Starting phenix.real_space_refine on Fri Feb 16 09:55:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkr_11259/02_2024/6zkr_11259_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkr_11259/02_2024/6zkr_11259.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkr_11259/02_2024/6zkr_11259_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkr_11259/02_2024/6zkr_11259_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkr_11259/02_2024/6zkr_11259_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkr_11259/02_2024/6zkr_11259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkr_11259/02_2024/6zkr_11259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkr_11259/02_2024/6zkr_11259_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zkr_11259/02_2024/6zkr_11259_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Fe 28 7.16 5 Zn 1 6.06 5 P 44 5.49 5 S 466 5.16 5 C 43597 2.51 5 N 11138 2.21 5 O 12078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 68": "NH1" <-> "NH2" Residue "1 ARG 237": "NH1" <-> "NH2" Residue "1 ARG 249": "NH1" <-> "NH2" Residue "1 ARG 339": "NH1" <-> "NH2" Residue "1 ARG 423": "NH1" <-> "NH2" Residue "2 ARG 187": "NH1" <-> "NH2" Residue "3 ARG 53": "NH1" <-> "NH2" Residue "3 TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 418": "NH1" <-> "NH2" Residue "3 TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 460": "NH1" <-> "NH2" Residue "3 TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 2": "NH1" <-> "NH2" Residue "4 TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 188": "NH1" <-> "NH2" Residue "4 TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 8": "NH1" <-> "NH2" Residue "5 ARG 12": "NH1" <-> "NH2" Residue "5 ARG 14": "NH1" <-> "NH2" Residue "5 PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 25": "NH1" <-> "NH2" Residue "6 ARG 77": "NH1" <-> "NH2" Residue "6 TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "6 ARG 174": "NH1" <-> "NH2" Residue "6 ARG 178": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 161": "NH1" <-> "NH2" Residue "L PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "M TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 103": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 77": "NH1" <-> "NH2" Residue "W ARG 115": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 165": "NH1" <-> "NH2" Residue "Z ARG 14": "NH1" <-> "NH2" Residue "Z TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d ARG 186": "NH1" <-> "NH2" Residue "d ARG 251": "NH1" <-> "NH2" Residue "d ARG 292": "NH1" <-> "NH2" Residue "d ARG 320": "NH1" <-> "NH2" Residue "d ARG 322": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "g ARG 32": "NH1" <-> "NH2" Residue "h ARG 17": "NH1" <-> "NH2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 95": "NH1" <-> "NH2" Residue "k ARG 305": "NH1" <-> "NH2" Residue "l ARG 68": "NH1" <-> "NH2" Residue "l ARG 82": "NH1" <-> "NH2" Residue "l ARG 104": "NH1" <-> "NH2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 49": "NH1" <-> "NH2" Residue "o ARG 50": "NH1" <-> "NH2" Residue "o ARG 120": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "p ARG 56": "NH1" <-> "NH2" Residue "p ARG 108": "NH1" <-> "NH2" Residue "q ARG 26": "NH1" <-> "NH2" Residue "q ARG 27": "NH1" <-> "NH2" Residue "q ARG 51": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "r ARG 19": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r ARG 37": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "s PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 103": "NH1" <-> "NH2" Residue "s ARG 110": "NH1" <-> "NH2" Residue "s ARG 114": "NH1" <-> "NH2" Residue "s ARG 117": "NH1" <-> "NH2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 37": "NH1" <-> "NH2" Residue "t ARG 44": "NH1" <-> "NH2" Residue "t ARG 64": "NH1" <-> "NH2" Residue "t ARG 92": "NH1" <-> "NH2" Residue "t ARG 121": "NH1" <-> "NH2" Residue "t ARG 128": "NH1" <-> "NH2" Residue "t ARG 134": "NH1" <-> "NH2" Residue "t ARG 176": "NH1" <-> "NH2" Residue "u ARG 19": "NH1" <-> "NH2" Residue "v ARG 70": "NH1" <-> "NH2" Residue "w ARG 25": "NH1" <-> "NH2" Residue "w ARG 84": "NH1" <-> "NH2" Residue "z PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 37": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67353 Number of models: 1 Model: "" Number of chains: 69 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: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3390 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 393} Chain breaks: 2 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: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 880 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain breaks: 1 Chain: "H" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2489 Classifications: {'peptide': 313} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 290} Chain breaks: 1 Chain: "J" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1273 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 1 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: 4806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4806 Classifications: {'peptide': 606} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 579} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 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: "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: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2372 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 15, 'TRANS': 281} Chain breaks: 3 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' K': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'3PE': 1, 'PC1': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "9" Number of atoms: 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: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'3PE': 1, 'PC1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 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: "K" 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: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 236 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "M" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 282 Unusual residues: {'3PE': 2, 'CDL': 1, 'PC1': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 251 Unusual residues: {'3PE': 2, 'CDL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 51 Chain: "W" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} 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: "Y" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 100 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "g" 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: "i" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "o" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 106 Unusual residues: {'3PE': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "p" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 26 Chain: "s" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'MYR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2715 