Starting phenix.real_space_refine (version: dev) on Sun Feb 26 02:30:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdm_14658/02_2023/7zdm_14658_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdm_14658/02_2023/7zdm_14658.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdm_14658/02_2023/7zdm_14658_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdm_14658/02_2023/7zdm_14658_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdm_14658/02_2023/7zdm_14658_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdm_14658/02_2023/7zdm_14658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdm_14658/02_2023/7zdm_14658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdm_14658/02_2023/7zdm_14658_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdm_14658/02_2023/7zdm_14658_updated.pdb" } resolution = 3.44 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= 0.009 sd= 0.028 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 Process input model Symmetric amino acids flipped Residue "2 ASP 52": "OD1" <-> "OD2" Residue "2 ASP 134": "OD1" <-> "OD2" Residue "3 ASP 118": "OD1" <-> "OD2" Residue "3 GLU 246": "OE1" <-> "OE2" Residue "4 GLU 227": "OE1" <-> "OE2" Residue "5 GLU 27": "OE1" <-> "OE2" Residue "5 ASP 55": "OD1" <-> "OD2" Residue "5 ASP 147": "OD1" <-> "OD2" Residue "6 TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 105": "OD1" <-> "OD2" Residue "9 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 84": "OE1" <-> "OE2" Residue "9 TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ASP 110": "OD1" <-> "OD2" Residue "a ASP 57": "OD1" <-> "OD2" Residue "a PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 9": "OE1" <-> "OE2" Residue "b ASP 20": "OD1" <-> "OD2" Residue "b GLU 37": "OE1" <-> "OE2" Residue "b ASP 60": "OD1" <-> "OD2" Residue "c GLU 28": "OE1" <-> "OE2" Residue "c GLU 107": "OE1" <-> "OE2" Residue "d GLU 52": "OE1" <-> "OE2" Residue "d ASP 77": "OD1" <-> "OD2" Residue "d PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 285": "OE1" <-> "OE2" Residue "e GLU 42": "OE1" <-> "OE2" Residue "g TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 74": "OD1" <-> "OD2" Residue "h ASP 57": "OD1" <-> "OD2" Residue "h GLU 61": "OE1" <-> "OE2" Residue "h GLU 104": "OE1" <-> "OE2" Residue "i GLU 136": "OE1" <-> "OE2" Residue "j ASP 13": "OD1" <-> "OD2" Residue "j TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 23": "OD1" <-> "OD2" Residue "j ASP 39": "OD1" <-> "OD2" Residue "j ASP 43": "OD1" <-> "OD2" Residue "j GLU 49": "OE1" <-> "OE2" Residue "j ASP 56": "OD1" <-> "OD2" Residue "j PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 64": "OD1" <-> "OD2" Residue "j ASP 78": "OD1" <-> "OD2" Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 192": "OE1" <-> "OE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 145": "OE1" <-> "OE2" Residue "L ASP 179": "OD1" <-> "OD2" Residue "L TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 503": "OE1" <-> "OE2" Residue "L GLU 559": "OE1" <-> "OE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "N PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 84": "OD1" <-> "OD2" Residue "V GLU 137": "OE1" <-> "OE2" Residue "W PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 54": "OE1" <-> "OE2" Residue "W ASP 81": "OD1" <-> "OD2" Residue "W GLU 102": "OE1" <-> "OE2" Residue "Y ASP 112": "OD1" <-> "OD2" Residue "Z ASP 5": "OD1" <-> "OD2" Residue "Z TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 72": "OD1" <-> "OD2" Residue "Z ASP 98": "OD1" <-> "OD2" Residue "k TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 61": "OD1" <-> "OD2" Residue "l ASP 83": "OD1" <-> "OD2" Residue "m GLU 15": "OE1" <-> "OE2" Residue "n GLU 24": "OE1" <-> "OE2" Residue "n GLU 84": "OE1" <-> "OE2" Residue "o ASP 16": "OD1" <-> "OD2" Residue "o GLU 17": "OE1" <-> "OE2" Residue "o TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 34": "OE1" <-> "OE2" Residue "p ASP 107": "OD1" <-> "OD2" Residue "p GLU 112": "OE1" <-> "OE2" Residue "q GLU 107": "OE1" <-> "OE2" Residue "r PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 124": "OD1" <-> "OD2" Residue "s TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 27": "OD1" <-> "OD2" Residue "s PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 32": "OE1" <-> "OE2" Residue "s ASP 85": "OD1" <-> "OD2" Residue "s GLU 118": "OE1" <-> "OE2" Residue "t GLU 67": "OE1" <-> "OE2" Residue "t GLU 94": "OE1" <-> "OE2" Residue "t PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 135": "OE1" <-> "OE2" Residue "t ASP 161": "OD1" <-> "OD2" Residue "u GLU 26": "OE1" <-> "OE2" Residue "v GLU 32": "OE1" <-> "OE2" Residue "v GLU 35": "OE1" <-> "OE2" Residue "v ASP 46": "OD1" <-> "OD2" Residue "v GLU 151": "OE1" <-> "OE2" Residue "w GLU 28": "OE1" <-> "OE2" Residue "w GLU 31": "OE1" <-> "OE2" Residue "w GLU 35": "OE1" <-> "OE2" Residue "w GLU 39": "OE1" <-> "OE2" Residue "w ASP 48": "OD1" <-> "OD2" Residue "w PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 114": "OD1" <-> "OD2" Residue "w GLU 122": "OE1" <-> "OE2" Residue "x GLU 6": "OE1" <-> "OE2" Residue "y ASP 31": "OD1" <-> "OD2" Residue "z GLU 49": "OE1" <-> "OE2" Residue "z GLU 67": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 67086 Number of models: 1 Model: "" Number of chains: 64 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: 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: 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: "4" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'PC1': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "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 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "L" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 159 Unusual residues: {'3PE': 1, 'PC1': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "V" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 37 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: "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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 104.837 55.067 239.442 1.00 48.18 S ATOM 3039 SG CYS 1 405 108.538 49.687 238.302 1.00 43.77 S ATOM 2695 SG CYS 1 362 107.609 54.937 234.412 1.00 28.83 S ATOM 2676 SG CYS 1 359 111.620 54.954 239.795 1.00 29.75 S ATOM 4116 SG CYS 2 103 102.568 48.624 258.467 1.00 56.16 S ATOM 4150 SG CYS 2 108 100.612 46.259 260.093 1.00 49.69 S ATOM 4430 SG CYS 2 144 104.556 45.212 254.722 1.00 63.19 S ATOM 4453 SG CYS 2 148 102.766 42.475 255.812 1.00 48.46 S ATOM 5793 SG CYS 3 114 106.634 74.421 225.737 1.00 32.96 S ATOM 5732 SG CYS 3 105 101.332 77.570 227.930 1.00 31.50 S ATOM 5753 SG CYS 3 108 107.225 79.407 229.861 1.00 27.33 S ATOM 6125 SG CYS 3 156 114.516 66.817 230.191 1.00 37.30 S ATOM 6102 SG CYS 3 153 112.223 69.543 235.669 1.00 14.76 S ATOM 6149 SG CYS 3 159 118.418 70.794 233.812 1.00 70.79 S ATOM 6479 SG CYS 3 203 113.937 73.195 230.379 1.00 68.48 S ATOM 5238 SG CYS 3 41 113.315 60.269 227.587 1.00 21.68 S ATOM 5324 SG CYS 3 52 109.749 61.064 226.835 1.00 47.00 S ATOM 5349 SG CYS 3 55 110.574 56.419 223.066 1.00 43.78 S ATOM 5450 SG CYS 3 69 113.959 56.571 224.563 1.00 47.32 S ATOM 16178 SG CYS 