Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 15:51:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdh_14648/04_2023/7zdh_14648_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdh_14648/04_2023/7zdh_14648.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdh_14648/04_2023/7zdh_14648_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdh_14648/04_2023/7zdh_14648_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdh_14648/04_2023/7zdh_14648_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdh_14648/04_2023/7zdh_14648.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdh_14648/04_2023/7zdh_14648.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdh_14648/04_2023/7zdh_14648_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdh_14648/04_2023/7zdh_14648_updated.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.012 sd= 0.034 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: 8 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 28 5.49 5 S 468 5.16 5 C 43418 2.51 5 N 11233 2.21 5 O 12042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 112": "OE1" <-> "OE2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J GLU 114": "OE1" <-> "OE2" Residue "K TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "L PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "V GLU 16": "OE1" <-> "OE2" Residue "V GLU 50": "OE1" <-> "OE2" Residue "V GLU 81": "OE1" <-> "OE2" Residue "V GLU 137": "OE1" <-> "OE2" Residue "X GLU 61": "OE1" <-> "OE2" Residue "Y ASP 36": "OD1" <-> "OD2" Residue "Y ASP 156": "OD1" <-> "OD2" Residue "Z ASP 72": "OD1" <-> "OD2" Residue "Z ASP 80": "OD1" <-> "OD2" Residue "k TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 4": "OD1" <-> "OD2" Residue "m ASP 59": "OD1" <-> "OD2" Residue "m ASP 64": "OD1" <-> "OD2" Residue "n ASP 42": "OD1" <-> "OD2" Residue "n TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 105": "OD1" <-> "OD2" Residue "p TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 6": "OE1" <-> "OE2" Residue "p GLU 27": "OE1" <-> "OE2" Residue "p GLU 60": "OE1" <-> "OE2" Residue "p GLU 117": "OE1" <-> "OE2" Residue "q ASP 63": "OD1" <-> "OD2" Residue "q ASP 79": "OD1" <-> "OD2" Residue "r GLU 16": "OE1" <-> "OE2" Residue "r GLU 98": "OE1" <-> "OE2" Residue "r GLU 114": "OE1" <-> "OE2" Residue "w ASP 34": "OD1" <-> "OD2" Residue "x GLU 41": "OE1" <-> "OE2" Residue "y GLU 32": "OE1" <-> "OE2" Residue "y GLU 47": "OE1" <-> "OE2" Residue "z ASP 51": "OD1" <-> "OD2" Residue "1 PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 427": "OE1" <-> "OE2" Residue "2 ASP 114": "OD1" <-> "OD2" Residue "2 GLU 118": "OE1" <-> "OE2" Residue "2 ASP 168": "OD1" <-> "OD2" Residue "2 GLU 170": "OE1" <-> "OE2" Residue "2 ASP 174": "OD1" <-> "OD2" Residue "3 TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 88": "OE1" <-> "OE2" Residue "4 ASP 160": "OD1" <-> "OD2" Residue "6 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 137": "OD1" <-> "OD2" Residue "9 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 172": "OD1" <-> "OD2" Residue "b GLU 37": "OE1" <-> "OE2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "c GLU 15": "OE1" <-> "OE2" Residue "c GLU 107": "OE1" <-> "OE2" Residue "d PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 240": "OD1" <-> "OD2" Residue "e ASP 34": "OD1" <-> "OD2" Residue "e TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 84": "OD1" <-> "OD2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "g GLU 33": "OE1" <-> "OE2" Residue "g ASP 60": "OD1" <-> "OD2" Residue "g GLU 110": "OE1" <-> "OE2" Residue "h GLU 109": "OE1" <-> "OE2" Residue "i TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 55": "OE1" <-> "OE2" Residue "j GLU 61": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 67219 Number of models: 1 Model: "" Number of chains: 66 Chain: "A" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 922 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2528 Classifications: {'peptide': 318} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 295} Chain: "J" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 3, 'TRANS': 171} Chain: "K" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 749 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4807 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3647 Classifications: {'peptide': 459} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 437} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2723 Classifications: {'peptide': 347} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 326} Chain: "V" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1028 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1155 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 10, 'TRANS': 128} Chain: "X" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 701 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "Y" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 12, 'TRANS': 158} Chain: "Z" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1441 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "k" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2596 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain: "l" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 874 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "m" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 626 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 11, 'TRANS': 68} Chain: "n" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 634 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "o" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1004 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 10, 'TRANS': 109} Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1059 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "q" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1142 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "r" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 846 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 86} Chain breaks: 1 Chain: "s" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1047 Classifications: {'peptide': 122} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 114} Chain: "t" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1520 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 16, 'TRANS': 160} Chain: "u" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 563 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "v" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1307 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 20, 'TRANS': 134} Chain: "w" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 846 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, 'TRANS': 92} Chain: "x" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 576 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3312 Classifications: {'peptide': 430} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 408} Chain: "2" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1655 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 191} Chain: "3" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5275 Classifications: {'peptide': 688} Link IDs: {'PTRANS': 32, 'TRANS': 655} Chain: "4" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3457 Classifications: {'peptide': 430} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 401} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1726 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "6" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1247 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "9" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1414 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "a" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "b" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 737 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "c" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "d" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2748 