SG CYS 1 365 102.268 53.473 246.981 1.00 43.60 S ATOM 2676 SG CYS 1 359 109.285 53.871 247.881 1.00 42.93 S ATOM 3039 SG CYS 1 405 106.092 47.712 246.363 1.00 37.41 S ATOM 4116 SG CYS 2 103 99.735 49.228 266.086 1.00 98.42 S ATOM 4150 SG CYS 2 108 97.292 47.124 268.137 1.00 50.11 S ATOM 4430 SG CYS 2 144 101.166 45.510 262.651 1.00 65.45 S ATOM 4453 SG CYS 2 148 99.399 42.791 263.915 1.00 89.47 S ATOM 5793 SG CYS 3 114 105.329 71.494 232.276 1.00 70.64 S ATOM 5732 SG CYS 3 105 100.051 75.104 233.873 1.00 60.59 S ATOM 5753 SG CYS 3 108 106.094 76.714 235.698 1.00 72.88 S ATOM 6125 SG CYS 3 156 112.410 64.113 237.084 1.00 43.36 S ATOM 6102 SG CYS 3 153 110.210 67.319 242.517 1.00 44.29 S ATOM 6149 SG CYS 3 159 116.307 68.021 240.827 1.00 62.59 S ATOM 6479 SG CYS 3 203 112.226 70.441 236.980 1.00 75.99 S ATOM 5238 SG CYS 3 41 111.528 57.578 234.957 1.00 51.36 S ATOM 5324 SG CYS 3 52 107.777 58.681 234.084 1.00 52.72 S ATOM 5349 SG CYS 3 55 108.073 53.600 230.988 1.00 41.80 S ATOM 5450 SG CYS 3 69 111.837 53.753 232.472 1.00 66.86 S ATOM 15607 SG CYS 6 54 84.428 94.689 207.698 1.00 82.29 S ATOM 17533 SG CYS 9 116 91.589 95.797 220.309 1.00 44.58 S ATOM 17580 SG CYS 9 122 92.071 91.456 225.057 1.00 27.48 S ATOM 17307 SG CYS 9 87 96.096 91.059 219.871 1.00 63.10 S ATOM 17609 SG CYS 9 126 94.114 88.175 232.431 1.00 70.19 S ATOM 17280 SG CYS 9 83 97.809 89.835 227.417 1.00 29.44 S ATOM 17238 SG CYS 9 77 99.793 91.677 233.156 1.00 22.31 S ATOM 17257 SG CYS 9 80 99.107 85.038 231.701 1.00 49.44 S ATOM 41151 SG CYS b 59 94.973 84.291 247.968 1.00 46.23 S ATOM 41329 SG CYS b 84 98.110 83.860 245.795 1.00 41.16 S ATOM 41351 SG CYS b 87 96.674 86.940 246.430 1.00 35.15 S Time building chain proxies: 26.67, per 1000 atoms: 0.40 Number of scatterers: 67353 At special positions: 0 Unit cell: (175.13, 198.37, 297.97, 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 466 16.00 P 44 15.00 O 12078 8.00 N 11138 7.00 C 43597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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=2.04 Simple disulfide: pdb=" SG CYS l 42 " - pdb=" SG CYS l 55 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.56 Conformation dependent library (CDL) restraints added in 8.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES 2 300 " pdb="FE2 FES 2 300 " - pdb=" SG CYS 2 148 " 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 2 144 " pdb=" FES 3 803 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 52 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 55 " pdb="FE1 FES 3 803 " - pdb=" SG CYS 3 41 " pdb="FE2 FES 3 803 " - pdb=" SG CYS 3 69 " pdb=" SF4 1 500 " pdb="FE1 SF4 1 500 " - pdb=" SG CYS 1 365 " pdb="FE3 SF4 1 500 " - pdb=" SG CYS 1 359 " pdb="FE4 SF4 1 500 " - pdb=" SG CYS 1 405 " pdb="FE2 SF4 1 500 " - 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="FE2 SF4 3 801 " - pdb=" SG CYS 3 105 " pdb="FE1 SF4 3 801 " - pdb=" SG CYS 3 114 " 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="FE4 SF4 6 201 " - pdb=" SG CYS 6 54 " pdb="FE3 SF4 6 201 " - pdb=" SG CYS 6 149 " pdb="FE2 SF4 6 201 " - pdb=" SG CYS 6 119 " pdb="FE1 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 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15330 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 322 helices and 28 sheets defined 50.0% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.32 Creating SS restraints... Processing helix chain '1' and resid 17 through 19 No H-bonds generated for 'chain '1' and resid 17 through 19' 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 81 removed outlier: 3.881A pdb=" N PHE 1 81 " --> pdb=" O LEU 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 113 Processing helix chain '1' and resid 115 through 127 Processing helix chain '1' and resid 143 through 158 Processing helix chain '1' and resid 166 through 168 No H-bonds generated for 'chain '1' and resid 166 through 168' Processing helix chain '1' and resid 185 through 187 No H-bonds generated for 'chain '1' and resid 185 through 187' Processing helix chain '1' and resid 189 through 196 Processing helix chain '1' and resid 215 through 217 No H-bonds generated for 'chain '1' and resid 215 through 217' Processing helix chain '1' and resid 225 through 229 Processing helix chain '1' and resid 231 through 237 Processing helix chain '1' and resid 239 through 244 Processing helix chain '1' and resid 276 through 282 Processing helix chain '1' and resid 291 through 293 No H-bonds generated for 'chain '1' and resid 291 through 293' Processing helix chain '1' and resid 319 through 323 Processing helix chain '1' and resid 343 through 356 Processing helix chain '1' and resid 363 through 381 removed outlier: 4.354A pdb=" N ASP 1 370 " --> pdb=" O ARG 1 366 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG 1 381 " --> pdb=" O ALA 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 388 through 399 Processing helix chain '1' and resid 407 through 436 Proline residue: 1 414 - end of helix Proline residue: 1 424 - end of helix Processing helix chain '2' and resid 25 through 37 removed outlier: 3.743A pdb=" N ASN 2 37 " --> pdb=" O ALA 2 33 " (cutoff:3.500A) Processing helix chain '2' and resid 43 through 58 removed outlier: 3.646A pdb=" N VAL 2 47 " --> pdb=" O ALA 2 44 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU 2 48 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) Proline residue: 2 49 - end of helix removed outlier: 3.546A pdb=" N ASN 2 58 " --> pdb=" O GLN 2 55 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 73 Processing helix chain '2' and resid 78 through 86 removed outlier: 4.017A pdb=" N VAL 2 83 " --> pdb=" O ARG 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 106 through 110 Processing helix chain '2' and resid 113 through 124 Processing helix chain '2' and resid 148 through 150 No H-bonds generated for 'chain '2' and resid 148 through 150' Processing helix chain '2' and resid 166 through 178 Processing helix chain '3' and resid 26 through 33 removed outlier: 4.079A pdb=" N VAL 3 33 " --> pdb=" O ALA 3 29 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 97 Processing helix chain '3' and resid 115 through 122 Processing helix chain '3' and resid 159 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 201 No H-bonds generated for 'chain '3' and resid 198 through 201' Processing helix chain '3' and resid 265 through 269 Processing helix chain '3' and resid 296 through 307 removed outlier: 3.865A pdb=" N MET 3 306 " --> pdb=" O ARG 3 302 " (cutoff:3.500A) Processing helix chain '3' and resid 325 through 337 Processing helix chain '3' and resid 360 through 362 No H-bonds generated for 'chain '3' and resid 360 through 362' Processing helix chain '3' and resid 369 through 372 Processing helix chain '3' and resid 384 through 387 No H-bonds generated for 'chain '3' and resid 384 through 387' Processing helix chain '3' and resid 389 through 401 Processing helix chain '3' and resid 426 through 433 