6 119 90.104 101.349 203.929 1.00 26.45 S ATOM 16408 SG CYS 6 149 87.440 98.945 209.054 1.00 67.15 S ATOM 15680 SG CYS 6 55 84.582 104.193 206.274 1.00 26.87 S ATOM 15674 SG CYS 6 54 83.851 98.614 203.629 1.00 24.01 S ATOM 17600 SG CYS 9 116 91.532 98.961 215.644 1.00 31.23 S ATOM 17647 SG CYS 9 122 92.452 94.479 220.286 1.00 20.09 S ATOM 17374 SG CYS 9 87 96.280 94.545 214.945 1.00 41.18 S ATOM 17676 SG CYS 9 126 94.611 90.701 227.561 1.00 22.70 S ATOM 17347 SG CYS 9 83 98.305 92.772 222.483 1.00 36.24 S ATOM 17305 SG CYS 9 77 100.201 93.946 228.490 1.00 27.87 S ATOM 17324 SG CYS 9 80 99.832 87.648 225.960 1.00 41.35 S ATOM 18923 SG CYS b 59 96.541 85.425 242.778 1.00 54.14 S ATOM 19101 SG CYS b 84 99.406 85.511 240.653 1.00 68.30 S ATOM 19123 SG CYS b 87 97.603 88.477 241.648 1.00 28.59 S Time building chain proxies: 27.40, per 1000 atoms: 0.41 Number of scatterers: 67086 At special positions: 0 Unit cell: (178.12, 202.52, 290.36, 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 25 15.00 O 12018 8.00 N 11230 7.00 C 43315 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=2.04 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: 21.72 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="FE1 FES 2 300 " - pdb=" SG CYS 2 108 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " 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 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb=" SF4 1 501 " pdb="FE1 SF4 1 501 " - pdb=" SG CYS 1 365 " pdb="FE4 SF4 1 501 " - pdb=" SG CYS 1 359 " pdb="FE2 SF4 1 501 " - pdb=" SG CYS 1 405 " 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="FE3 SF4 3 802 " - pdb=" SG CYS 3 159 " pdb="FE4 SF4 3 802 " - pdb=" SG CYS 3 203 " 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="FE1 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 55 " pdb=" SF4 9 402 " pdb="FE3 SF4 9 402 " - pdb=" SG CYS 9 122 " pdb="FE2 SF4 9 402 " - pdb=" SG CYS 9 116 " pdb="FE4 SF4 9 402 " - pdb=" SG CYS 9 87 " pdb="FE1 SF4 9 402 " - pdb=" SG CYS 9 119 " pdb=" SF4 9 403 " pdb="FE2 SF4 9 403 " - pdb=" SG CYS 9 83 " pdb="FE4 SF4 9 403 " - pdb=" SG CYS 9 80 " pdb="FE1 SF4 9 403 " - pdb=" SG CYS 9 126 " pdb="FE3 SF4 9 403 " - 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 87 " pdb="ZN ZN b 300 " - pdb=" SG CYS b 84 " 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: 333 helices and 31 sheets defined 50.8% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... 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 63 Processing helix chain '1' and resid 75 through 82 removed outlier: 4.400A pdb=" N MET 1 82 " --> pdb=" O LYS 1 78 " (cutoff:3.500A) 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 228 No H-bonds generated for 'chain '1' and resid 225 through 228' Processing helix chain '1' and resid 231 through 237 Processing helix chain '1' and resid 239 through 244 Processing helix chain '1' and resid 276 through 283 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 311 through 314 removed outlier: 3.703A pdb=" N THR 1 314 " --> pdb=" O VAL 1 311 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 311 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: 4.620A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 399 removed outlier: 3.531A pdb=" N ILE 1 399 " --> pdb=" O SER 1 396 " (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 37 Processing helix chain '2' and resid 43 through 58 removed outlier: 3.557A pdb=" N VAL 2 47 " --> pdb=" O ALA 2 44 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) 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 177 Processing helix chain '3' and resid 26 through 33 Processing helix chain '3' and resid 84 through 97 Processing helix chain '3' and resid 115 through 122 Processing helix chain '3' and resid 158 through 165 Processing helix chain '3' and resid 178 through 180 No H-bonds generated for 'chain '3' and resid 178 through 180' Processing helix chain '3' and resid 198 through 202 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: 3.815A 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 359 through 362 removed outlier: 4.051A pdb=" N TYR 3 362 " --> pdb=" O ARG 3 359 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 359 through 362' Processing helix chain '3' and resid 369 through 372 Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 434 removed outlier: 3.683A pdb=" N ALA 3 433 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 444 Processing helix chain '3' and resid 456 through 459 removed outlier: 3.521A pdb=" N GLN 3 459 " --> pdb=" O SER 3 456 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 456 through 459' Processing helix chain '3' and resid 463 through 478 Processing helix chain '3' and resid 499 through 505 Processing helix chain '3' and resid 512 through 516 Processing helix chain '3' and resid 534 through 536 No H-bonds generated for 'chain '3' and resid 534 through 536' 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: 3.688A pdb=" N LYS 3 650 " --> pdb=" O SER 3 646 " (cutoff:3.500A) Processing helix chain '3' and resid 668 through 670 No H-bonds generated for 'chain '3' and resid 668 through 670' 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 15 removed outlier: 3.993A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY 4 15 " --> pdb=" O ALA 4 11 " (cutoff:3.500A) Processing helix chain '4' and resid 24 through 26 No H-bonds generated for 'chain '4' and resid 24 through 26' 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 103 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: 4.622A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 229 removed outlier: 4.272A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 4.985A 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 258 through 262 Processing helix chain '4' and resid 269 through 272 No H-bonds generated for 'chain '4' and resid 269 through 272' Processing helix chain '4' and resid 293 through 316 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: 4.352A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 4.812A 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 429 Processing helix chain '5' and resid 16 through 32 Processing helix chain '5' and resid 54 through 66 removed outlier: 3.631A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ILE 5 58 " --> pdb=" O ASP 5 55 " (cutoff:3.500A) Proline residue: 5 59 - end of helix Processing helix chain '5' and resid 127 through 138 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 26 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 94 through 105 Proline residue: 6 98 - end of helix Processing helix chain '6' and resid 117 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 41 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 172 removed outlier: 5.647A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 45 Processing helix chain 'a' and resid 50 through 60 removed outlier: 4.416A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.596A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) 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 20 through 23 No H-bonds generated for 'chain 'c' and resid 20 through 