid 123 through 140 removed outlier: 3.586A pdb=" N ILE U 132 " --> pdb=" O PHE U 128 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU U 139 " --> pdb=" O GLU U 135 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 43 Processing helix chain 'V' and resid 75 through 81 Processing helix chain 'V' and resid 85 through 89 Processing helix chain 'Z' and resid 4 through 7 No H-bonds generated for 'chain 'Z' and resid 4 through 7' Processing helix chain 'Z' and resid 12 through 24 removed outlier: 4.128A pdb=" N LYS Z 23 " --> pdb=" O GLU Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 27 through 29 No H-bonds generated for 'chain 'Z' and resid 27 through 29' Processing helix chain 'Z' and resid 51 through 55 Processing helix chain 'Z' and resid 62 through 71 Processing helix chain 'Z' and resid 92 through 105 removed outlier: 4.602A pdb=" N VAL Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) Processing helix chain 'Z' and resid 109 through 123 removed outlier: 3.876A pdb=" N ALA Z 113 " --> pdb=" O PHE Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 157 through 160 No H-bonds generated for 'chain 'Z' and resid 157 through 160' Processing helix chain '0' and resid 5 through 7 No H-bonds generated for 'chain '0' and resid 5 through 7' Processing helix chain '0' and resid 17 through 27 removed outlier: 3.811A pdb=" N LYS 0 21 " --> pdb=" O LYS 0 17 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG 0 22 " --> pdb=" O TRP 0 18 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG 0 25 " --> pdb=" O LYS 0 21 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 0 26 " --> pdb=" O ARG 0 22 " (cutoff:3.500A) Processing helix chain '0' and resid 29 through 32 No H-bonds generated for 'chain '0' and resid 29 through 32' Processing helix chain '3' and resid 13 through 20 Processing helix chain '3' and resid 24 through 27 No H-bonds generated for 'chain '3' and resid 24 through 27' Processing helix chain '3' and resid 40 through 45 Processing helix chain '3' and resid 66 through 72 removed outlier: 4.222A pdb=" N GLU 3 71 " --> pdb=" O PRO 3 67 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU 3 72 " --> pdb=" O PRO 3 68 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 87 No H-bonds generated for 'chain '3' and resid 84 through 87' Processing helix chain '3' and resid 108 through 121 removed outlier: 4.489A pdb=" N MET 3 116 " --> pdb=" O GLU 3 112 " (cutoff:3.500A) Processing helix chain '6' and resid 93 through 95 No H-bonds generated for 'chain '6' and resid 93 through 95' Processing helix chain '6' and resid 102 through 104 No H-bonds generated for 'chain '6' and resid 102 through 104' Processing helix chain '7' and resid 22 through 30 Processing helix chain '7' and resid 38 through 43 Processing helix chain '7' and resid 75 through 77 No H-bonds generated for 'chain '7' and resid 75 through 77' Processing helix chain '7' and resid 101 through 109 removed outlier: 3.717A pdb=" N LEU 7 105 " --> pdb=" O MET 7 101 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER 7 106 " --> pdb=" O ALA 7 102 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY 7 107 " --> pdb=" O THR 7 103 " (cutoff:3.500A) Processing helix chain '7' and resid 127 through 139 removed outlier: 4.118A pdb=" N GLU 7 131 " --> pdb=" O PRO 7 127 " (cutoff:3.500A) Processing helix chain '7' and resid 156 through 170 Processing helix chain '7' and resid 191 through 201 Processing helix chain '7' and resid 303 through 305 No H-bonds generated for 'chain '7' and resid 303 through 305' Processing helix chain '7' and resid 307 through 309 No H-bonds generated for 'chain '7' and resid 307 through 309' Processing helix chain '8' and resid 5 through 14 removed outlier: 4.031A pdb=" N GLU 8 9 " --> pdb=" O LYS 8 5 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N MET 8 10 " --> pdb=" O GLU 8 6 " (cutoff:3.500A) Processing helix chain '8' and resid 58 through 61 No H-bonds generated for 'chain '8' and resid 58 through 61' Processing helix chain '8' and resid 65 through 69 Processing helix chain '8' and resid 90 through 100 removed outlier: 4.074A pdb=" N THR 8 94 " --> pdb=" O GLN 8 90 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG 8 98 " --> pdb=" O THR 8 94 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N PHE 8 99 " --> pdb=" O LEU 8 95 " (cutoff:3.500A) Processing helix chain '9' and resid 43 through 45 No H-bonds generated for 'chain '9' and resid 43 through 45' Processing helix chain '9' and resid 54 through 57 No H-bonds generated for 'chain '9' and resid 54 through 57' Processing helix chain '9' and resid 87 through 113 removed outlier: 3.608A pdb=" N ARG 9 91 " --> pdb=" O ASP 9 87 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LYS 9 92 " --> pdb=" O ASP 9 88 " (cutoff:3.500A) Processing helix chain '9' and resid 119 through 124 Processing helix chain '9' and resid 136 through 141 Processing helix chain '9' and resid 148 through 153 Processing helix chain '9' and resid 161 through 166 Processing helix chain '9' and resid 192 through 203 Processing helix chain '9' and resid 207 through 210 No H-bonds generated for 'chain '9' and resid 207 through 210' Processing helix chain '9' and resid 239 through 256 removed outlier: 4.134A pdb=" N GLN 9 245 " --> pdb=" O GLU 9 241 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE 9 246 " --> pdb=" O ALA 9 242 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE 9 253 " --> pdb=" O ASN 9 249 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU 9 256 " --> pdb=" O LYS 9 252 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 Processing sheet with id= B, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.597A pdb=" N PHE A 69 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 68 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY A 85 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N GLN A 70 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N PHE A 83 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 12.681A pdb=" N LYS A 82 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 11.847A pdb=" N GLY A 193 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LYS A 84 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 191 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 188 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 190 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS A 117 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 103 through 105 Processing sheet with id= D, first strand: chain 'B' and resid 68 through 71 removed outlier: 6.902A pdb=" N ARG B 90 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N SER B 71 " --> pdb=" O ARG B 90 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE B 92 " --> pdb=" O SER B 71 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 32 through 35 removed outlier: 6.932A pdb=" N VAL B 42 " --> pdb=" O TYR B 33 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.593A pdb=" N PHE C 30 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 130 through 132 removed outlier: 3.630A pdb=" N THR D 153 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 42 through 44 Processing sheet with id= I, first strand: chain 'E' and resid 90 through 93 removed outlier: 3.652A pdb=" N GLU E 98 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS E 113 " --> pdb=" O ARG E 101 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 122 through 126 removed outlier: 3.500A pdb=" N MET E 166 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 129 through 133 removed outlier: 3.539A pdb=" N HIS E 148 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 184 through 186 removed outlier: 3.687A pdb=" N GLY E 197 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR E 214 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ILE E 202 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL E 212 " --> pdb=" O ILE E 202 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 121 through 123 removed outlier: 3.685A pdb=" N ASP F 67 " --> pdb=" O LEU F 86 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ALA F 88 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE F 65 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 145 through 149 Processing sheet with id= O, first strand: chain 'G' and resid 16 through 18 removed outlier: 3.836A pdb=" N ASN G 120 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY G 65 " --> pdb=" O ASN G 120 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS G 122 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE G 63 " --> pdb=" O LYS G 122 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL G 124 " --> pdb=" O MET G 61 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N MET G 61 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 83 through 88 removed outlier: 3.774A pdb=" N ARG G 103 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 135 through 138 Processing sheet with id= R, first strand: chain 'I' and resid 24 through 27 Processing sheet with id= S, first strand: chain 'I' and resid 71 through 74 removed outlier: 