removed outlier: 3.927A pdb=" N ILE 3 432 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA 3 433 " --> pdb=" O GLN 3 430 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 445 removed outlier: 3.957A pdb=" N VAL 3 442 " --> pdb=" O PRO 3 438 " (cutoff:3.500A) Processing helix chain '3' and resid 463 through 478 Processing helix chain '3' and resid 499 through 504 Processing helix chain '3' and resid 511 through 516 removed outlier: 4.016A pdb=" N LYS 3 516 " --> pdb=" O ALA 3 513 " (cutoff:3.500A) Processing helix chain '3' and resid 566 through 568 No H-bonds generated for 'chain '3' and resid 566 through 568' Processing helix chain '3' and resid 596 through 607 Processing helix chain '3' and resid 616 through 626 Processing helix chain '3' and resid 642 through 651 removed outlier: 4.094A pdb=" N LEU 3 651 " --> pdb=" O GLU 3 647 " (cutoff:3.500A) Processing helix chain '3' and resid 669 through 671 No H-bonds generated for 'chain '3' and resid 669 through 671' Processing helix chain '3' and resid 682 through 692 Processing helix chain '4' and resid 8 through 14 removed outlier: 3.506A pdb=" N GLN 4 13 " --> pdb=" O GLU 4 9 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR 4 14 " --> pdb=" O TRP 4 10 " (cutoff:3.500A) Processing helix chain '4' and resid 87 through 93 removed outlier: 4.866A pdb=" N GLU 4 92 " --> pdb=" O GLU 4 88 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR 4 93 " --> pdb=" O LYS 4 89 " (cutoff:3.500A) Processing helix chain '4' and resid 96 through 100 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: 4.006A pdb=" N GLU 4 172 " --> pdb=" O PHE 4 168 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU 4 173 " --> pdb=" O TRP 4 169 " (cutoff:3.500A) Processing helix chain '4' and resid 208 through 229 removed outlier: 3.804A pdb=" N ASN 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER 4 219 " --> pdb=" O SER 4 215 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU 4 220 " --> pdb=" O LYS 4 216 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG 4 221 " --> pdb=" O ASN 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 237 Processing helix chain '4' and resid 247 through 252 Processing helix chain '4' and resid 257 through 263 removed outlier: 4.456A pdb=" N GLY 4 262 " --> pdb=" O MET 4 259 " (cutoff:3.500A) 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: 4.440A pdb=" N ASP 4 403 " --> pdb=" O LEU 4 399 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LYS 4 404 " --> pdb=" O ALA 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 414 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: 3.915A pdb=" N VAL 5 57 " --> pdb=" O PRO 5 54 " (cutoff:3.500A) removed outlier: 4.199A 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 125 through 137 removed outlier: 3.823A pdb=" N ASN 5 128 " --> pdb=" O LYS 5 125 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TRP 5 129 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU 5 131 " --> pdb=" O ASN 5 128 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG 5 132 " --> pdb=" O TRP 5 129 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET 5 137 " --> pdb=" O ILE 5 134 " (cutoff:3.500A) Processing helix chain '6' and resid 25 through 42 Processing helix chain '6' and resid 54 through 62 Processing helix chain '6' and resid 69 through 72 Processing helix chain '6' and resid 97 through 105 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: 5.770A pdb=" N ALA 9 163 " --> pdb=" O ASP 9 159 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLU 9 164 " --> pdb=" O LYS 9 160 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ALA 9 167 " --> pdb=" O ALA 9 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 53 through 80 Proline residue: A 74 - end of helix removed outlier: 5.673A pdb=" N TRP A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.929A 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 10 Processing helix chain 'H' and resid 12 through 32 removed outlier: 3.546A pdb=" N THR H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 44 No H-bonds generated for 'chain 'H' and resid 42 through 44' Processing helix chain 'H' and resid 47 through 56 Processing helix chain 'H' and resid 68 through 83 Proline residue: H 75 - end of helix Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.640A pdb=" N ALA H 112 " --> pdb=" O MET H 108 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TYR H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER H 115 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 157 removed outlier: 3.910A pdb=" N VAL H 144 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR H 145 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N MET H 156 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 169 removed outlier: 4.104A 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 217 through 242 Processing helix chain 'H' and resid 252 through 273 Processing helix chain 'H' and resid 282 through 290 Processing helix chain 'H' and resid 293 through 310 Proline residue: H 308 - end of helix Processing helix chain 'J' and resid 2 through 21 removed outlier: 4.983A pdb=" N VAL J 6 " --> pdb=" O THR J 3 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE J 20 " --> pdb=" O PHE J 17 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER J 21 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 47 removed outlier: 3.999A pdb=" N PHE J 47 " --> pdb=" O ILE J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 73 removed outlier: 4.098A pdb=" N LEU J 61 " --> pdb=" O PHE J 57 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY J 62 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N MET J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL J 66 " --> pdb=" O GLY J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 110 Processing helix chain 'J' and resid 138 through 148 removed outlier: 4.048A pdb=" N LEU J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N TYR J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 4.375A 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 19 Processing helix chain 'K' and resid 26 through 50 Processing helix chain 'K' and resid 54 through 84 removed outlier: 3.932A pdb=" N MET K 58 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Proline residue: K 60 - end of helix removed outlier: 3.600A pdb=" N PHE K 66 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA K 67 " --> pdb=" O LEU K 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 23 removed outlier: 3.551A pdb=" N LEU L 12 " --> pdb=" O THR L 8 " (cutoff:3.500A) Proline residue: L 18 - end of helix Processing helix chain 'L' and resid 32 through 57 removed outlier: 3.844A pdb=" N ILE L 49 " --> pdb=" O ILE L 45 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.545A pdb=" N THR L 57 " --> pdb=" O MET L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 107 Proline residue: L 91 - end of helix removed outlier: 3.734A pdb=" N TRP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 