23' Processing helix chain 'c' and resid 27 through 31 removed outlier: 4.424A pdb=" N LYS c 31 " --> pdb=" O GLU c 28 " (cutoff:3.500A) 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: 4.027A pdb=" N MET d 41 " --> pdb=" O HIS d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 55 No H-bonds generated for 'chain 'd' and resid 53 through 55' Processing helix chain 'd' and resid 57 through 62 Proline residue: d 61 - end of helix No H-bonds generated for 'chain 'd' and resid 57 through 62' Processing helix chain 'd' and resid 78 through 85 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 188 removed outlier: 4.223A pdb=" N ARG d 186 " --> pdb=" O PHE d 182 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N TRP d 187 " --> pdb=" O ALA d 183 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE d 188 " --> pdb=" O ASN d 184 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 197 No H-bonds generated for 'chain 'd' and resid 195 through 197' Processing helix chain 'd' and resid 207 through 219 Processing helix chain 'd' and resid 221 through 223 No H-bonds generated for 'chain 'd' and resid 221 through 223' Processing helix chain 'd' and resid 238 through 249 Processing helix chain 'd' and resid 260 through 272 removed outlier: 3.611A pdb=" N TRP d 265 " --> pdb=" O PHE d 261 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE d 272 " --> pdb=" O ARG d 268 " (cutoff:3.500A) Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 300 through 303 Processing helix chain 'd' and resid 310 through 312 No H-bonds generated for 'chain 'd' and resid 310 through 312' Processing helix chain 'd' and resid 314 through 321 removed outlier: 5.545A pdb=" N ARG d 320 " --> pdb=" O GLU d 316 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N HIS d 321 " --> pdb=" O VAL d 317 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 46 removed outlier: 6.438A pdb=" N VAL e 41 " --> pdb=" O GLU e 37 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLU e 42 " --> pdb=" O LYS e 38 " (cutoff:3.500A) 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: 4.290A 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 64 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 69 removed outlier: 4.422A pdb=" N ASN g 69 " --> pdb=" O MET g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.583A 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 'i' and resid 2 through 17 removed outlier: 3.659A 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 79 through 81 No H-bonds generated for 'chain 'i' and resid 79 through 81' Processing helix chain 'i' and resid 84 through 90 removed outlier: 4.210A 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 44 through 58 Processing helix chain 'j' and resid 64 through 67 No H-bonds generated for 'chain 'j' and resid 64 through 67' Processing helix chain 'j' and resid 73 through 83 Processing helix chain 'A' and resid 2 through 19 removed outlier: 3.585A pdb=" N LEU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 80 Proline residue: A 74 - end of helix removed outlier: 5.500A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 Processing helix chain 'H' and resid 2 through 30 Proline residue: H 12 - end of helix Processing helix chain 'H' and resid 47 through 56 removed outlier: 3.541A pdb=" N PHE H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 86 Proline residue: H 75 - end of helix removed outlier: 4.256A pdb=" N TRP H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 122 removed outlier: 3.846A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 156 removed outlier: 5.265A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 169 removed outlier: 3.914A pdb=" N GLN H 169 " --> 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: 3.785A 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 286 through 289 No H-bonds generated for 'chain 'H' and resid 286 through 289' Processing helix chain 'H' and resid 294 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 2 through 20 removed outlier: 5.005A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE J 20 " --> pdb=" O PHE J 17 " (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 138 through 148 removed outlier: 4.500A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.062A 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 3 through 20 Processing helix chain 'K' and resid 26 through 50 Processing helix chain 'K' and resid 54 through 84 removed outlier: 3.907A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix Processing helix chain 'K' and resid 90 through 92 No H-bonds generated for 'chain 'K' and resid 90 through 92' Processing helix chain 'L' and resid 4 through 23 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 224 Processing helix chain 'L' and resid 231 through 238 removed outlier: 4.381A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 5.554A 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 255 through 262 Processing helix chain 'L' and resid 264 through 268 Processing helix chain 'L' and resid 271 through 293 Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 350 removed outlier: 4.293A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) 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 367 through 380 Processing helix chain 'L' and resid 387 through 400 removed outlier: 3.588A pdb=" N TYR L 390 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER L 391 " --> pdb=" O GLY L 388 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS L 392 " --> pdb=" O PHE L 389 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ASP L 393 " --> pdb=" O TYR L 390 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU L 394 " --> pdb=" O SER L 391 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 431 Processing helix chain 'L' and resid 448 through 471 removed outlier: 6.026A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.508A 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: 3.853A 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 547 removed outlier: 3.591A pdb=" N TYR L 529 " --> pdb=" O LEU L 526 " (cutoff:3.500A) Proline residue: L 530 - end of helix removed outlier: 5.521A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU L 536 " --> pdb=" O MET L 533 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 3.508A pdb=" N LEU L 542 " --> pdb=" O TYR L 539 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN L 546 " --> pdb=" O THR L 543 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS L 547 " --> pdb=" O MET L 544 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 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 Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 23 through 42 removed outlier: 4.345A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 79 Proline residue: M 64 - end of helix Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 110 Processing helix chain 'M' and resid 115 through 135 removed outlier: 4.526A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.419A 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 171 Proline residue: M 159 - end of helix 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: 