3.621A pdb=" N TYR I 128 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG I 124 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE I 103 " --> pdb=" O ILE I 126 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR I 128 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE I 101 " --> pdb=" O TYR I 128 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY I 109 " --> pdb=" O THR I 106 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 43 through 48 Processing sheet with id= U, first strand: chain 'J' and resid 122 through 124 removed outlier: 3.710A pdb=" N ILE J 100 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG J 79 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 4 through 9 removed outlier: 3.573A pdb=" N ILE K 14 " --> pdb=" O GLN K 67 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 26 through 28 removed outlier: 6.468A pdb=" N ILE K 62 " --> pdb=" O ARG K 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 43 through 49 removed outlier: 3.638A pdb=" N THR L 49 " --> pdb=" O ASP L 62 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 80 through 84 Processing sheet with id= Z, first strand: chain 'N' and resid 102 through 105 removed outlier: 6.838A pdb=" N ARG N 74 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS N 57 " --> pdb=" O ALA N 72 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA N 72 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA N 59 " --> pdb=" O ARG N 70 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ARG N 70 " --> pdb=" O ALA N 59 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'R' and resid 33 through 37 removed outlier: 3.603A pdb=" N ILE R 88 " --> pdb=" O PHE R 34 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA R 104 " --> pdb=" O LEU R 87 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA R 89 " --> pdb=" O VAL R 102 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL R 102 " --> pdb=" O ALA R 89 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'R' and resid 46 through 56 removed outlier: 3.628A pdb=" N ALA R 72 " --> pdb=" O VAL R 47 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'T' and resid 80 through 82 removed outlier: 3.754A pdb=" N ILE T 81 " --> pdb=" O VAL T 92 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'U' and resid 79 through 81 removed outlier: 3.917A pdb=" N ARG U 89 " --> pdb=" O LYS U 81 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'U' and resid 111 through 114 removed outlier: 3.502A pdb=" N GLY U 118 " --> pdb=" O VAL U 114 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'V' and resid 2 through 11 removed outlier: 6.341A pdb=" N TYR V 20 " --> pdb=" O THR V 6 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL V 8 " --> pdb=" O GLU V 18 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU V 18 " --> pdb=" O VAL V 8 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLU V 10 " --> pdb=" O ARG V 16 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG V 16 " --> pdb=" O GLU V 10 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE V 21 " --> pdb=" O GLY V 67 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY V 67 " --> pdb=" O PHE V 21 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS V 70 " --> pdb=" O ILE V 53 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILE V 53 " --> pdb=" O LYS V 70 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'X' and resid 7 through 9 removed outlier: 3.623A pdb=" N TYR X 7 " --> pdb=" O LEU X 57 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'X' and resid 40 through 46 removed outlier: 3.549A pdb=" N GLY X 16 " --> pdb=" O GLN X 26 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS X 28 " --> pdb=" O ILE X 14 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE X 14 " --> pdb=" O LYS X 28 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'Z' and resid 33 through 38 removed outlier: 3.504A pdb=" N GLY Z 41 " --> pdb=" O THR Z 38 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Z' and resid 144 through 147 removed outlier: 4.459A pdb=" N GLY Z 127 " --> pdb=" O MET Z 183 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain '3' and resid 51 through 53 removed outlier: 3.730A pdb=" N ILE 3 53 " --> pdb=" O ILE 3 78 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '6' and resid 23 through 26 Processing sheet with id= AM, first strand: chain '6' and resid 47 through 49 removed outlier: 4.063A pdb=" N ARG 6 47 " --> pdb=" O VAL 6 39 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN 6 30 " --> pdb=" O ASP 6 38 