131 Processing helix chain 'L' and resid 137 through 155 Processing helix chain 'L' and resid 162 through 193 removed outlier: 3.940A pdb=" N GLY L 181 " --> pdb=" O ILE L 177 " (cutoff:3.500A) 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: 3.629A pdb=" N MET L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU L 238 " --> pdb=" O PRO L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 250 removed outlier: 4.621A pdb=" N SER L 249 " --> pdb=" O ALA L 245 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 264 through 267 No H-bonds generated for 'chain 'L' and resid 264 through 267' Processing helix chain 'L' and resid 271 through 293 removed outlier: 3.683A pdb=" N ALA L 289 " --> pdb=" O THR L 285 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 318 Processing helix chain 'L' and resid 322 through 349 removed outlier: 4.436A pdb=" N PHE L 334 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE L 335 " --> pdb=" O THR L 331 " (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 381 Processing helix chain 'L' and resid 389 through 400 removed outlier: 5.114A pdb=" N LEU L 394 " --> pdb=" O TYR L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 430 removed outlier: 3.740A pdb=" N ALA L 420 " --> pdb=" O THR L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 471 removed outlier: 3.614A pdb=" N LEU L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY L 465 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 5.748A 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 508 removed outlier: 3.638A pdb=" N THR L 508 " --> pdb=" O ILE L 504 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 547 Proline residue: L 530 - end of helix removed outlier: 4.488A pdb=" N MET L 533 " --> pdb=" O PRO L 530 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N HIS L 534 " --> pdb=" O THR L 531 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG L 535 " --> pdb=" O ILE L 532 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N THR L 537 " --> pdb=" O HIS L 534 " (cutoff:3.500A) Proline residue: L 538 - end of helix removed outlier: 4.539A pdb=" N THR L 543 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN L 546 " --> pdb=" O THR L 543 " (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 removed outlier: 3.991A pdb=" N MET M 12 " --> pdb=" O THR M 8 " (cutoff:3.500A) Proline residue: M 13 - end of helix Processing helix chain 'M' and resid 25 through 42 removed outlier: 4.234A pdb=" N LEU M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU M 41 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU M 42 " --> pdb=" O SER M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 79 removed outlier: 3.762A pdb=" N LEU M 73 " --> pdb=" O THR M 69 " (cutoff:3.500A) Proline residue: M 74 - end of helix Processing helix chain 'M' and resid 89 through 107 Processing helix chain 'M' and resid 115 through 135 removed outlier: 4.677A pdb=" N LEU M 126 " --> pdb=" O PHE M 122 " (cutoff:3.500A) removed outlier: 4.730A 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 140 through 151 removed outlier: 3.754A pdb=" N LEU M 143 " --> pdb=" O THR M 140 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA M 145 " --> pdb=" O ARG M 142 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE M 151 " --> pdb=" O TYR M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 170 Proline residue: M 159 - end of helix removed outlier: 3.554A pdb=" N VAL M 162 " --> pdb=" O LEU M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 179 No H-bonds generated for 'chain 'M' and resid 176 through 179' Processing helix chain 'M' and resid 191 through 206 removed outlier: 4.942A pdb=" N ALA M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE M 203 " --> pdb=" O CYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 219 No H-bonds generated for 'chain 'M' and resid 216 through 219' Processing helix chain 'M' and resid 225 through 233 Processing helix chain 'M' and resid 237 through 246 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 277 removed outlier: 4.244A pdb=" N ILE M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER M 273 " --> pdb=" O MET M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 303 removed outlier: 4.373A pdb=" N LEU M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL M 297 " --> pdb=" O HIS M 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 337 removed outlier: 4.193A pdb=" N ARG M 336 " --> pdb=" O SER M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 366 Processing helix chain 'M' and resid 373 through 388 Processing helix chain 'M' and resid 392 through 415 Processing helix chain 'M' and resid 431 through 446 Proline residue: M 443 - end of helix Processing helix chain 'M' and resid 451 through 453 No H-bonds generated for 'chain 'M' and resid 451 through 453' Processing helix chain 'N' and resid 3 through 22 Processing helix chain 'N' and resid 26 through 44 Proline residue: N 42 - end of helix Processing helix chain 'N' and resid 50 through 81 Processing helix chain 'N' and resid 92 through 106 Processing helix chain 'N' and resid 115 through 121 Processing helix chain 'N' and resid 124 through 132 Processing helix chain 'N' and resid 135 through 144 removed outlier: 3.622A pdb=" N MET N 139 " --> pdb=" O LYS N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 148 No H-bonds generated for 'chain 'N' and resid 146 through 148' Processing helix chain 'N' and resid 151 through 169 removed outlier: 4.027A pdb=" N GLY N 169 " --> pdb=" O GLY N 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 193 removed outlier: 3.877A pdb=" N VAL N 193 " --> pdb=" O TRP N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 222 Processing helix chain 'N' and resid 227 through 233 removed outlier: 4.148A pdb=" N THR N 233 " --> pdb=" O SER N 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 251 removed outlier: 3.600A pdb=" N ILE N 242 " --> pdb=" O PRO N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 270 Proline residue: N 262 - end of helix Processing helix chain 'N' and resid 277 through 300 removed outlier: 3.613A pdb=" N LEU N 287 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU N 288 " --> pdb=" O ILE N 284 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 310 through 316 removed outlier: 3.553A pdb=" N TRP N 315 " --> pdb=" O LYS N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 334 removed outlier: 3.516A pdb=" N SER N 333 " --> pdb=" O MET N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 337 through 346 Proline residue: N 341 - end of helix removed outlier: 3.787A 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 87 through 103 Processing helix chain 'V' and resid 108 through 129 Processing helix chain 'W' and resid 16 through 46 removed outlier: 4.316A 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 63 through 65 No H-bonds generated for 'chain 'W' and resid 63 through 65' Processing helix chain 'W' and resid 70 through 78 Processing helix chain 'W' and