4.474A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 219 Proline residue: M 217 - end of helix Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 249 removed outlier: 4.754A pdb=" N LEU M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU M 249 " --> pdb=" O ARG M 245 " (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: 3.677A 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 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 390 through 415 removed outlier: 3.555A pdb=" N LEU M 408 " --> pdb=" O LEU M 405 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR M 413 " --> pdb=" O MET M 410 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN M 415 " --> pdb=" O ILE M 412 " (cutoff:3.500A) Processing helix chain 'M' and resid 431 through 448 Proline residue: M 443 - end of helix removed outlier: 4.213A pdb=" N SER M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 454 removed outlier: 3.536A pdb=" N ILE M 454 " --> pdb=" O PRO M 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 451 through 454' Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 40 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: 4.350A pdb=" N GLU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 144 removed outlier: 4.942A pdb=" N LYS N 135 " --> pdb=" O LEU N 131 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU N 136 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA N 137 " --> pdb=" O TRP N 133 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 151 through 170 removed outlier: 4.187A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 191 Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 235 removed outlier: 4.277A pdb=" N HIS N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N TRP N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN N 235 " --> pdb=" O SER N 231 " (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 removed outlier: 3.596A pdb=" N MET N 270 " --> pdb=" O ILE N 267 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 300 Processing helix chain 'N' and resid 311 through 315 Processing helix chain 'N' and resid 326 through 334 Processing helix chain 'N' and resid 340 through 346 removed outlier: 3.507A pdb=" N SER N 344 " --> pdb=" O PRO N 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 9 Processing helix chain 'V' and resid 17 through 42 Processing helix chain 'V' and resid 48 through 80 Processing helix chain 'V' and resid 86 through 104 Processing helix chain 'V' and resid 107 through 130 Processing helix chain 'W' and resid 16 through 46 removed outlier: 4.145A 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 'X' and resid 8 through 20 Processing helix chain 'X' and resid 27 through 29 No H-bonds generated for 'chain 'X' and resid 27 through 29' Processing helix chain 'X' and resid 36 through 39 No H-bonds generated for 'chain 'X' and resid 36 through 39' 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 57 through 76 removed outlier: 3.830A 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 113 Processing helix chain 'Z' and resid 28 through 39 Processing helix chain 'Z' and resid 41 through 57 removed outlier: 3.847A 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 142 removed outlier: 4.510A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY Z 117 " --> pdb=" O GLN Z 113 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU Z 118 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER Z 119 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS Z 120 " --> pdb=" O GLU Z 116 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ARG Z 121 " --> pdb=" O GLY Z 117 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN Z 123 " --> pdb=" O SER Z 119 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA Z 125 " --> pdb=" O ARG Z 121 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LYS Z 126 " --> pdb=" O GLN Z 122 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLU Z 127 " --> pdb=" O ASN Z 123 " (cutoff:3.500A) Processing helix chain 'Z' and resid 151 through 172 Processing helix chain 'k' and resid 5 through 10 Processing helix chain 'k' and resid 35 through 46 removed outlier: 4.246A pdb=" N ALA k 39 " --> pdb=" O SEP k 36 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU k 46 " --> pdb=" O ALA k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 62 No H-bonds generated for 'chain 'k' and resid 59 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: 4.580A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 5.777A 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 191 through 193 No H-bonds generated for 'chain 'k' and resid 191 through 193' Processing helix chain 'k' and resid 196 through 208 Processing helix chain 'k' and resid 210 through 214 Processing helix chain 'k' and resid 225 through 229 removed outlier: 3.543A pdb=" N GLU k 229 " --> pdb=" O ALA k 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 225 through 229' Processing helix chain 'k' and resid 231 through 238 Processing helix chain 'k' and resid 253 through 264 Processing helix chain 'k' and resid 266 through 269 No H-bonds generated for 'chain 'k' and resid 266 through 269' Processing helix chain 'k' and resid 286 through 298 Processing helix chain 'k' and resid 310 through 312 No H-bonds generated for 'chain 'k' and resid 310 through 312' Processing helix chain 'k' and resid 317 through 319 No H-bonds generated for 'chain 'k' and resid 317 through 319' Processing helix chain 'l' and resid 6 through 9 No H-bonds generated for 'chain 'l' and resid 6 through 9' Processing helix chain 'l' and resid 33 through 42 Processing helix chain 'l' and resid 47 through 54 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 34 Proline residue: m 32 - end of helix 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 45 through 48 No H-bonds generated for 'chain 'n' and resid 45 through 48' 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 87 Processing helix 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 15 through 17 No H-bonds generated for 'chain 'p' and resid 15 through 17' Processing helix chain 'p' and resid 19 through 22 removed outlier: 3.699A pdb=" N TYR p 22 " --> pdb=" O PRO p 19 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'p' and resid 83 through 93 Processing helix chain 'p' and resid 95 through 117 removed outlier: 3.889A 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: 3.517A pdb=" N ALA q 94 " --> pdb=" O LEU q 90 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR q 95 " --> pdb=" O GLU q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 120 through 123 No H-bonds generated for 'chain 'q' and resid 120 through 123' Processing helix chain 'q' and resid 129 through 135 Processing helix chain 'q' and resid 138 through 141 No H-bonds generated for 'chain 'q' and resid 138 through 141' 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 88 Processing helix chain 's' and resid 2 through 7 Processing helix chain 's' and resid 42 through 47 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 81 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 50 removed outlier: 4.147A pdb=" N HIS t 50 " --> pdb=" O