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 21, 'TRANS': 318} Chain: "e" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "f" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 917 Classifications: {'peptide': 113} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 104} Chain: "g" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 969 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "h" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 11, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1209 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 660 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 190 Unusual residues: {'3PE': 2, 'PC1': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "M" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "N" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "V" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Chain: "o" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "p" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 23 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "9" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 40651 SG CYS 1 365 103.994 55.039 241.035 1.00 42.11 S ATOM 40975 SG CYS 1 405 107.691 49.710 240.207 1.00 51.22 S ATOM 40631 SG CYS 1 362 106.890 54.867 236.018 1.00 29.46 S ATOM 40612 SG CYS 1 359 110.802 55.063 241.442 1.00 38.96 S ATOM 42052 SG CYS 2 103 101.562 48.647 260.232 1.00 78.72 S ATOM 42086 SG CYS 2 108 99.671 46.274 262.151 1.00 39.80 S ATOM 42366 SG CYS 2 144 103.404 45.503 256.668 1.00 73.42 S ATOM 42389 SG CYS 2 148 101.823 42.520 257.758 1.00 86.69 S ATOM 43729 SG CYS 3 114 105.888 74.209 227.105 1.00 35.21 S ATOM 43668 SG CYS 3 105 100.645 77.429 229.419 1.00 37.25 S ATOM 43689 SG CYS 3 108 106.644 79.259 231.055 1.00 35.20 S ATOM 44061 SG CYS 3 156 113.889 66.613 231.731 1.00 35.77 S ATOM 44038 SG CYS 3 153 111.477 69.414 237.113 1.00 43.02 S ATOM 44085 SG CYS 3 159 117.772 70.466 235.443 1.00 76.82 S ATOM 44415 SG CYS 3 203 113.282 73.031 231.920 1.00 74.07 S ATOM 43174 SG CYS 3 41 112.379 60.161 229.332 1.00 40.01 S ATOM 43260 SG CYS 3 52 108.851 60.767 228.548 1.00 83.72 S ATOM 43285 SG CYS 3 55 109.780 56.168 224.755 1.00 37.25 S ATOM 43386 SG CYS 3 69 113.138 56.304 226.205 1.00 32.89 S ATOM 54114 SG CYS 6 119 89.731 101.015 205.126 1.00 99.38 S ATOM 54344 SG CYS 6 149 86.863 98.537 210.106 1.00 31.94 S ATOM 53616 SG CYS 6 55 84.198 103.961 207.419 1.00 38.41 S ATOM 53610 SG CYS 6 54 83.446 98.440 204.616 1.00 39.31 S ATOM 55536 SG CYS 9 116 91.071 98.842 216.950 1.00 36.34 S ATOM 55583 SG CYS 9 122 91.898 94.313 221.573 1.00 24.77 S ATOM 55310 SG CYS 9 87 95.692 94.350 216.191 1.00 21.08 S ATOM 55612 SG CYS 9 126 93.947 90.637 228.757 1.00 34.74 S ATOM 55283 SG CYS 9 83 97.680 92.568 223.746 1.00 40.35 S ATOM 55241 SG CYS 9 77 99.702 93.565 229.835 1.00 40.39 S ATOM 55260 SG CYS 9 80 99.154 87.389 227.237 1.00 46.39 S ATOM 56859 SG CYS b 59 95.905 85.164 244.393 1.00 58.30 S ATOM 57037 SG CYS b 84 98.620 85.532 241.950 1.00 64.63 S ATOM 57059 SG CYS b 87 97.288 88.100 243.046 1.00 67.93 S Time building chain proxies: 26.35, per 1000 atoms: 0.39 Number of scatterers: 67219 At special positions: 0 Unit cell: (178.12, 201.3, 294.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 K 1 19.00 S 468 16.00 P 28 15.00 O 12042 8.00 N 11233 7.00 C 43418 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS V 94 " - pdb=" SG CYS V 114 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 112 " - pdb=" SG CYS Z 124 " distance=2.03 Simple disulfide: pdb=" SG CYS l 32 " - pdb=" SG CYS l 65 " distance=2.03 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.03 Simple disulfide: pdb=" SG CYS s 58 " - pdb=" SG CYS s 89 " distance=2.03 Simple disulfide: pdb=" SG CYS s 68 " - pdb=" SG CYS s 79 " distance=2.03 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.05 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 103 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " pdb="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 144 " pdb=" FES 3 803 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 405 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE3 SF4 1 501 " - pdb=" SG CYS 1 362 " pdb=" SF4 3 801 " pdb="FE3 SF4 3 801 " - pdb=" NE2 HIS 3 101 " pdb="FE4 SF4 3 801 " - pdb=" SG CYS 3 108 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " pdb="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb=" SF4 3 802 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " pdb="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE1 SF4 3 802 " - pdb=" SG CYS 3 156 " pdb="FE2 SF4 3 802 " - pdb=" SG CYS 3 153 " pdb=" SF4 6 201 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE1 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 201 " pdb="FE3 SF4 9 201 " - pdb=" SG CYS 9 122 " pdb="FE2 SF4 9 201 " - pdb=" SG CYS 9 116 " pdb="FE4 SF4 9 201 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 201 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 202 " pdb="FE2 SF4 9 202 " - pdb=" SG CYS 9 83 " pdb="FE1 SF4 9 202 " - pdb=" SG CYS 9 126 " pdb="FE4 SF4 9 202 " - pdb=" SG CYS 9 80 " pdb="FE3 SF4 9 202 " - pdb=" SG CYS 9 77 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN b 300 " pdb="ZN ZN b 300 " - pdb=" NE2 HIS b 68 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 59 " Number of angles added : 3 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15462 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 338 helices and 30 sheets defined 50.8% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 2 through 23 removed outlier: 3.739A pdb=" N LEU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 75 removed outlier: 4.319A pdb=" N LEU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 77 through 80 Processing helix chain 'A' and resid 85 through 107 Processing helix chain 'H' and resid 2 through 32 Proline residue: H 12 - end of helix Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 55 Processing helix chain 'H' and resid 68 through 83 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 122 removed outlier: 4.069A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 153 removed outlier: 5.353A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 170 removed outlier: 3.729A pdb=" N ILE H 166 " --> pdb=" O SER H 163 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR H 168 " --> pdb=" O LEU H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 192 Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 219 through 242 removed outlier: 3.798A pdb=" N PHE H 223 " --> pdb=" O PRO H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 274 Processing helix chain 'H' and resid 284 through 289 Processing helix chain 'H' and resid 293 through 311 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 2 through 21 removed outlier: 5.087A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE J 20 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER J 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 46 Processing helix chain 'J' and resid 50 through 73 Processing helix chain 'J' and resid 87 through 107 Processing helix chain 'J' and resid 124 through 127 Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.152A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 171 Processing helix chain 'K' and resid 4 through 20 Processing helix chain 'K' and resid 26 through 51 Processing helix chain 'K' and resid 55 through 84 removed outlier: 3.989A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 6.075A pdb=" N ALA K 72 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL K 79 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N MET K 80 " --> pdb=" O LEU K 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 24 Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 56 Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix Processing helix chain 'L' and resid 114 through 132 Processing helix chain 'L' and resid 137 through 