resid 83 through 116 Processing helix chain 'W' and resid 130 through 132 No H-bonds generated for 'chain 'W' and resid 130 through 132' Processing helix chain 'X' and resid 8 through 19 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 9 through 11 No H-bonds generated for 'chain 'Y' and resid 9 through 11' Processing helix chain 'Y' and resid 21 through 26 Processing helix chain 'Y' and resid 28 through 34 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 52 through 74 removed outlier: 4.158A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 53 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLU Y 57 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA Y 66 " --> pdb=" O ASN Y 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 90 removed outlier: 3.729A pdb=" N CYS Y 87 " --> pdb=" O GLU Y 83 " (cutoff:3.500A) 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 58 removed outlier: 4.211A pdb=" N ASN Z 58 " --> pdb=" O GLN Z 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 73 through 75 No H-bonds generated for 'chain 'Z' and resid 73 through 75' Processing helix chain 'Z' and resid 81 through 123 removed outlier: 4.295A pdb=" N GLU Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU Z 118 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N SER Z 119 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N HIS Z 120 " --> pdb=" O GLU Z 116 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG Z 121 " --> pdb=" O GLY Z 117 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLN Z 122 " --> pdb=" O GLU Z 118 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 142 Processing helix chain 'Z' and resid 151 through 171 Processing helix chain 'a' and resid 42 through 45 removed outlier: 3.659A pdb=" N ASP a 45 " --> pdb=" O GLN a 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 42 through 45' Processing helix chain 'a' and resid 50 through 60 removed outlier: 4.941A pdb=" N LYS a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.781A pdb=" N ARG b 27 " --> pdb=" O ARG b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 44 Processing helix chain 'c' and resid 78 through 81 removed outlier: 4.436A pdb=" N ASN c 81 " --> pdb=" O PRO c 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 78 through 81' Processing helix chain 'c' and resid 89 through 98 Processing helix chain 'c' and resid 119 through 122 removed outlier: 3.534A pdb=" N PHE c 122 " --> pdb=" O GLY c 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 119 through 122' Processing helix chain 'd' and resid 30 through 39 Processing helix chain 'd' and resid 53 through 62 removed outlier: 5.110A pdb=" N HIS d 58 " --> pdb=" O ASP d 55 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU d 59 " --> pdb=" O THR d 56 " (cutoff:3.500A) Proline residue: d 61 - end of helix Processing helix chain 'd' and resid 78 through 87 removed outlier: 3.521A pdb=" N GLU d 86 " --> pdb=" O ARG d 82 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N HIS d 87 " --> pdb=" O ARG d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 110 Processing helix chain 'd' and resid 112 through 124 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 179 through 184 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 248 Processing helix chain 'd' and resid 281 through 287 Processing helix chain 'd' and resid 301 through 303 No H-bonds generated for 'chain 'd' and resid 301 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: 5.122A pdb=" N ARG d 320 " --> pdb=" O GLU d 316 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N HIS d 321 " --> pdb=" O VAL d 317 " (cutoff:3.500A) Processing helix chain 'e' and resid 27 through 38 removed outlier: 4.563A pdb=" N GLY e 31 " --> pdb=" O GLY e 28 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 46 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: 4.522A pdb=" N HIS f 36 " --> pdb=" O ASP f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 59 Processing helix chain 'f' and resid 65 through 71 Processing helix chain 'f' and resid 76 through 96 removed outlier: 4.078A pdb=" N GLN f 95 " --> pdb=" O ARG f 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 48 Proline residue: g 43 - end of helix Processing helix chain 'g' and resid 55 through 68 Processing helix chain 'g' and resid 75 through 93 Processing helix chain 'g' and resid 99 through 105 removed outlier: 4.701A 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 3 through 14 Processing helix chain 'i' and resid 19 through 30 Processing helix chain 'i' and resid 84 through 90 removed outlier: 3.854A pdb=" N ARG i 88 " --> pdb=" O PRO i 84 " (cutoff:3.500A) removed outlier: 4.590A 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 73 through 82 Processing helix chain 'k' and resid 5 through 10 Processing helix chain 'k' and resid 38 through 45 Processing helix chain 'k' and resid 58 through 62 Processing helix chain 'k' and resid 79 through 84 Processing helix chain 'k' and resid 92 through 117 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 removed outlier: 3.745A pdb=" N ALA k 137 " --> pdb=" O VAL k 133 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 162 removed outlier: 4.562A pdb=" N CYS k 161 " --> pdb=" O LYS k 157 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLU k 162 " --> pdb=" O VAL k 158 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 184 Processing helix chain 'k' and resid 196 through 214 removed outlier: 5.856A pdb=" N LEU k 211 " --> pdb=" O LYS k 207 " (cutoff:3.500A) Proline residue: k 212 - end of helix Processing helix chain 'k' and resid 226 through 228 No H-bonds generated for 'chain 'k' and resid 226 through 228' Processing helix chain 'k' and resid 231 through 239 Processing helix chain 'k' and resid 253 through 263 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 297 Processing helix chain 'l' and resid 5 through 8 No H-bonds generated for 'chain 'l' and resid 5 through 8' Processing helix chain 'l' and resid 25 through 27 No H-bonds generated for 'chain 'l' and resid 25 through 27' Processing helix chain 'l' and resid 33 through 43 Processing helix chain 'l' and resid 47 through 54 removed outlier: 3.937A pdb=" N LYS l 53 " --> pdb=" O ILE l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 67 Processing helix chain 'l' and resid 69 through 87 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 7 through 14 Processing helix chain 'm' and resid 16 through 33 Proline residue: m 32 - end of helix Processing helix chain 'm' and resid 38 through 47 removed outlier: 3.714A pdb=" N LEU m 42 " --> pdb=" O THR m 38 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA m 47 " --> pdb=" O MET m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 82 Processing helix chain 'n' and resid 27 through 36 Processing helix chain 'n' and resid 49 through 52 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 5 through 7 No H-bonds generated for 'chain 'o' and resid 5 through 7' Processing helix chain 'o' and resid 16 through 