ARG t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 56 through 72 Processing helix chain 't' and resid 93 through 95 No H-bonds generated for 'chain 't' and resid 93 through 95' Processing helix chain 't' and resid 100 through 105 removed outlier: 3.701A pdb=" N LEU t 103 " --> pdb=" O GLU t 100 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP t 105 " --> pdb=" O CYS t 102 " (cutoff:3.500A) 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: 5.167A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.924A 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 120 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 51 through 64 Processing helix chain 'w' and resid 71 through 78 Processing helix chain 'w' and resid 83 through 102 removed outlier: 3.783A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG w 100 " --> pdb=" O VAL w 97 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA w 102 " --> pdb=" O TYR w 99 " (cutoff:3.500A) Processing helix chain 'x' and resid 14 through 46 Processing helix chain 'y' and resid 14 through 33 removed outlier: 3.619A pdb=" N GLU y 32 " --> pdb=" O ARG y 28 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS y 33 " --> pdb=" O LYS y 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 4 No H-bonds generated for 'chain 'z' and resid 2 through 4' Processing helix chain 'z' and resid 6 through 29 Proline residue: z 19 - end of helix Processing helix chain 'z' and resid 42 through 55 Processing sheet with id= A, first strand: chain '1' and resid 91 through 96 removed outlier: 7.619A pdb=" N VAL 1 94 " --> pdb=" O PRO 1 219 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR 1 221 " --> pdb=" O VAL 1 94 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ASN 1 96 " --> pdb=" O THR 1 221 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA 1 223 " --> pdb=" O ASN 1 96 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '1' and resid 133 through 138 removed outlier: 6.626A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain '1' and resid 266 through 271 Processing sheet with id= D, first strand: chain '2' and resid 137 through 142 removed outlier: 6.638A pdb=" N TYR 2 98 " --> pdb=" O THR 2 138 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE 2 140 " --> pdb=" O TYR 2 98 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE 2 100 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL 2 142 " --> pdb=" O ILE 2 100 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL 2 102 " --> pdb=" O VAL 2 142 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N CYS 2 103 " --> pdb=" O MET 2 153 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N MET 2 153 " --> pdb=" O CYS 2 103 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 9 through 13 Processing sheet with id= F, first strand: chain '3' and resid 146 through 148 Processing sheet with id= G, first strand: chain '3' and resid 173 through 175 Processing sheet with id= H, first strand: chain '3' and resid 223 through 228 Processing sheet with id= I, first strand: chain '3' and resid 283 through 285 Processing sheet with id= J, first strand: chain '3' and resid 343 through 345 removed outlier: 8.538A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU 3 561 " --> pdb=" O GLY 3 547 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain '3' and resid 490 through 493 removed outlier: 8.463A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP 3 420 " --> pdb=" O LEU 3 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain '3' and resid 572 through 574 Processing sheet with id= M, first strand: chain '4' and resid 47 through 51 removed outlier: 6.269A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL 4 73 " --> pdb=" O SER 4 69 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '4' and resid 361 through 369 Processing sheet with id= O, first strand: chain '5' and resid 74 through 82 removed outlier: 6.931A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA 5 80 " --> pdb=" O GLU 5 91 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU 5 91 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N TYR 5 110 " --> pdb=" O ILE 5 50 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N ILE 5 52 " --> pdb=" O TYR 5 110 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '5' and resid 172 through 177 Processing sheet with id= Q, first strand: chain '6' and resid 85 through 89 removed outlier: 6.429A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE 6 144 " --> pdb=" O SER 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '9' and resid 65 through 67 Processing sheet with id= S, first strand: chain '9' and resid 92 through 98 removed outlier: 5.690A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= U, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= V, first strand: chain 'c' and resid 103 through 106 removed outlier: 6.816A pdb=" N ALA c 35 " --> pdb=" O ASP c 104 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N GLU c 106 " --> pdb=" O ALA c 35 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE c 37 " --> pdb=" O GLU c 106 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'c' and resid 64 through 66 Processing sheet with id= X, first strand: chain 'd' and resid 227 through 230 removed outlier: 7.999A pdb=" N PHE d 228 " --> pdb=" O ALA d 163 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE d 129 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE d 166 " --> pdb=" O PHE d 129 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N HIS d 131 " --> pdb=" O ILE d 166 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N SER d 133 " --> pdb=" O PRO d 168 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'd' and resid 192 through 194 removed outlier: 6.643A pdb=" N TYR d 256 " --> pdb=" O LEU d 193 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'e' and resid 51 through 57 removed outlier: 6.843A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'i' and resid 60 through 63 removed outlier: 6.461A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 112 through 115 Processing sheet with id= AC, first strand: chain 'L' and resid 69 through 71 Processing sheet with id= AD, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.679A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'k' and resid 122 through 125 removed outlier: 6.610A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) 2845 hydrogen bonds defined for protein. 