157 Processing helix chain 'L' and resid 162 through 193 Processing helix chain 'L' and resid 198 through 204 Processing helix chain 'L' and resid 210 through 223 Processing helix chain 'L' and resid 231 through 238 removed outlier: 4.128A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 247 Processing helix chain 'L' and resid 252 through 262 removed outlier: 4.548A pdb=" N GLY L 256 " --> pdb=" O VAL L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 272 through 293 Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 350 Processing helix chain 'L' and resid 356 through 358 No H-bonds generated for 'chain 'L' and resid 356 through 358' Processing helix chain 'L' and resid 362 through 365 No H-bonds generated for 'chain 'L' and resid 362 through 365' Processing helix chain 'L' and resid 367 through 381 Processing helix chain 'L' and resid 389 through 400 removed outlier: 5.168A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 Processing helix chain 'L' and resid 448 through 471 removed outlier: 6.156A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N PHE L 466 " --> pdb=" O LEU L 462 " (cutoff:3.500A) Processing helix chain 'L' and resid 484 through 487 No H-bonds generated for 'chain 'L' and resid 484 through 487' Processing helix chain 'L' and resid 489 through 509 removed outlier: 4.026A pdb=" N HIS L 509 " --> pdb=" O SER L 505 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 546 Proline residue: L 530 - end of helix removed outlier: 4.452A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix Processing helix chain 'L' and resid 558 through 561 No H-bonds generated for 'chain 'L' and resid 558 through 561' Processing helix chain 'L' and resid 563 through 577 Processing helix chain 'L' and resid 584 through 600 Processing helix chain 'M' and resid 5 through 16 removed outlier: 4.271A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 4.178A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 81 Proline residue: M 74 - end of helix removed outlier: 3.714A pdb=" N GLN M 81 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 109 Processing helix chain 'M' and resid 115 through 135 removed outlier: 4.644A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL M 127 " --> pdb=" O GLU M 123 " (cutoff:3.500A) Proline residue: M 128 - end of helix Processing helix chain 'M' and resid 142 through 168 removed outlier: 3.560A pdb=" N LEU M 147 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE M 149 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU M 150 " --> pdb=" O GLY M 146 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR M 152 " --> pdb=" O TYR M 148 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR M 153 " --> pdb=" O PHE M 149 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA M 155 " --> pdb=" O PHE M 151 " (cutoff:3.500A) Proline residue: M 159 - end of helix removed outlier: 3.882A pdb=" N VAL M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 179 No H-bonds generated for 'chain 'M' and resid 176 through 179' Processing helix chain 'M' and resid 190 through 206 removed outlier: 4.517A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 221 removed outlier: 3.882A pdb=" N VAL M 221 " --> pdb=" O PRO M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 250 removed outlier: 4.788A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU M 249 " --> pdb=" O ARG M 245 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU M 250 " --> pdb=" O ILE M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 257 No H-bonds generated for 'chain 'M' and resid 254 through 257' Processing helix chain 'M' and resid 259 through 278 removed outlier: 4.242A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG M 278 " --> pdb=" O SER M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 303 Processing helix chain 'M' and resid 306 through 337 Processing helix chain 'M' and resid 348 through 350 No H-bonds generated for 'chain 'M' and resid 348 through 350' Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 392 through 415 removed outlier: 4.155A pdb=" N ASN M 399 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU M 408 " --> pdb=" O ALA M 404 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR M 409 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR M 414 " --> pdb=" O MET M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 446 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 451 through 454 Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 113 through 121 removed outlier: 4.421A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 133 Processing helix chain 'N' and resid 137 through 144 Processing helix chain 'N' and resid 146 through 148 No H-bonds generated for 'chain 'N' and resid 146 through 148' Processing helix chain 'N' and resid 151 through 171 removed outlier: 4.194A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 192 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 236 removed outlier: 4.730A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS N 236 " --> pdb=" O HIS N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 Processing helix chain 'N' and resid 258 through 270 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 4.278A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix Processing helix chain 'V' and resid 3 through 10 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 79 Processing helix chain 'V' and resid 86 through 104 Processing helix chain 'V' and resid 108 through 130 Processing helix chain 'W' and resid 16 through 46 removed outlier: 4.459A pdb=" N THR W 32 " --> pdb=" O TYR W 28 " (cutoff:3.500A) Proline residue: W 35 - end of helix Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 117 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'X' and resid 8 through 20 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 64 through 67 No H-bonds generated for 'chain 'X' and resid 64 through 67' Processing helix chain 'X' and resid 73 through 84 Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 56 through 76 removed outlier: 3.989A pdb=" N HIS Y 76 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 Processing helix chain 'Y' and resid 100 through 114 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 57 removed outlier: 3.751A pdb=" N LYS Z 57 " --> pdb=" O ARG Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 123 removed outlier: 4.778A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY Z 117 " --> pdb=" O GLN Z 113 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU Z 118 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N SER Z 119 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N HIS Z 120 " --> pdb=" O GLU Z 116 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG Z 121 " --> pdb=" O GLY Z 117 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 171 Processing helix chain 'k' and resid 5 through 10 Processing helix chain 'k' and resid 35 through 43 removed outlier: 4.802A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 118 Processing helix chain 'k' and resid 128 through 130 No H-bonds generated for 'chain 'k' and resid 128 through 130' Processing helix chain 'k' and resid 132 through 140 Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.320A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 186 Processing helix chain 'k' and resid 189 through 193 removed outlier: 3.587A pdb=" N LYS k 193 " --> pdb=" O HIS k 190 " (cutoff:3.500A) Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 210 through 214 Processing helix chain 'k' and resid 227 through 229 No H-bonds generated for 'chain 'k' and resid 227 through 229' Processing helix chain 'k' and resid 231 through 240 removed outlier: 3.607A pdb=" N TYR k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) Processing helix chain 'k' and resid 253 through 264 Processing helix chain 'k' and resid 266 through 271 Processing helix chain 'k' and resid 286 through 297 Processing helix chain 'l' and resid 5 