20 removed outlier: 3.566A pdb=" N ARG o 19 " --> pdb=" O ASP o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 29 through 48 Processing helix chain 'o' and resid 58 through 96 removed outlier: 3.958A pdb=" N TYR o 74 " --> pdb=" O PHE o 70 " (cutoff:3.500A) 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 26 through 50 removed outlier: 3.941A pdb=" N GLN p 49 " --> pdb=" O GLU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 62 through 73 removed outlier: 3.607A pdb=" N SER p 72 " --> pdb=" O THR p 68 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA p 73 " --> pdb=" O CYS p 69 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 92 Processing helix chain 'p' and resid 95 through 117 removed outlier: 3.808A pdb=" N GLU p 117 " --> pdb=" O LYS p 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 31 through 96 removed outlier: 3.540A pdb=" N PHE q 35 " --> pdb=" O GLY q 31 " (cutoff:3.500A) Proline residue: q 72 - end of helix 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 136 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 24 Processing helix chain 'r' and resid 69 through 72 No H-bonds generated for 'chain 'r' and resid 69 through 72' Processing helix chain 'r' and resid 75 through 87 Processing helix chain 's' and resid 2 through 8 Processing helix chain 's' and resid 42 through 46 Processing helix chain 's' and resid 59 through 71 Processing helix chain 's' and resid 80 through 121 Processing helix chain 't' and resid 11 through 29 Processing helix chain 't' and resid 33 through 48 Processing helix chain 't' and resid 57 through 72 Processing helix chain 't' and resid 92 through 95 removed outlier: 4.336A pdb=" N CYS t 95 " --> pdb=" O ARG t 92 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 92 through 95' Processing helix chain 't' and resid 100 through 105 removed outlier: 3.550A pdb=" N LEU t 103 " --> pdb=" O GLU t 100 " (cutoff:3.500A) removed outlier: 3.582A 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: 4.160A pdb=" N GLN t 123 " --> pdb=" O ALA t 119 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP t 124 " --> pdb=" O LYS t 120 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU t 133 " --> pdb=" O ARG t 129 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ARG t 134 " --> pdb=" O GLU t 130 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU t 141 " --> pdb=" O LYS t 137 " (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 98 through 121 Processing helix chain 'v' and resid 134 through 138 Processing helix chain 'w' and resid 51 through 66 Processing helix chain 'w' and resid 69 through 78 Processing helix chain 'w' and resid 83 through 100 removed outlier: 4.161A pdb=" N GLN w 86 " --> pdb=" O TYR w 83 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLU w 87 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU w 92 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL w 97 " --> pdb=" O GLU w 94 " (cutoff:3.500A) Processing helix chain 'w' and resid 115 through 117 No H-bonds generated for 'chain 'w' and resid 115 through 117' Processing helix chain 'x' and resid 14 through 45 Processing helix chain 'y' and resid 11 through 14 removed outlier: 3.690A pdb=" N VAL y 14 " --> pdb=" O TRP y 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 11 through 14' Processing helix chain 'y' and resid 16 through 33 Processing helix chain 'z' and resid 2 through 29 removed outlier: 3.562A pdb=" N VAL z 5 " --> pdb=" O TRP z 2 " (cutoff:3.500A) Proline residue: z 7 - end of helix removed outlier: 4.969A pdb=" N ILE z 18 " --> pdb=" O CYS z 15 " (cutoff:3.500A) Proline residue: z 19 - end of helix removed outlier: 3.528A pdb=" N ARG z 28 " --> pdb=" O ARG z 25 " (cutoff:3.500A) Processing helix chain 'z' and resid 42 through 54 Processing sheet with id= A, first strand: chain '1' and resid 219 through 224 removed outlier: 3.526A pdb=" N THR 1 221 " --> pdb=" O TYR 1 92 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ALA 1 133 " --> pdb=" O LEU 1 93 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL 1 95 " --> pdb=" O ALA 1 133 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR 1 135 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA 1 97 " --> pdb=" O TYR 1 135 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR 1 137 " --> pdb=" O ALA 1 97 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP 1 174 " --> pdb=" O ALA 1 134 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE 1 136 " --> pdb=" O ASP 1 174 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE 1 176 " --> pdb=" O ILE 1 136 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE 1 138 " --> pdb=" O PHE 1 176 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL 1 178 " --> pdb=" O ILE 1 138 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 266 through 271 Processing sheet with id= C, first strand: chain '2' and resid 98 through 103 Processing sheet with id= D, first strand: chain '2' and resid 154 through 156 removed outlier: 3.509A pdb=" N ASN 2 159 " --> pdb=" O ILE 2 156 " (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 removed outlier: 3.603A pdb=" N ARG 3 249 " --> pdb=" O SER 3 241 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 282 through 285 Processing sheet with id= J, first strand: chain '3' and resid 343 through 345 removed outlier: 8.530A pdb=" N CYS 3 344 " --> pdb=" O VAL 3 315 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA 3 317 " --> pdb=" O CYS 3 344 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET 3 521 " --> pdb=" O ALA 3 316 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE 3 318 " --> pdb=" O MET 3 521 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE 3 523 " --> pdb=" O ILE 3 318 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE 3 542 " --> pdb=" O LEU 3 522 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU 3 524 " --> pdb=" O PHE 3 542 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL 3 544 " --> pdb=" O LEU 3 524 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL 3 559 " --> pdb=" O TYR 3 545 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY 3 547 " --> pdb=" O VAL 3 559 " (cutoff:3.500A) removed outlier: 6.112A 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: 8.365A pdb=" N ASN 3 491 " --> pdb=" O PRO 3 449 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL 3 451 " --> pdb=" O ASN 3 491 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU 3 493 " --> pdb=" O VAL 3 451 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU 3 453 " --> pdb=" O LEU 3 493 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL 3 376 " --> pdb=" O MET 3 450 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL 3 452 " --> pdb=" O VAL 3 376 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU 3 378 " --> pdb=" O VAL 3 452 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLY 3 454 " --> pdb=" O LEU 3 378 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL 3 380 " --> pdb=" O GLY 3 454 