8067 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: 21.89 Time building geometry restraints manager: 23.72 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: 28350 1.42 - 1.64: 39592 1.64 - 1.86: 761 1.86 - 2.08: 1 2.08 - 2.31: 80 Bond restraints: 68784 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.605 0.228 3.80e-02 6.93e+02 3.59e+01 bond pdb=" C16 ZMP j 101 " pdb=" N2 ZMP j 101 " ideal model delta sigma weight residual 1.452 1.332 0.120 2.00e-02 2.50e+03 3.57e+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 3.23e+01 bond pdb=" C13 ZMP X 101 " pdb=" N1 ZMP X 101 " ideal model delta sigma weight residual 1.451 1.341 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C16 ZMP X 101 " pdb=" N2 ZMP X 101 " ideal model delta sigma weight residual 1.452 1.346 0.106 2.00e-02 2.50e+03 2.79e+01 ... (remaining 68779 not shown) Histogram of bond angle deviations from ideal: 69.41 - 82.79: 78 82.79 - 96.17: 3 96.17 - 109.55: 8052 109.55 - 122.93: 80354 122.93 - 136.31: 4686 Bond angle restraints: 93173 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 74.05 46.55 3.00e+00 1.11e-01 2.41e+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 70.88 38.42 3.00e+00 1.11e-01 1.64e+02 angle pdb=" PA NDP d 401 " pdb=" O3 NDP d 401 " pdb=" PN NDP d 401 " ideal model delta sigma weight residual 107.74 131.36 -23.62 1.95e+00 2.62e-01 1.46e+02 angle pdb=" C5B NDP d 401 " pdb=" O5B NDP d 401 " pdb=" PA NDP d 401 " ideal model delta sigma weight residual 103.84 118.62 -14.78 1.91e+00 2.73e-01 5.96e+01 angle pdb=" O3 NAI 1 503 " pdb=" PA NAI 1 503 " pdb=" O5B NAI 1 503 " ideal model delta sigma weight residual 98.63 120.37 -21.74 3.00e+00 1.11e-01 5.25e+01 ... (remaining 93168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.79: 39703 33.79 - 67.58: 1516 67.58 - 101.37: 102 101.37 - 135.16: 5 135.16 - 168.96: 1 Dihedral angle restraints: 41327 sinusoidal: 17352 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 -114.38 -65.62 0 5.00e+00 4.00e-02 1.72e+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 -135.93 -44.07 0 5.00e+00 4.00e-02 7.77e+01 dihedral pdb=" CB CYS s 68 " pdb=" SG CYS s 68 " pdb=" SG CYS s 79 " pdb=" CB CYS s 79 " ideal model delta sinusoidal sigma weight residual -86.00 -161.88 75.88 1 1.00e+01 1.00e-02 7.26e+01 ... (remaining 41324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.246: 10147 4.246 - 8.491: 0 8.491 - 12.737: 0 12.737 - 16.982: 0 16.982 - 21.228: 24 Chirality restraints: 10171 Sorted by residual: 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 -10.67 21.23 2.00e-01 2.50e+01 1.13e+04 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 10.64 -21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE3 SF4 3 801 " pdb=" S1 SF4 3 801 " pdb=" S2 SF4 3 801 " pdb=" S4 SF4 3 801 " both_signs ideal model delta sigma weight residual False -10.55 10.58 -21.14 2.00e-01 2.50e+01 1.12e+04 ... (remaining 10168 not shown) Planarity restraints: 11709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 218 " 0.078 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO H 219 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO H 219 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO H 219 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP u 55 " -0.062 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO u 56 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO u 56 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO u 56 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 115 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C ILE J 115 " 0.064 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 ... (remaining 11706 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.78: 15653 2.78 - 3.37: 71026 3.37 - 3.96: 130150 3.96 - 4.55: 184490 4.55 - 5.14: 275194 Nonbonded interactions: 676513 Sorted by model distance: nonbonded pdb=" OH TYR k 108 " pdb=" O LEU k 164 " model vdw 2.195 2.440 nonbonded pdb=" O ILE L 561 " pdb=" OG1 THR L 565 " model vdw 2.213 2.440 nonbonded pdb=" OE2 GLU M 123 " pdb=" OG SER M 157 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR H 114 " pdb=" O LEU J 61 " model vdw 2.214 2.440 nonbonded pdb=" O PHE H 293 " pdb=" OG1 THR H 297 " model vdw 2.223 2.440 ... (remaining 676508 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 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 25 5.49 5 S 468 5.16 5 C 43315 2.51 5 N 11230 2.21 5 O 12018 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.300 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: 0.060 Extract box with map and model: 6.130 Check model and map are aligned: 0.720 Process input model: 150.750 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.470 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:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.228 68784 Z= 0.387 Angle : 0.854 46.545 93173 Z= 0.419 Chirality : 1.026 21.228 10171 Planarity : 0.006 0.117 11709 Dihedral : 16.677 168.955 25847 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.76 % Favored : 96.22 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.01 % 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: -0.65 (0.09), residues: 8122 helix: 0.13 (0.07), residues: 4271 sheet: -0.48 (0.24), residues: 447 loop : -1.05 (0.10), residues: 3404 *********************** 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 974 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 949 time to evaluate : 6.679 Fit side-chains outliers start: 25 outliers final: 14 residues processed: 962 average time/residue: 0.6711 time to fit residues: 1099.7883 Evaluate side-chains 920 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 906 time to evaluate : 5.933 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5116 time to fit residues: 21.6807 ------------------------------------------------------------------------------- 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: 10.0000 chunk 607 optimal weight: 10.0000 chunk 337 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 410 optimal weight: 0.9990 chunk 324 optimal weight: 9.9990 chunk 628 optimal weight: 9.9990 chunk 243 optimal weight: 10.0000 chunk 382 optimal weight: 9.9990 chunk 467 optimal weight: 10.0000 chunk 728 optimal weight: 30.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 148 ASN 1 436 GLN 2 42 HIS ** 2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 127 ASN 5 145 HIS 9 65 HIS f 82 GLN g 98 GLN H 32 GLN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 ASN L 175 ASN L 194 ASN M 399 ASN ** Y 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 55 HIS ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 59 HIS ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.263 68784 Z= 0.626 Angle : 1.585 50.897 93173 Z= 1.022 Chirality : 0.310 6.420 10171 Planarity : 0.005 0.090 11709 Dihedral : 7.412 168.615 9584 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.56 % Favored : 96.42 % Rotamer Outliers : 3.31 % 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: -0.05 (0.09), residues: 8122 helix: 0.75 (0.08), residues: 4279 sheet: -0.56 (0.24), residues: 435 loop : -0.90 (0.10), residues: 3408 *********************** 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 1162 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 924 time to evaluate : 6.211 Fit side-chains revert: symmetry clash outliers start: 238 outliers final: 148 residues processed: 1097 average time/residue: 0.6568 time to fit residues: 1246.4150 Evaluate side-chains 1030 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 882 time to evaluate : 5.955 Switching outliers to nearest non-outliers outliers start: 148 outliers final: 0 residues processed: 148 average time/residue: 0.5076 time to fit residues: 152.0716 ------------------------------------------------------------------------------- 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: 