through 9 Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 42 Processing helix chain 'l' and resid 48 through 54 removed outlier: 4.266A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 88 Processing helix chain 'l' and resid 95 through 97 No H-bonds generated for 'chain 'l' and resid 95 through 97' Processing helix chain 'm' and resid 5 through 14 Processing helix chain 'm' and resid 16 through 30 Processing helix chain 'm' and resid 38 through 46 Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 38 Processing helix chain 'n' and resid 48 through 50 No H-bonds generated for 'chain 'n' and resid 48 through 50' Processing helix chain 'n' and resid 54 through 56 No H-bonds generated for 'chain 'n' and resid 54 through 56' Processing helix chain 'n' and resid 62 through 66 Processing helix chain 'n' and resid 70 through 88 Processing helix chain 'o' and resid 16 through 20 removed outlier: 3.773A pdb=" N ARG o 19 " --> pdb=" O ASP o 16 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER o 20 " --> pdb=" O GLU o 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 16 through 20' Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 Processing helix chain 'p' and resid 19 through 22 Processing helix chain 'p' and resid 26 through 50 Processing helix chain 'p' and resid 62 through 72 removed outlier: 3.538A pdb=" N SER p 72 " --> pdb=" O THR p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 93 Processing helix chain 'p' and resid 95 through 117 removed outlier: 3.521A pdb=" N GLU p 117 " --> pdb=" O LYS p 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 31 through 96 Proline residue: q 72 - end of helix removed outlier: 3.689A pdb=" N ALA q 94 " --> pdb=" O LEU q 90 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR q 95 " --> pdb=" O GLU q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 120 through 126 removed outlier: 3.509A pdb=" N GLY q 125 " --> pdb=" O GLY q 121 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU q 126 " --> pdb=" O GLU q 122 " (cutoff:3.500A) Processing helix chain 'q' and resid 129 through 135 Processing helix chain 'r' and resid 5 through 25 Processing helix chain 'r' and resid 69 through 72 No H-bonds generated for 'chain 'r' and resid 69 through 72' Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 2 through 8 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 49 Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 92 through 95 removed outlier: 4.013A pdb=" N CYS t 95 " --> pdb=" O ARG t 92 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 92 through 95' Processing helix chain 't' and resid 100 through 105 Processing helix chain 't' and resid 108 through 111 No H-bonds generated for 'chain 't' and resid 108 through 111' Processing helix chain 't' and resid 115 through 142 removed outlier: 5.040A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) Processing helix chain 't' and resid 167 through 170 No H-bonds generated for 'chain 't' and resid 167 through 170' Processing helix chain 'u' and resid 19 through 42 Processing helix chain 'u' and resid 56 through 58 No H-bonds generated for 'chain 'u' and resid 56 through 58' Processing helix chain 'v' and resid 6 through 8 No H-bonds generated for 'chain 'v' and resid 6 through 8' Processing helix chain 'v' and resid 17 through 26 Processing helix chain 'v' and resid 55 through 57 No H-bonds generated for 'chain 'v' and resid 55 through 57' Processing helix chain 'v' and resid 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 37 through 40 No H-bonds generated for 'chain 'w' and resid 37 through 40' Processing helix chain 'w' and resid 51 through 66 removed outlier: 3.629A pdb=" N PHE w 66 " --> pdb=" O PHE w 62 " (cutoff:3.500A) Processing helix chain 'w' and resid 71 through 78 Processing helix chain 'w' and resid 83 through 100 removed outlier: 5.735A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA w 89 " --> pdb=" O GLN w 86 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 46 Processing helix chain 'y' and resid 11 through 14 removed outlier: 3.689A pdb=" N VAL y 14 " --> pdb=" O TRP y 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 11 through 14' Processing helix chain 'y' and resid 16 through 33 removed outlier: 3.677A pdb=" N GLU y 32 " --> pdb=" O ARG y 28 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS y 33 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 29 Proline residue: z 7 - end of helix removed outlier: 4.902A pdb=" N ILE z 18 " --> pdb=" O CYS z 15 " (cutoff:3.500A) Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 55 Processing helix chain '1' and resid 33 through 37 Processing helix chain '1' and resid 45 through 51 Processing helix chain '1' and resid 53 through 62 Processing helix chain '1' and resid 75 through 80 Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 129 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 229 Processing helix chain '1' and resid 231 through 237 Processing helix chain '1' and resid 239 through 243 Processing helix chain '1' and resid 276 through 282 Processing helix chain '1' and resid 291 through 293 No H-bonds generated for 'chain '1' and resid 291 through 293' Processing helix chain '1' and resid 309 through 314 removed outlier: 3.757A pdb=" N GLU 1 313 " --> pdb=" O LYS 1 309 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N THR 1 314 " --> pdb=" O SER 1 310 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 309 through 314' Processing helix chain '1' and resid 319 through 323 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.584A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 398 removed outlier: 4.093A pdb=" N ASP 1 390 " --> pdb=" O PRO 1 386 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER 1 391 " --> pdb=" O ALA 1 387 " (cutoff:3.500A) Processing helix chain '1' and resid 407 through 437 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 36 Processing helix chain '2' and resid 43 through 58 Proline residue: 2 49 - end of helix Processing helix chain '2' and resid 65 through 73 Processing helix chain '2' and resid 77 through 86 Processing helix chain '2' and resid 106 through 109 No H-bonds generated for 'chain '2' and resid 106 through 109' Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 148 through 150 No H-bonds generated for 'chain '2' and resid 148 through 150' Processing helix chain '2' and resid 166 through 178 Processing helix chain '3' and resid 26 through 33 Processing helix chain '3' and resid 84 through 99 Processing helix chain '3' and resid 105 through 107 No H-bonds generated for 'chain '3' and resid 105 through 107' Processing helix chain '3' and resid 115 through 122 Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 198 through 201 No H-bonds generated for 'chain '3' and resid 198 through 201' Processing helix chain '3' and resid 219 through 221 No H-bonds generated for 'chain '3' and resid 219 through 221' Processing helix chain '3' and resid 265 through 269 Processing helix chain '3' and resid 271 through 274 No H-bonds generated for 'chain '3' and resid 271 through 274' Processing helix chain '3' and resid 296 through 309 removed outlier: 3.792A pdb=" N SER 3 309 " --> pdb=" O GLY 3 305 " (cutoff:3.500A) Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 369 through 372 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 434 Processing helix chain '3' and resid 438 through 445 Processing helix chain '3' and resid 457 through 459 No H-bonds generated for 'chain '3' and resid 457 through 459' Processing helix chain '3' and resid 463 through 478 Processing helix chain '3' and resid 500 through 504 Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 596 through 606 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 628 through 630 No H-bonds generated for 'chain '3' and resid 628 through 630' Processing helix chain '3' and resid 642 through 650 removed outlier: 3.854A pdb=" N LYS 3 650 " --> pdb=" O SER 3 646 " (cutoff:3.500A) Processing