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS 3 405 " --> pdb=" O VAL 3 377 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU 3 379 " --> pdb=" O LYS 3 405 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA 3 407 " --> pdb=" O LEU 3 379 " (cutoff:3.500A) removed outlier: 6.266A 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 571 through 574 removed outlier: 3.517A pdb=" N ALA 3 571 " --> pdb=" O THR 3 583 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '4' and resid 47 through 51 removed outlier: 6.458A pdb=" N SER 4 69 " --> pdb=" O VAL 4 73 " (cutoff:3.500A) removed outlier: 6.583A 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 removed outlier: 3.748A pdb=" N GLY 4 361 " --> pdb=" O SER 4 380 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG 4 388 " --> pdb=" O VAL 4 379 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '5' and resid 74 through 79 removed outlier: 6.759A pdb=" N ASN 5 95 " --> pdb=" O ALA 5 76 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU 5 78 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL 5 93 " --> pdb=" O LEU 5 78 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE 5 105 " --> pdb=" O LEU 5 96 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU 5 48 " --> pdb=" O ARG 5 106 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LYS 5 108 " --> pdb=" O LEU 5 48 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE 5 50 " --> pdb=" O LYS 5 108 " (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 47 through 51 removed outlier: 6.591A pdb=" N VAL 6 85 " --> pdb=" O MET 6 48 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N PHE 6 50 " --> pdb=" O VAL 6 85 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE 6 87 " --> pdb=" O PHE 6 50 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR 6 112 " --> pdb=" O MET 6 86 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL 6 88 " --> pdb=" O TYR 6 112 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL 6 114 " --> pdb=" O VAL 6 88 " (cutoff:3.500A) removed outlier: 6.473A 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: 5.741A pdb=" N GLU 9 97 " --> pdb=" O THR 9 106 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR 9 106 " --> pdb=" O GLU 9 97 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 112 through 114 Processing sheet with id= U, first strand: chain 'L' and resid 61 through 67 removed outlier: 6.612A pdb=" N LEU L 78 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= W, first strand: chain 'b' and resid 56 through 59 Processing sheet with id= X, first strand: chain 'c' and resid 102 through 106 removed outlier: 4.520A pdb=" N VAL c 39 " --> pdb=" O GLU c 106 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU c 84 " --> pdb=" O MET c 57 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'd' and resid 227 through 230 removed outlier: 7.688A pdb=" N PHE d 228 " --> pdb=" O ALA d 163 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE d 165 " --> pdb=" O PHE d 228 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N PHE d 230 " --> pdb=" O ILE d 165 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS d 167 " --> pdb=" O PHE d 230 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE d 129 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ILE d 166 " --> pdb=" O PHE d 129 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N HIS d 131 " --> pdb=" O ILE d 166 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER d 133 " --> pdb=" O PRO d 168 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE d 132 " --> pdb=" O ASN d 93 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL d 90 " --> pdb=" O VAL d 20 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLN d 44 " --> pdb=" O ALA d 21 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL d 23 " --> pdb=" O GLN d 44 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE d 46 " --> pdb=" O VAL d 23 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'e' and resid 51 through 57 removed outlier: 3.724A pdb=" N LEU e 22 " --> pdb=" O ARG e 55 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG e 67 " --> pdb=" O ARG e 16 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE e 18 " --> pdb=" O TRP e 65 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP e 65 " --> pdb=" O ILE e 18 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE e 20 " --> pdb=" O LYS e 63 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS e 63 " --> pdb=" O ILE e 20 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA e 66 " --> pdb=" O LYS e 74 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'i' and resid 60 through 63 removed outlier: 3.708A pdb=" N GLY i 40 " --> pdb=" O TYR i 48 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLU i 50 " --> pdb=" O LEU i 38 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU i 38 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'k' and resid 122 through 125 removed outlier: 6.703A pdb=" N VAL k 168 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASP k 28 " --> pdb=" O VAL k 168 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE k 170 " --> pdb=" O ASP k 28 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU k 219 " --> pdb=" O VAL k 169 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N TYR k 171 " --> pdb=" O GLU k 219 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU k 221 " --> pdb=" O TYR k 171 " (cutoff:3.500A) 2744 hydrogen bonds defined for protein. 7740 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: 22.74 Time building geometry restraints manager: 22.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.43: 28275 1.43 - 1.66: 39883 1.66 - 1.89: 758 1.89 - 2.13: 0 2.13 - 2.36: 80 Bond restraints: 68996 Sorted by residual: bond pdb=" O2B NDP d 401 " pdb=" P2B NDP d 401 " ideal model delta sigma weight residual 1.833 1.591 0.242 3.80e-02 6.93e+02 4.06e+01 bond pdb=" C16 ZMP g 201 " pdb=" N2 ZMP g 201 " ideal model delta sigma weight residual 1.452 1.335 0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" OB3 CDL z 101 " pdb=" PB2 CDL z 101 " ideal model delta sigma weight residual 1.529 1.472 0.057 1.00e-02 1.00e+04 3.29e+01 bond pdb=" OB3 CDL W 201 " pdb=" PB2 CDL W 201 " ideal model delta sigma weight residual 1.529 1.472 0.057 1.00e-02 1.00e+04 3.23e+01 bond pdb=" OB3 CDL L1003 " pdb=" PB2 CDL L1003 " ideal model delta sigma weight residual 1.529 1.473 0.056 1.00e-02 1.00e+04 3.18e+01 ... (remaining 68991 not shown) Histogram of bond angle deviations from ideal: 61.43 - 76.63: 71 76.63 - 91.82: 9 91.82 - 107.02: 3036 107.02 - 122.21: 79157 122.21 - 137.40: 10959 Bond angle restraints: 93232 Sorted by residual: angle pdb=" S1 FES 3 803 " pdb="FE2 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.36 13.97 1.14e+00 7.69e-01 1.50e+02 angle pdb=" S1 FES 3 803 " pdb="FE1 FES 3 803 " pdb=" S2 FES 3 803 " ideal model delta sigma weight residual 104.33 90.13 14.20 1.20e+00 6.94e-01 1.40e+02 angle pdb=" S1 FES 2 300 " pdb="FE2 FES 2 300 " pdb=" S2 FES 2 300 " ideal model delta