10.0000 chunk 226 optimal weight: 6.9990 chunk 606 optimal weight: 7.9990 chunk 495 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 729 optimal weight: 10.0000 chunk 788 optimal weight: 0.9990 chunk 649 optimal weight: 2.9990 chunk 723 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 585 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 ASN g 98 GLN j 74 GLN ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 295 GLN L 296 ASN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 42 GLN ** s 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 77 GLN x 34 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.255 68784 Z= 0.560 Angle : 1.562 51.003 93173 Z= 1.013 Chirality : 0.308 6.353 10171 Planarity : 0.004 0.084 11709 Dihedral : 7.157 168.172 9584 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Rotamer Outliers : 2.07 % 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: 0.26 (0.09), residues: 8122 helix: 1.03 (0.08), residues: 4275 sheet: -0.52 (0.24), residues: 436 loop : -0.79 (0.11), residues: 3411 *********************** 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 1090 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 941 time to evaluate : 7.220 Fit side-chains revert: symmetry clash outliers start: 149 outliers final: 67 residues processed: 1047 average time/residue: 0.6618 time to fit residues: 1200.0794 Evaluate side-chains 954 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 887 time to evaluate : 6.012 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.5278 time to fit residues: 74.8660 ------------------------------------------------------------------------------- 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: 7.9990 chunk 548 optimal weight: 5.9990 chunk 378 optimal weight: 30.0000 chunk 80 optimal weight: 30.0000 chunk 348 optimal weight: 20.0000 chunk 489 optimal weight: 4.9990 chunk 732 optimal weight: 5.9990 chunk 775 optimal weight: 20.0000 chunk 382 optimal weight: 10.0000 chunk 693 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 82 ASN 3 198 ASN g 98 GLN h 20 GLN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN L 295 GLN L 296 ASN l 26 HIS ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN t 77 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.248 68784 Z= 0.600 Angle : 1.575 50.969 93173 Z= 1.018 Chirality : 0.309 6.499 10171 Planarity : 0.005 0.084 11709 Dihedral : 7.204 167.541 9584 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.01 % Favored : 95.96 % Rotamer Outliers : 2.53 % 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: 0.30 (0.09), residues: 8122 helix: 1.06 (0.08), residues: 4275 sheet: -0.42 (0.25), residues: 415 loop : -0.76 (0.11), residues: 3432 *********************** 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 1102 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 920 time to evaluate : 6.272 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 182 outliers final: 103 residues processed: 1043 average time/residue: 0.6578 time to fit residues: 1188.2779 Evaluate side-chains 992 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 889 time to evaluate : 5.977 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 0 residues processed: 103 average time/residue: 0.5241 time to fit residues: 110.3937 ------------------------------------------------------------------------------- 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: 8.9990 chunk 11 optimal weight: 5.9990 chunk 577 optimal weight: 0.8980 chunk 319 optimal weight: 2.9990 chunk 661 optimal weight: 4.9990 chunk 535 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 395 optimal weight: 7.9990 chunk 695 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 79 ASN g 98 GLN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 295 GLN L 296 ASN ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 58 ASN t 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.249 68784 Z= 0.541 Angle : 1.555 50.761 93173 Z= 1.010 Chirality : 0.309 6.397 10171 Planarity : 0.004 0.081 11709 Dihedral : 7.006 167.811 9584 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.49 % Rotamer Outliers : 1.43 % 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: 0.49 (0.09), residues: 8122 helix: 1.23 (0.08), residues: 4281 sheet: -0.55 (0.24), residues: 444 loop : -0.66 (0.11), residues: 3397 *********************** 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 1039 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 936 time to evaluate : 5.944 Fit side-chains revert: symmetry clash outliers start: 103 outliers final: 45 residues processed: 1005 average time/residue: 0.6579 time to fit residues: 1137.1868 Evaluate side-chains 939 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 894 time to evaluate : 5.946 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.5378 time to fit residues: 52.8775 ------------------------------------------------------------------------------- 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: 7.9990 chunk 153 optimal weight: 1.9990 chunk 455 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 775 optimal weight: 20.0000 chunk 644 optimal weight: 10.0000 chunk 359 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 256 optimal weight: 8.9990 chunk 407 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 ASN ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 ASN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN l 26 HIS x 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.246 68784 Z= 0.591 Angle : 1.573 50.873 93173 Z= 1.017 Chirality : 0.309 6.493 10171 Planarity : 0.004 0.082 11709 Dihedral : 7.113 167.907 9584 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.11 % Favored : 95.86 % Rotamer Outliers : 1.67 % 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: 0.42 (0.09), residues: 8122 helix: 1.16 (0.08), residues: 4279 sheet: -0.62 (0.24), residues: 444 loop : -0.68 (0.11), residues: 3399 *********************** 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 1023 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 903 time to evaluate : 6.569 Fit side-chains outliers start: 120 outliers final: 71 residues processed: 983 average time/residue: 0.6605 time to fit residues: 1118.8363 Evaluate side-chains 948 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 877 time to evaluate : 5.960 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.5150 time to fit residues: 77.3553 ------------------------------------------------------------------------------- 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: 6.9990 chunk 87 optimal weight: 4.9990 chunk 442 optimal weight: 0.6980 chunk 566 optimal weight: 20.0000 chunk 439 optimal weight: 6.9990 chunk 653 optimal weight: 10.0000 chunk 433 optimal weight: 9.9990 chunk 772 optimal weight: 10.0000 chunk 483 optimal weight: 0.0570 chunk 471 optimal weight: 0.7980 chunk 356 optimal weight: 10.0000 overall best weight: 2.