helix chain '3' and resid 669 through 671 No H-bonds generated for 'chain '3' and resid 669 through 671' Processing helix chain '3' and resid 676 through 679 No H-bonds generated for 'chain '3' and resid 676 through 679' Processing helix chain '3' and resid 682 through 692 Processing helix chain '4' and resid 8 through 11 No H-bonds generated for 'chain '4' and resid 8 through 11' Processing helix chain '4' and resid 13 through 15 No H-bonds generated for 'chain '4' and resid 13 through 15' Processing helix chain '4' and resid 87 through 90 No H-bonds generated for 'chain '4' and resid 87 through 90' Processing helix chain '4' and resid 96 through 102 Proline residue: 4 101 - end of helix Processing helix chain '4' and resid 111 through 126 Processing helix chain '4' and resid 132 through 161 Processing helix chain '4' and resid 165 through 185 removed outlier: 4.208A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 4.303A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 237 Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 257 through 263 removed outlier: 4.085A pdb=" N GLY 4 262 " --> pdb=" O MET 4 259 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 317 Processing helix chain '4' and resid 335 through 338 No H-bonds generated for 'chain '4' and resid 335 through 338' Processing helix chain '4' and resid 342 through 353 Processing helix chain '4' and resid 394 through 405 removed outlier: 4.339A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 411 through 420 Processing helix chain '4' and resid 425 through 428 No H-bonds generated for 'chain '4' and resid 425 through 428' Processing helix chain '5' and resid 17 through 32 Processing helix chain '5' and resid 54 through 66 removed outlier: 5.052A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix removed outlier: 4.596A pdb=" N THR 5 62 " --> pdb=" O PRO 5 59 " (cutoff:3.500A) Processing helix chain '5' and resid 126 through 137 removed outlier: 5.114A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) Processing helix chain '5' and resid 207 through 209 No H-bonds generated for 'chain '5' and resid 207 through 209' Processing helix chain '6' and resid 25 through 42 Processing helix chain '6' and resid 54 through 62 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 80 through 82 No H-bonds generated for 'chain '6' and resid 80 through 82' Processing helix chain '6' and resid 97 through 106 Processing helix chain '6' and resid 119 through 122 No H-bonds generated for 'chain '6' and resid 119 through 122' Processing helix chain '6' and resid 124 through 126 No H-bonds generated for 'chain '6' and resid 124 through 126' Processing helix chain '6' and resid 136 through 138 No H-bonds generated for 'chain '6' and resid 136 through 138' Processing helix chain '6' and resid 153 through 168 Processing helix chain '6' and resid 172 through 178 Processing helix chain '9' and resid 14 through 26 Processing helix chain '9' and resid 28 through 42 removed outlier: 3.738A pdb=" N PHE 9 42 " --> pdb=" O LEU 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 86 Processing helix chain '9' and resid 121 through 125 Processing helix chain '9' and resid 145 through 147 No H-bonds generated for 'chain '9' and resid 145 through 147' Processing helix chain '9' and resid 151 through 175 removed outlier: 5.694A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU 9 174 " --> pdb=" O GLN 9 170 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N TYR 9 175 " --> pdb=" O ALA 9 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 45 Processing helix chain 'a' and resid 50 through 61 removed outlier: 4.466A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE a 61 " --> pdb=" O ASP a 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 27 Processing helix chain 'b' and resid 40 through 45 Processing helix chain 'b' and resid 64 through 66 No H-bonds generated for 'chain 'b' and resid 64 through 66' Processing helix chain 'c' and resid 27 through 31 removed outlier: 4.237A pdb=" N LYS c 31 " --> pdb=" O GLU c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 50 through 52 No H-bonds generated for 'chain 'c' and resid 50 through 52' Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 119 through 122 Processing helix chain 'd' and resid 30 through 41 removed outlier: 3.930A pdb=" N MET d 41 " --> pdb=" O HIS d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 62 removed outlier: 4.240A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) Proline residue: d 61 - end of helix Processing helix chain 'd' and resid 78 through 84 Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 187 removed outlier: 4.499A pdb=" N ARG d 186 " --> pdb=" O PHE d 182 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TRP d 187 " --> pdb=" O ALA d 183 " (cutoff:3.500A) Processing helix chain 'd' and resid 194 through 197 Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 238 through 248 Processing helix chain 'd' and resid 260 through 267 removed outlier: 3.666A pdb=" N ARG d 264 " --> pdb=" O HIS d 260 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP d 265 " --> pdb=" O PHE d 261 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE d 266 " --> pdb=" O ALA d 262 " (cutoff:3.500A) Processing helix chain 'd' and resid 270 through 272 No H-bonds generated for 'chain 'd' and resid 270 through 272' Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 310 through 321 removed outlier: 5.145A pdb=" N ILE d 315 " --> pdb=" O GLU d 311 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLU d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG d 320 " --> pdb=" O GLU d 316 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N HIS d 321 " --> pdb=" O VAL d 317 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 38 removed outlier: 5.151A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 44 No H-bonds generated for 'chain 'e' and resid 41 through 44' Processing helix chain 'e' and resid 69 through 71 No H-bonds generated for 'chain 'e' and resid 69 through 71' Processing helix chain 'e' and resid 83 through 96 Processing helix chain 'f' and resid 19 through 36 removed outlier: 4.161A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 60 Processing helix chain 'f' and resid 65 through 71 Processing helix chain 'f' and resid 76 through 96 Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 68 Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.554A pdb=" N PHE g 105 " --> pdb=" O HIS g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 117 through 123 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 53 through 55 No H-bonds generated for 'chain 'h' and resid 53 through 55' Processing helix chain 'h' and resid 59 through 61 No H-bonds generated for 'chain 'h' and resid 59 through 61' Processing helix chain 'i' and resid 3 through 17 removed outlier: 3.990A pdb=" N HIS i 17 " --> pdb=" O GLN i 13 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 30 Processing helix chain 'i' and resid 84 through 90 removed outlier: 4.303A pdb=" N TRP i 89 " --> pdb=" O GLU i 85 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 21 Processing helix chain 'j' and resid 27 through 29 No H-bonds generated for 'chain 'j' and resid 27 through 29' Processing helix chain 'j' and resid 36 through 39 No H-bonds generated for 'chain 'j' and resid 36 through 39' Processing helix chain 'j' and resid 44 through 58 Processing helix chain 'j' and resid 64 through 69 removed outlier: 3.563A pdb=" N GLU j 68 " --> pdb=" O ASP j 64 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS j 69 " --> pdb=" O ILE j 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 64 through 69' Processing helix chain 'j' and resid 73 through 83 Processing sheet with id= A, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= B, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= C, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.447A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'k' and