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '7' and resid 13 through 15 removed outlier: 6.041A pdb=" N ILE 7 145 " --> pdb=" O LEU 7 116 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N VAL 7 118 " --> pdb=" O ILE 7 145 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL 7 147 " --> pdb=" O VAL 7 118 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '7' and resid 219 through 221 Processing sheet with id= AP, first strand: chain '7' and resid 246 through 248 Processing sheet with id= AQ, first strand: chain '7' and resid 272 through 275 Processing sheet with id= AR, first strand: chain '7' and resid 259 through 263 removed outlier: 3.883A pdb=" N LEU 7 259 " --> pdb=" O GLU 7 270 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER 7 268 " --> pdb=" O VAL 7 261 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain '7' and resid 324 through 326 removed outlier: 3.975A pdb=" N LEU 7 326 " --> pdb=" O VAL 7 386 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL 7 386 " --> pdb=" O LEU 7 326 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain '7' and resid 377 through 381 removed outlier: 7.618A pdb=" N ILE 7 397 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TRP 7 410 " --> pdb=" O THR 7 395 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR 7 395 " --> pdb=" O TRP 7 410 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLN 7 400 " --> pdb=" O THR 7 356 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N THR 7 356 " --> pdb=" O GLN 7 400 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU 7 379 " --> pdb=" O THR 7 371 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain '7' and resid 53 through 58 removed outlier: 4.067A pdb=" N ARG 7 87 " --> pdb=" O ILE 7 56 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL 7 58 " --> pdb=" O PHE 7 85 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N PHE 7 85 " --> pdb=" O VAL 7 58 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain '7' and resid 214 through 217 removed outlier: 4.718A pdb=" N GLN 7 244 " --> pdb=" O VAL 7 214 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU 7 216 " --> pdb=" O ILE 7 242 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE 7 242 " --> pdb=" O LEU 7 216 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain '8' and resid 73 through 75 removed outlier: 4.031A pdb=" N ASN 8 74 " --> pdb=" O VAL 8 82 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL 8 82 " --> pdb=" O ASN 8 74 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain '8' and resid 114 through 116 Processing sheet with id= AY, first strand: chain '9' and resid 37 through 41 removed outlier: 3.652A pdb=" N GLY 9 26 " --> pdb=" O PHE 9 23 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER 9 30 " --> pdb=" O VAL 9 19 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL 9 19 " --> pdb=" O SER 9 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP 9 79 " --> pdb=" O ILE 9 69 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL 9 71 " --> pdb=" O THR 9 77 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR 9 77 " --> pdb=" O VAL 9 71 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain '9' and resid 259 through 263 815 hydrogen bonds defined for protein. 2280 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1050 hydrogen bonds 1884 hydrogen bond angles 0 basepair planarities 383 basepair parallelities 839 stacking parallelities Total time for adding SS restraints: 48.57 Time building geometry restraints manager: 26.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 7494 1.29 - 1.43: 29422 1.43 - 1.56: 35056 1.56 - 1.70: 3189 1.70 - 1.83: 222 Bond restraints: 75383 Sorted by residual: bond pdb=" C4 B8H 2 938 " pdb=" C5 B8H 2 938 " ideal model delta sigma weight residual 1.834 1.372 0.462 2.00e-02 2.50e+03 5.35e+02 bond pdb=" N1 B8H 2 938 " pdb=" C6 B8H 2 938 " ideal model delta sigma weight residual 1.682 1.347 0.335 2.00e-02 2.50e+03 2.80e+02 bond pdb=" C4 5MU 4 54 " pdb=" C5 5MU 4 54 " ideal model delta sigma weight residual 1.802 1.476 0.326 2.00e-02 2.50e+03 2.66e+02 bond pdb=" N1 5MU 4 54 " pdb=" C6 5MU 4 54 " ideal model delta sigma weight residual 1.635 1.336 0.299 2.00e-02 2.50e+03 2.23e+02 bond pdb=" C1' GNP 7 501 " pdb=" C2' GNP 7 501 " ideal model delta sigma weight residual 1.273 1.531 -0.258 2.00e-02 2.50e+03 1.67e+02 ... (remaining 75378 not shown) Histogram of bond angle deviations from ideal: 98.63 - 106.94: 11559 106.94 - 115.25: 47577 115.25 - 123.55: 41841 123.55 - 131.86: 8399 131.86 - 140.17: 244 Bond