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 ASN e 79 ASN g 98 GLN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 190 HIS l 26 HIS l 96 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.248 68784 Z= 0.529 Angle : 1.550 50.764 93173 Z= 1.008 Chirality : 0.308 6.421 10171 Planarity : 0.004 0.080 11709 Dihedral : 6.887 168.029 9584 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.21 % Favored : 96.76 % Rotamer Outliers : 1.21 % 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: 0.64 (0.10), residues: 8122 helix: 1.34 (0.08), residues: 4284 sheet: -0.57 (0.24), residues: 454 loop : -0.57 (0.11), residues: 3384 *********************** 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 1034 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 947 time to evaluate : 6.055 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 34 residues processed: 1006 average time/residue: 0.6966 time to fit residues: 1210.5270 Evaluate side-chains 929 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 895 time to evaluate : 5.943 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.5809 time to fit residues: 43.8280 ------------------------------------------------------------------------------- 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: 9.9990 chunk 308 optimal weight: 0.8980 chunk 461 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 chunk 491 optimal weight: 5.9990 chunk 526 optimal weight: 10.0000 chunk 382 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 607 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 ASN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS l 96 HIS z 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.250 68784 Z= 0.556 Angle : 1.562 50.828 93173 Z= 1.013 Chirality : 0.309 6.474 10171 Planarity : 0.004 0.080 11709 Dihedral : 6.913 168.058 9584 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.84 % Favored : 96.13 % Rotamer Outliers : 0.93 % 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: 0.61 (0.10), residues: 8122 helix: 1.32 (0.08), residues: 4280 sheet: -0.63 (0.24), residues: 456 loop : -0.58 (0.11), residues: 3386 *********************** 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 984 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 917 time to evaluate : 6.057 Fit side-chains revert: symmetry clash outliers start: 67 outliers final: 40 residues processed: 955 average time/residue: 0.6778 time to fit residues: 1110.8465 Evaluate side-chains 927 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 887 time to evaluate : 6.250 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.5117 time to fit residues: 47.8696 ------------------------------------------------------------------------------- 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: 4.9990 chunk 740 optimal weight: 10.0000 chunk 675 optimal weight: 9.9990 chunk 720 optimal weight: 8.9990 chunk 433 optimal weight: 1.9990 chunk 313 optimal weight: 9.9990 chunk 565 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 chunk 650 optimal weight: 10.0000 chunk 681 optimal weight: 7.9990 chunk 717 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 444 GLN c 51 ASN e 79 ASN ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN l 26 HIS t 77 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.248 68784 Z= 0.582 Angle : 1.574 50.813 93173 Z= 1.017 Chirality : 0.309 6.460 10171 Planarity : 0.004 0.080 11709 Dihedral : 7.046 167.801 9584 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.05 % Rotamer Outliers : 0.67 % 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: 0.53 (0.09), residues: 8122 helix: 1.25 (0.08), residues: 4275 sheet: -0.63 (0.24), residues: 444 loop : -0.62 (0.11), residues: 3403 *********************** 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 950 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 902 time to evaluate : 6.087 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 27 residues processed: 930 average time/residue: 0.6814 time to fit residues: 1091.0121 Evaluate side-chains 908 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 881 time to evaluate : 6.008 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.5448 time to fit residues: 36.2192 ------------------------------------------------------------------------------- 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: 2.9990 chunk 761 optimal weight: 8.9990 chunk 464 optimal weight: 3.9990 chunk 361 optimal weight: 6.9990 chunk 529 optimal weight: 2.9990 chunk 798 optimal weight: 9.9990 chunk 735 optimal weight: 10.0000 chunk 636 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 491 optimal weight: 0.9980 chunk 390 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 51 ASN e 80 ASN g 98 GLN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS t 77 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.252 68784 Z= 0.530 Angle : 1.555 50.768 93173 Z= 1.010 Chirality : 0.308 6.421 10171 Planarity : 0.004 0.079 11709 Dihedral : 6.839 167.977 9584 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.39 % Favored : 96.59 % Rotamer Outliers : 0.21 % 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: 0.71 (0.10), residues: 8122 helix: 1.40 (0.08), residues: 4276 sheet: -0.56 (0.24), residues: 445 loop : -0.54 (0.11), residues: 3401 ********************** 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 939 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 924 time to evaluate : 6.286 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 931 average time/residue: 0.6996 time to fit residues: 1117.3200 Evaluate side-chains 905 residues out of total 7189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 899 time to evaluate : 5.935 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.6234 time to fit residues: 14.7398 ------------------------------------------------------------------------------- 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: 2.9990 chunk 677 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 586 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 637 optimal weight: 8.9990 chunk 266 optimal weight: 8.9990 chunk 654 optimal weight: 10.0000 chunk 80 optimal weight: 30.0000 chunk 117 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 121 GLN c 51 ASN e 79 ASN ** g 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 74 GLN ** H 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 26 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.074988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.066840 restraints weight = 146463.353| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.49 r_work: 0.2833 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.247 68784 Z= 0.579 Angle : 1.575 50.820 93173 Z= 1.017 Chirality : 0.309 6.427 10171 Planarity : 0.004 0.079 11709 Dihedral : 6.985 167.662 9584 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.17 % Favored : 95.80 % Rotamer Outliers : 0.39 % 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: 0.60 (0.10), residues: 8122 helix: 1.32 (0.08), residues: 4261 sheet: -0.62 (0.24), residues: 437 loop : -0.60 (0.11), residues: 3424 =============================================================================== Job complete usr+sys time: 17258.72 seconds wall clock time: 304 minutes 4.30 seconds (18244.30 seconds total)