resid 123 through 125 removed outlier: 6.557A pdb=" N ILE k 25 " --> pdb=" O LEU k 124 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ASP k 173 " --> pdb=" O LEU k 221 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR k 223 " --> pdb=" O ASP k 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain '1' and resid 219 through 224 removed outlier: 6.338A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '1' and resid 266 through 271 Processing sheet with id= G, first strand: chain '2' and resid 137 through 142 removed outlier: 6.903A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS 2 103 " --> pdb=" O MET 2 153 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N MET 2 153 " --> pdb=" O CYS 2 103 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 9 through 13 Processing sheet with id= I, first strand: chain '3' and resid 56 through 58 Processing sheet with id= J, first strand: chain '3' and resid 146 through 148 Processing sheet with id= K, first strand: chain '3' and resid 173 through 175 Processing sheet with id= L, first strand: chain '3' and resid 223 through 228 Processing sheet with id= M, first strand: chain '3' and resid 283 through 285 Processing sheet with id= N, first strand: chain '3' and resid 343 through 345 removed outlier: 8.565A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain '3' and resid 405 through 409 Processing sheet with id= P, first strand: chain '3' and resid 572 through 574 Processing sheet with id= Q, first strand: chain '4' and resid 47 through 51 removed outlier: 5.660A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL 4 73 " --> pdb=" O SER 4 69 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '4' and resid 361 through 369 Processing sheet with id= S, first strand: chain '5' and resid 74 through 82 removed outlier: 6.805A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 104 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 52 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '5' and resid 172 through 177 Processing sheet with id= U, first strand: chain '6' and resid 85 through 89 removed outlier: 6.585A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain '9' and resid 65 through 67 Processing sheet with id= W, first strand: chain '9' and resid 92 through 98 removed outlier: 5.698A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= Y, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= Z, first strand: chain 'c' and resid 102 through 105 Processing sheet with id= AA, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= AB, first strand: chain 'd' and resid 227 through 230 removed outlier: 6.418A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'e' and resid 51 through 57 removed outlier: 7.054A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.753A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) 2860 hydrogen bonds defined for protein. 8022 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.88 Time building geometry restraints manager: 23.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 28362 1.42 - 1.64: 39709 1.64 - 1.86: 763 1.86 - 2.08: 0 2.08 - 2.31: 80 Bond restraints: 68914 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.612 0.221 3.80e-02 6.93e+02 3.38e+01 bond pdb=" C13 ZMP j 101 " pdb=" N1 ZMP j 101 " ideal model delta sigma weight residual 1.451 1.337 0.114 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C16 ZMP j 101 " pdb=" N2 ZMP j 101 " ideal model delta sigma weight residual 1.452 1.338 0.114 2.00e-02 2.50e+03 3.24e+01 bond pdb=" C13 ZMP X 101 " pdb=" N1 ZMP X 101 " ideal model delta sigma weight residual 1.451 1.340 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C16 ZMP X 101 " pdb=" N2 ZMP X 101 " ideal model delta sigma weight residual 1.452 1.347 0.105 2.00e-02 2.50e+03 2.73e+01 ... (remaining 68909 not shown) Histogram of bond angle deviations from ideal: 69.76 - 83.20: 78 83.20 - 96.64: 2 96.64 - 110.09: 12287 110.09 - 123.53: 78615 123.53 - 136.97: 2336 Bond angle restraints: 93318 Sorted by residual: angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O2A NAI 1 503 " ideal model delta sigma weight residual 120.60 73.79 46.81 3.00e+00 1.11e-01 2.44e+02 angle pdb=" O1A NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 109.30 70.99 38.31 3.00e+00 1.11e-01 1.63e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 131.34 -23.60 1.95e+00 2.62e-01 1.46e+02 angle pdb=" CA PRO 3 63 " pdb=" N PRO 3 63 " pdb=" CD PRO 3 63 " ideal model delta sigma weight residual 112.00 98.03 13.97 1.40e+00 5.10e-01 9.95e+01 angle pdb=" C5B NDP d 401 " pdb=" O5B NDP d 401 " pdb=" PA NDP d 401 " ideal model delta sigma weight residual 103.84 119.42 -15.58 1.91e+00 2.73e-01 6.62e+01 ... (remaining 93313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.98: 40011 33.98 - 67.97: 1327 67.97 - 101.95: 76 101.95 - 135.93: 3 135.93 - 169.92: 1 Dihedral angle restraints: 41418 sinusoidal: 17443 harmonic: 23975 Sorted by residual: dihedral pdb=" CA ILE J 115 " pdb=" C ILE J 115 " pdb=" N VAL J 116 " pdb=" CA VAL J 116 " ideal model delta harmonic sigma weight residual -180.00 -117.16 -62.84 0 5.00e+00 4.00e-02 1.58e+02 dihedral pdb=" CA TYR 4 275 " pdb=" C TYR 4 275 " pdb=" N ASP 4 276 " pdb=" CA ASP 4 276 " ideal model delta harmonic sigma weight residual 180.00 -139.18 -40.82 0 5.00e+00 4.00e-02 6.67e+01 dihedral pdb=" C10 FMN 1 502 " pdb=" C1' FMN 1 502 " pdb=" N10 FMN 1 502 " pdb=" C2' FMN 1 502 " ideal model delta sinusoidal sigma weight residual 257.59 87.68 169.92 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 41415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.246: 10150 4.246 - 8.492: 0 8.492 - 12.738: 0 12.738 - 16.984: 0 16.984 - 21.230: 24 Chirality restraints: 10174 Sorted by residual: chirality pdb="FE3 SF4 6 201 " pdb=" S1 SF4 6 201 " pdb=" S2 SF4 6 201 " pdb=" S4 SF4 6 201 " both_signs ideal model delta sigma weight residual False -10.55 10.68 -21.23 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE4 SF4 6 201 " pdb=" S1 SF4 6 201 " pdb=" S2 SF4 6 201 " pdb=" S3 SF4 6 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 9 202 " pdb=" S1 SF4 9 202 " pdb=" S2 SF4 9 202 " pdb=" S3 SF4 9 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.59 21.15 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10171 not shown) Planarity restraints: 11715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA 3 62 " 0.073 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO 3 63 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO 3 63 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO 3 63 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 115 " -0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C ILE J 115 " 0.065 2.00e-02 2.50e+03 pdb=" O ILE J 115 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL J 116 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP k 226 " -0.019 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP k 226 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP k 226 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP k 226 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP k 226 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP k 226 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP k 226 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP k 226 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP k 226 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP k 226 " -0.000 2.00e-02 2.50e+03 ... (remaining 11712 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 19433 2.82 - 3.40: 70391 3.40 - 3.98: 129627 3.98 - 4.56: 184388 4.56 - 5.14: 270734 Nonbonded interactions: 674573 Sorted by model distance: nonbonded pdb=" O PHE H 293 " pdb=" OG1 THR H 297 " model vdw 2.238 2.440 nonbonded pdb=" O MET 4 152 " pdb=" OG1 THR 4 156 " model vdw 2.244 2.440 nonbonded pdb=" O TYR N 298 " pdb=" OG1 THR N 303 " model vdw 2.246 2.440 nonbonded pdb=" OH TYR H 114 " pdb=" O LEU J 61 " model vdw 2.249 2.440 nonbonded pdb=" O GLY 1 76 " pdb=" OG SER 1 80 " model vdw 2.256 2.440 ... (remaining 674568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'X' and (resid 5 through 86 or resid 101)) selection = (chain 'j' and (resid 5 through 86 or (resid 101 and (name C10 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 o \ r name C19 or name C2 or name C20 or name C21 or name C3 or name C4 or name C5 o \ r name C6 or name C7 or name C8 or name C9 or name N1 or name N2 or name O1 or n \ ame O2 or name O3 or name O4 or name O5 or name O6 or name O7 or name P1 or name \ S1 )))) } 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 6.210 Check model and map are aligned: 0.740 Set scattering table: 0.450 Process input model: 146.080 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.210 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:2.