angle restraints: 109620 Sorted by residual: angle pdb=" C ALA 7 2 " pdb=" N TRP 7 3 " pdb=" CA TRP 7 3 " ideal model delta sigma weight residual 120.83 140.17 -19.34 1.43e+00 4.89e-01 1.83e+02 angle pdb=" C1' A2M 2 373 " pdb=" N9 A2M 2 373 " pdb=" C8 A2M 2 373 " ideal model delta sigma weight residual 88.50 123.58 -35.08 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N6 A2M 2 373 " pdb=" C6 A2M 2 373 " pdb=" N1 A2M 2 373 " ideal model delta sigma weight residual 92.14 121.36 -29.22 3.00e+00 1.11e-01 9.49e+01 angle pdb=" C ASP 7 93 " pdb=" N ALA 7 94 " pdb=" CA ALA 7 94 " ideal model delta sigma weight residual 122.48 136.03 -13.55 1.62e+00 3.81e-01 6.99e+01 angle pdb=" O3' C 4 74 " pdb=" C3' C 4 74 " pdb=" C2' C 4 74 " ideal model delta sigma weight residual 109.50 120.81 -11.31 1.50e+00 4.44e-01 5.69e+01 ... (remaining 109615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 43469 35.30 - 70.59: 4122 70.59 - 105.89: 526 105.89 - 141.19: 10 141.19 - 176.49: 5 Dihedral angle restraints: 48132 sinusoidal: 35156 harmonic: 12976 Sorted by residual: dihedral pdb=" O4' C 4 17 " pdb=" C1' C 4 17 " pdb=" N1 C 4 17 " pdb=" C2 C 4 17 " ideal model delta sinusoidal sigma weight residual 200.00 56.20 143.80 1 1.50e+01 4.44e-03 7.71e+01 dihedral pdb=" O4' C 21132 " pdb=" C1' C 21132 " pdb=" N1 C 21132 " pdb=" C2 C 21132 " ideal model delta sinusoidal sigma weight residual 200.00 66.74 133.26 1 1.50e+01 4.44e-03 7.19e+01 dihedral pdb=" O4' C 21498 " pdb=" C1' C 21498 " pdb=" N1 C 21498 " pdb=" C2 C 21498 " ideal model delta sinusoidal sigma weight residual -128.00 48.49 -176.49 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 48129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 13226 0.151 - 0.302: 128 0.302 - 0.454: 0 0.454 - 0.605: 1 0.605 - 0.756: 1 Chirality restraints: 13356 Sorted by residual: chirality pdb=" C3' C 4 74 " pdb=" C4' C 4 74 " pdb=" O3' C 4 74 " pdb=" C2' C 4 74 " both_signs ideal model delta sigma weight residual False -2.74 -1.99 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" C1' B8H 2 938 " pdb=" O4' B8H 2 938 " pdb=" C2' B8H 2 938 " pdb=" C5 B8H 2 938 " both_signs ideal model delta sigma weight residual False 2.55 2.04 0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" C1' G 2 987 " pdb=" O4' G 2 987 " pdb=" C2' G 2 987 " pdb=" N9 G 2 987 " both_signs ideal model delta sigma weight residual False 2.46 2.17 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 13353 not shown) Planarity restraints: 7943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' H2U 4 20 " -0.847 2.00e-02 2.50e+03 5.83e-01 7.64e+03 pdb=" C4' H2U 4 20 " 0.222 2.00e-02 2.50e+03 pdb=" O4' H2U 4 20 " 0.640 2.00e-02 2.50e+03 pdb=" C3' H2U 4 20 " -0.195 2.00e-02 2.50e+03 pdb=" O3' H2U 4 20 " 0.950 2.00e-02 2.50e+03 pdb=" C2' H2U 4 20 " -0.623 2.00e-02 2.50e+03 pdb=" O2' H2U 4 20 " -0.613 2.00e-02 2.50e+03 pdb=" C1' H2U 4 20 " 0.418 2.00e-02 2.50e+03 pdb=" N1 H2U 4 20 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 21376 " 0.043 2.00e-02 2.50e+03 5.79e-01 7.55e+03 pdb=" C4' OMC 21376 " 0.451 2.00e-02 2.50e+03 pdb=" O4' OMC 21376 " 0.638 2.00e-02 2.50e+03 pdb=" C3' OMC 21376 " -0.579 2.00e-02 2.50e+03 pdb=" O3' OMC 21376 " -0.592 2.00e-02 2.50e+03 pdb=" C2' OMC 21376 " -0.207 2.00e-02 2.50e+03 pdb=" O2' OMC 21376 " 0.918 2.00e-02 2.50e+03 pdb=" C1' OMC 21376 " 0.215 2.00e-02 2.50e+03 pdb=" N1 OMC 21376 " -0.888 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GNP 7 501 " 0.445 2.00e-02 2.50e+03 5.70e-01 7.30e+03 pdb=" C2' GNP 7 501 " -0.612 2.00e-02 2.50e+03 pdb=" C3' GNP 7 501 " -0.268 2.00e-02 2.50e+03 pdb=" C4' GNP 7 501 " 0.202 2.00e-02 2.50e+03 pdb=" C5' GNP 7 501 " -0.855 2.00e-02 2.50e+03 pdb=" N9 GNP 7 501 " -0.024 2.00e-02 2.50e+03 pdb=" O2' GNP 7 501 " -0.482 2.00e-02 2.50e+03 pdb=" O3' GNP 7 501 " 0.788 2.00e-02 2.50e+03 pdb=" O4' GNP 7 501 " 0.806 2.00e-02 2.50e+03 ... (remaining 7940 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 292 2.44 - 3.05: 41615 3.05 - 3.67: 107431 3.67 - 4.28: 174513 4.28 - 4.90: 263258 Nonbonded interactions: 587109 Sorted by model distance: nonbonded pdb=" OP2 G 2 727 " pdb="MG MG 21608 " model vdw 1.823 2.170 nonbonded pdb=" OP1 C 2 586 " pdb="MG MG 21612 " model vdw 1.854 2.170 nonbonded pdb=" OP1 A 2 587 " pdb="MG MG 21606 " model vdw 1.879 2.170 nonbonded pdb=" OP2 C 21294 " pdb="MG MG 21630 " model vdw 1.898 2.170 nonbonded pdb=" OP1 U 21198 " pdb="MG MG 21628 " model vdw 1.899 2.170 ... (remaining 587104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.060 Extract box with map and model: 10.990 Check model and map are aligned: 0.750 Set scattering table: 0.490 Process input model: 186.180 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 204.