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 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 : 0.005 0.221 68914 Z= 0.304 Angle : 0.773 46.814 93318 Z= 0.379 Chirality : 1.027 21.230 10174 Planarity : 0.006 0.101 11715 Dihedral : 15.811 169.915 25938 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.13 % Favored : 96.86 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.09), residues: 8122 helix: 0.25 (0.07), residues: 4212 sheet: 0.07 (0.26), residues: 409 loop : -0.83 (0.10), residues: 3501 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 602 time to evaluate : 6.969 Fit side-chains outliers start: 20 outliers final: 7 residues processed: 616 average time/residue: 0.6713 time to fit residues: 713.3172 Evaluate side-chains 576 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 569 time to evaluate : 6.081 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5371 time to fit residues: 15.1345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 677 optimal weight: 8.9990 chunk 607 optimal weight: 20.0000 chunk 337 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 410 optimal weight: 6.9990 chunk 324 optimal weight: 5.9990 chunk 628 optimal weight: 8.9990 chunk 243 optimal weight: 9.9990 chunk 382 optimal weight: 20.0000 chunk 467 optimal weight: 20.0000 chunk 728 optimal weight: 2.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 ASN M 51 ASN M 366 ASN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 ASN l 26 HIS 1 437 HIS ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 150 ASN 3 43 HIS 9 65 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.264 68914 Z= 0.529 Angle : 1.556 51.173 93318 Z= 1.010 Chirality : 0.310 6.465 10174 Planarity : 0.004 0.066 11715 Dihedral : 7.044 171.463 9675 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.83 % Favored : 97.16 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.09), residues: 8122 helix: 1.03 (0.08), residues: 4248 sheet: 0.14 (0.26), residues: 393 loop : -0.66 (0.10), residues: 3481 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 574 time to evaluate : 6.258 Fit side-chains revert: symmetry clash outliers start: 170 outliers final: 95 residues processed: 704 average time/residue: 0.6494 time to fit residues: 794.2616 Evaluate side-chains 652 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 557 time to evaluate : 6.030 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 0.5071 time to fit residues: 99.4287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 404 optimal weight: 3.9990 chunk 226 optimal weight: 20.0000 chunk 606 optimal weight: 5.9990 chunk 495 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 729 optimal weight: 30.0000 chunk 788 optimal weight: 6.9990 chunk 649 optimal weight: 6.9990 chunk 723 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 585 optimal weight: 0.5980 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 210 ASN L 270 ASN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 46 ASN ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 113 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.251 68914 Z= 0.511 Angle : 1.541 50.928 93318 Z= 1.004 Chirality : 0.309 6.486 10174 Planarity : 0.004 0.066 11715 Dihedral : 6.818 170.516 9675 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.88 % Favored : 97.11 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.09), residues: 8122 helix: 1.34 (0.08), residues: 4248 sheet: 0.11 (0.26), residues: 393 loop : -0.54 (0.11), residues: 3481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 587 time to evaluate : 6.175 Fit side-chains outliers start: 104 outliers final: 49 residues processed: 675 average time/residue: 0.6631 time to fit residues: 777.3852 Evaluate side-chains 609 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 560 time to evaluate : 6.067 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.5069 time to fit residues: 55.8019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 720 optimal weight: 9.9990 chunk 548 optimal weight: 20.0000 chunk 378 optimal weight: 40.0000 chunk 80 optimal weight: 9.9990 chunk 348 optimal weight: 30.0000 chunk 489 optimal weight: 3.9990 chunk 732 optimal weight: 30.0000 chunk 775 optimal weight: 6.9990 chunk 382 optimal weight: 7.9990 chunk 693 optimal weight: 9.9990 chunk 208 optimal weight: 40.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 317 GLN L 194 ASN L 434 GLN L 603 ASN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 GLN m 61 ASN s 54 GLN w 41 ASN ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 321 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.248 68914 Z= 0.554 Angle : 1.560 51.138 93318 Z= 1.012 Chirality : 0.309 6.517 10174 Planarity : 0.004 0.068 11715 Dihedral : 6.945 170.068 9675 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.32 % Favored : 96.66 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.09), residues: 8122 helix: 1.34 (0.08), residues: 4259 sheet: -0.02 (0.26), residues: 405 loop : -0.58 (0.11), residues: 3458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 559 time to evaluate : 6.101 Fit side-chains revert: symmetry clash outliers start: 134 outliers final: 73 residues processed: 669 average time/residue: 0.6637 time to fit residues: 766.3550 Evaluate side-chains 626 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 553 time to evaluate : 6.041 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.5332 time to fit residues: 81.0256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 645 optimal weight: 10.0000 chunk 440 optimal weight: 0.0570 chunk 11 optimal weight: 7.9990 chunk 577 optimal weight: 20.0000 chunk 319 optimal weight: 6.9990 chunk 661 optimal weight: 4.9990 chunk 535 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 395 optimal weight: 7.9990 chunk 695 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 overall best weight: 3.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 135 ASN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 199 GLN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 287 HIS r 82 HIS 1 437 HIS ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.247 68914 Z= 0.503 Angle : 1.539 50.654 93318 Z= 1.003 Chirality : 0.309 6.441 10174 Planarity : 0.004 0.065 11715 Dihedral : 6.727 170.095 9675 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.93 % Favored : 97.06 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.10), residues: 8122 helix: 1.52 (0.08), residues: 4245 sheet: -0.16 (0.25), residues: 425 loop : -0.45 (0.11), residues: 3452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 582 time to evaluate : 6.047 Fit side-chains outliers start: 81 outliers final: 38 residues processed: 649 average time/residue: 0.6835 time to fit residues: 770.5125 Evaluate side-chains 593 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 555 time to evaluate : 6.091 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.5440 time to fit residues: 47.2360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 260 optimal weight: 20.0000 chunk 698 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 