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 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 0.462 75383 Z= 0.762 Angle : 0.960 35.078 109620 Z= 0.477 Chirality : 0.052 0.756 13356 Planarity : 0.018 0.583 7943 Dihedral : 22.238 176.486 39778 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.42 % Favored : 86.56 % Rotamer: Outliers : 0.13 % Allowed : 11.27 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -5.19 (0.10), residues: 4448 helix: -3.48 (0.11), residues: 1182 sheet: -3.02 (0.16), residues: 785 loop : -3.69 (0.10), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 184 HIS 0.012 0.002 HIS 7 132 PHE 0.025 0.003 PHE K 71 TYR 0.031 0.003 TYR 7 51 ARG 0.010 0.001 ARG V 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 3870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 719 time to evaluate : 4.201 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: L 100 LEU cc_start: 0.8357 (pt) cc_final: 0.8068 (pt) REVERT: N 77 LEU cc_start: 0.7824 (mt) cc_final: 0.7507 (mp) REVERT: W 6 ASN cc_start: 0.7522 (p0) cc_final: 0.7128 (p0) REVERT: Y 1 MET cc_start: 0.1867 (tpp) cc_final: 0.0536 (ttp) REVERT: 7 101 MET cc_start: -0.0160 (mmt) cc_final: -0.0865 (tpp) REVERT: 7 171 LYS cc_start: 0.5131 (mmtm) cc_final: 0.3874 (ttpp) outliers start: 5 outliers final: 3 residues processed: 723 average time/residue: 0.6964 time to fit residues: 839.6595 Evaluate side-chains 494 residues out of total 3870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 491 time to evaluate : 4.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain 7 residue 295 VAL Chi-restraints excluded: chain 4 residue 101 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 501 optimal weight: 6.9990 chunk 450 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 303 optimal weight: 9.9990 chunk 240 optimal weight: 5.9990 chunk 465 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 346 optimal weight: 2.9990 chunk 539 optimal weight: 40.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 18 HIS B 145 ASN ** B 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN D 123 GLN D 135 GLN E 99 HIS E 192 ASN F 181 GLN F 207 ASN G 46 ASN G 110 ASN G 118 GLN G 120 ASN H 48 HIS H 193 ASN I 9 ASN J 121 ASN K 120 ASN ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 ASN N 130 ASN S 6 GLN S 48 ASN T 84 HIS W 27 GLN W 40 ASN X 26 GLN ** Z 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 148 GLN ** 7 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 132 HIS 7 148 GLN 7 187 HIS 7 224 ASN 7 244 GLN 7 251 GLN 7 400 GLN 9 249 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 75383 Z= 0.257 Angle : 0.757 48.090 109620 Z= 0.383 Chirality : 0.040 0.239 13356 Planarity : 0.006 0.123 7943 Dihedral : 23.057 173.719 30259 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.56 % Allowed : 16.55 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.11), residues: 4448 helix: -2.28 (0.13), residues: 1211 sheet: -2.35 (0.16), residues: 801 loop : -3.01 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 5 HIS 0.006 0.001 HIS 7 20 PHE 0.019 0.001 PHE Y 21 TYR 0.017 0.001 TYR 7 51 ARG 0.007 0.000 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 534 time to evaluate : 4.151 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 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 303, in __init__ self.caller(self.optimize_sidechains) 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 609, in optimize_sidechains log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 83, in __init__ rotatable_hd = self.rotatable_hd) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 189, in run_one pdb_hierarchy = self.run_one_one(args=args) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 133, in run_one_one log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 108, in __init__ self.loop(function = self.one_residue_iteration) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 284, in loop function(residue = residue) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residues.py", line 271, in one_residue_iteration log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 172, in __init__ self.fit_proline() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/fit_residue.py", line 217, in fit_proline for rotamer, sites_cart in rotamer_iterator: TypeError: 'NoneType' object is not iterable