455 optimal weight: 30.0000 chunk 191 optimal weight: 5.9990 chunk 775 optimal weight: 2.9990 chunk 644 optimal weight: 20.0000 chunk 359 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 256 optimal weight: 8.9990 chunk 407 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 63 GLN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 94 GLN m 61 ASN 1 437 HIS ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.245 68914 Z= 0.537 Angle : 1.555 50.799 93318 Z= 1.009 Chirality : 0.309 6.426 10174 Planarity : 0.004 0.065 11715 Dihedral : 6.829 169.303 9675 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.48 % Favored : 96.50 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.10), residues: 8122 helix: 1.49 (0.08), residues: 4251 sheet: -0.10 (0.25), residues: 415 loop : -0.52 (0.11), residues: 3456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 558 time to evaluate : 6.353 Fit side-chains revert: symmetry clash outliers start: 89 outliers final: 44 residues processed: 624 average time/residue: 0.6759 time to fit residues: 731.2931 Evaluate side-chains 595 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 551 time to evaluate : 6.101 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.5731 time to fit residues: 55.2603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 748 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 442 optimal weight: 7.9990 chunk 566 optimal weight: 30.0000 chunk 439 optimal weight: 0.9990 chunk 653 optimal weight: 7.9990 chunk 433 optimal weight: 0.8980 chunk 772 optimal weight: 10.0000 chunk 483 optimal weight: 5.9990 chunk 471 optimal weight: 10.0000 chunk 356 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 61 ASN s 49 GLN v 126 GLN 1 356 HIS ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.248 68914 Z= 0.500 Angle : 1.540 51.018 93318 Z= 1.004 Chirality : 0.308 6.466 10174 Planarity : 0.004 0.064 11715 Dihedral : 6.665 169.426 9675 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.88 % Favored : 97.11 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.10), residues: 8122 helix: 1.63 (0.08), residues: 4240 sheet: -0.15 (0.25), residues: 427 loop : -0.37 (0.11), residues: 3455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 572 time to evaluate : 6.093 Fit side-chains outliers start: 40 outliers final: 11 residues processed: 603 average time/residue: 0.6838 time to fit residues: 720.0559 Evaluate side-chains 564 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 553 time to evaluate : 6.042 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5114 time to fit residues: 19.2217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 478 optimal weight: 20.0000 chunk 308 optimal weight: 9.9990 chunk 461 optimal weight: 20.0000 chunk 232 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 491 optimal weight: 10.0000 chunk 526 optimal weight: 30.0000 chunk 382 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 607 optimal weight: 8.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS l 44 HIS m 61 ASN ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.244 68914 Z= 0.541 Angle : 1.559 50.891 93318 Z= 1.011 Chirality : 0.309 6.446 10174 Planarity : 0.004 0.065 11715 Dihedral : 6.857 168.617 9675 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.44 % Favored : 96.55 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.10), residues: 8122 helix: 1.54 (0.08), residues: 4252 sheet: -0.09 (0.26), residues: 415 loop : -0.48 (0.11), residues: 3455 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 556 time to evaluate : 6.110 Fit side-chains outliers start: 53 outliers final: 24 residues processed: 590 average time/residue: 0.6701 time to fit residues: 683.9514 Evaluate side-chains 571 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 547 time to evaluate : 6.034 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.5051 time to fit residues: 31.4596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 703 optimal weight: 9.9990 chunk 740 optimal weight: 9.9990 chunk 675 optimal weight: 7.9990 chunk 720 optimal weight: 20.0000 chunk 433 optimal weight: 0.7980 chunk 313 optimal weight: 9.9990 chunk 565 optimal weight: 7.9990 chunk 221 optimal weight: 10.0000 chunk 650 optimal weight: 9.9990 chunk 681 optimal weight: 8.9990 chunk 717 optimal weight: 20.0000 overall best weight: 7.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 61 ASN 1 437 HIS ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.247 68914 Z= 0.544 Angle : 1.561 51.009 93318 Z= 1.012 Chirality : 0.309 6.541 10174 Planarity : 0.004 0.064 11715 Dihedral : 7.039 168.862 9675 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.30 % Favored : 96.69 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.10), residues: 8122 helix: 1.50 (0.08), residues: 4244 sheet: -0.16 (0.25), residues: 415 loop : -0.51 (0.11), residues: 3463 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 558 time to evaluate : 6.182 Fit side-chains outliers start: 30 outliers final: 13 residues processed: 578 average time/residue: 0.6845 time to fit residues: 684.1188 Evaluate side-chains 558 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 545 time to evaluate : 6.206 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5758 time to fit residues: 22.1073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 473 optimal weight: 7.9990 chunk 761 optimal weight: 8.9990 chunk 464 optimal weight: 8.9990 chunk 361 optimal weight: 9.9990 chunk 529 optimal weight: 6.9990 chunk 798 optimal weight: 5.9990 chunk 735 optimal weight: 20.0000 chunk 636 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 491 optimal weight: 9.9990 chunk 390 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 61 ASN 1 437 HIS ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.245 68914 Z= 0.544 Angle : 1.563 50.909 93318 Z= 1.012 Chirality : 0.309 6.471 10174 Planarity : 0.004 0.065 11715 Dihedral : 7.118 168.983 9675 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.50 % Favored : 96.49 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.10), residues: 8122 helix: 1.49 (0.08), residues: 4247 sheet: -0.10 (0.26), residues: 405 loop : -0.52 (0.11), residues: 3470 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16244 Ramachandran restraints generated. 8122 Oldfield, 0 Emsley, 8122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 546 time to evaluate : 6.190 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 557 average time/residue: 0.6972 time to fit residues: 671.0101 Evaluate side-chains 546 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 540 time to evaluate : 6.155 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5628 time to fit residues: 14.5707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 802 random chunks: chunk 505 optimal weight: 8.9990 chunk 677 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 586 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 637 optimal weight: 5.9990 chunk 266 optimal weight: 5.9990 chunk 654 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 61 ASN r 88 HIS ** 2 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.061544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.054003 restraints weight = 200276.041| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.69 r_work: 0.2867 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.246 68914 Z= 0.519 Angle : 1.554 50.860 93318 Z= 1.009 Chirality : 0.309 6.449 10174 Planarity : 0.004 0.065 11715 Dihedral : 7.056 169.130 9675 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.07 % Favored : 96.92 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.10), residues: 8122 helix: 1.57 (0.08), residues: 4241 sheet: -0.07 (0.26), residues: 405 loop : -0.46 (0.11), residues: 3476 =============================================================================== Job complete usr+sys time: 12833.95 seconds wall clock time: 228 minutes 38.32 seconds (13718.32 seconds total)