sigma weight residual 104.33 91.47 12.86 1.14e+00 7.69e-01 1.27e+02 angle pdb=" S1 FES 2 300 " pdb="FE1 FES 2 300 " pdb=" S2 FES 2 300 " ideal model delta sigma weight residual 104.33 91.07 13.26 1.20e+00 6.94e-01 1.22e+02 angle pdb="FE1 FES 3 803 " pdb=" S2 FES 3 803 " pdb="FE2 FES 3 803 " ideal model delta sigma weight residual 75.66 87.64 -11.98 1.14e+00 7.69e-01 1.10e+02 ... (remaining 93227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.24: 41073 33.24 - 66.48: 820 66.48 - 99.71: 63 99.71 - 132.95: 3 132.95 - 166.19: 5 Dihedral angle restraints: 41964 sinusoidal: 18204 harmonic: 23760 Sorted by residual: 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 -130.86 -49.14 0 5.00e+00 4.00e-02 9.66e+01 dihedral pdb=" CA ASN 3 259 " pdb=" C ASN 3 259 " pdb=" N GLU 3 260 " pdb=" CA GLU 3 260 " ideal model delta harmonic sigma weight residual 180.00 -131.53 -48.47 0 5.00e+00 4.00e-02 9.40e+01 dihedral pdb=" CA VAL A 29 " pdb=" C VAL A 29 " pdb=" N TYR A 30 " pdb=" CA TYR A 30 " ideal model delta harmonic sigma weight residual -180.00 -137.21 -42.79 0 5.00e+00 4.00e-02 7.32e+01 ... (remaining 41961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.225: 10072 4.225 - 8.449: 5 8.449 - 12.674: 0 12.674 - 16.898: 0 16.898 - 21.123: 24 Chirality restraints: 10101 Sorted by residual: chirality pdb="FE4 SF4 3 802 " pdb=" S1 SF4 3 802 " pdb=" S2 SF4 3 802 " pdb=" S3 SF4 3 802 " both_signs ideal model delta sigma weight residual False 10.55 -10.57 21.12 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 10.54 -21.09 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE3 SF4 9 403 " pdb=" S1 SF4 9 403 " pdb=" S2 SF4 9 403 " pdb=" S4 SF4 9 403 " both_signs ideal model delta sigma weight residual False -10.55 10.53 -21.08 2.00e-01 2.50e+01 1.11e+04 ... (remaining 10098 not shown) Planarity restraints: 11630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 9 40 " 0.019 2.00e-02 2.50e+03 2.79e-02 1.56e+01 pdb=" CG TYR 9 40 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR 9 40 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR 9 40 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR 9 40 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR 9 40 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR 9 40 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR 9 40 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 106 " -0.023 2.00e-02 2.50e+03 2.36e-02 1.40e+01 pdb=" CG TRP A 106 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A 106 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 106 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 106 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 106 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 106 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 106 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 106 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP A 106 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 29 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C VAL A 29 " 0.064 2.00e-02 2.50e+03 pdb=" O VAL A 29 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR A 30 " -0.022 2.00e-02 2.50e+03 ... (remaining 11627 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 20434 2.83 - 3.41: 72045 3.41 - 3.98: 134965 3.98 - 4.56: 191244 4.56 - 5.14: 279914 Nonbonded interactions: 698602 Sorted by model distance: nonbonded pdb=" OG SER 5 119 " pdb=" OE2 GLU 5 131 " model vdw 2.249 2.440 nonbonded pdb=" O GLU c 28 " pdb=" OG1 THR c 32 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR s 8 " pdb=" O PRO v 123 " model vdw 2.261 2.440 nonbonded pdb=" O VAL 3 413 " pdb=" OH TYR 3 419 " model vdw 2.262 2.440 nonbonded pdb=" OG SER k 22 " pdb=" O GLY k 119 " model vdw 2.263 2.440 ... (remaining 698597 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) selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 6.730 Check model and map are aligned: 0.730 Set scattering table: 0.470 Process input model: 160.940 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 174.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 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 : 0.008 0.242 68996 Z= 0.522 Angle : 1.010 19.901 93232 Z= 0.539 Chirality : 1.025 21.123 10101 Planarity : 0.008 0.079 11630 Dihedral : 12.655 166.191 26619 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.08 % Allowed : 2.27 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.07), residues: 8036 helix: -2.10 (0.06), residues: 4295 sheet: -2.38 (0.23), residues: 398 loop : -2.28 (0.09), residues: 3343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP 1 371 HIS 0.018 0.002 HIS 4 157 PHE 0.047 0.003 PHE J 17 TYR 0.064 0.003 TYR 9 40 ARG 0.021 0.001 ARG L 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2142 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 2136 time to evaluate : 5.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 251 SER cc_start: 0.8626 (m) cc_final: 0.8326 (p) REVERT: 1 272 MET cc_start: 0.8371 (tpt) cc_final: 0.8164 (tpt) REVERT: 1 327 THR cc_start: 0.8830 (t) cc_final: 0.8341 (p) REVERT: 1 385 ARG cc_start: 0.8369 (ptt90) cc_final: 0.8064 (ptp90) REVERT: 1 425 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8065 (tp30) REVERT: 1 435 GLN cc_start: 0.7982 (pp30) cc_final: 0.6334 (mt0) REVERT: 2 98 TYR cc_start: 0.9061 (m-80) cc_final: 0.8778 (m-80) REVERT: 2 170 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7911 (mt-10) REVERT: 2 174 ASP cc_start: 0.8274 (m-30) cc_final: 0.7894 (m-30) REVERT: 2 204 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8443 (mm-30) REVERT: 3 35 MET cc_start: 0.9178 (tmt) cc_final: 0.8775 (tmm) REVERT: 3 82 ASN cc_start: 0.9035 (t0) cc_final: 0.8750 (m-40) REVERT: 3 131 LEU cc_start: 0.9069 (mt) cc_final: 0.8758 (tt) REVERT: 3 196 SER cc_start: 0.9220 (p) cc_final: 0.8831 (t) REVERT: 3 231 MET cc_start: 0.9317 (mmt) cc_final: 0.9044 (mmm) REVERT: 3 420 ASP cc_start: 0.8384 (m-30) cc_final: 0.8072 (t0) REVERT: 3 585 VAL cc_start: 0.8949 (t) cc_final: 0.8693 (p) REVERT: 3 642 PHE cc_start: 0.7256 (m-80) cc_final: 0.6531 (t80) REVERT: 3 654 GLN cc_start: 0.7382 (tp-100) cc_final: 0.7102 (mp10) REVERT: 4 182 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8480 (tm-30) REVERT: 4 290 ARG cc_start: 0.8532 (mtp180) cc_final: 0.8297 (ttm-80) REVERT: 4 318 MET cc_start: 0.8956 (tpp) cc_final: 0.8751 (tpp) REVERT: 4 407 LYS cc_start: 0.8550 (mtpm) cc_final: 0.8166 (ptmt) REVERT: 5 16 ASP cc_start: 0.7975 (m-30) cc_final: 0.7774 (m-30) REVERT: 5 92 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8772 (mt) REVERT: 5 102 ASN cc_start: 0.9352 (t0) cc_final: 0.9119 (t0) REVERT: 5 108 LYS cc_start: 0.9236 (mtpt) cc_final: 0.9035 (mtpp) REVERT: 5 115 THR cc_start: 0.8984 (m) cc_final: 0.8610 (p) REVERT: 5 125 LYS cc_start: 0.9262 (mmtm) cc_final: 0.8957 (mtpt) REVERT: 5 150 ARG cc_start: 0.8938 (ptp-110) cc_final: 0.8689 (ptp90) REVERT: 6 44 SER cc_start: 0.9016 (t) cc_final: 0.8721 (t) REVERT: 6 81 ARG cc_start: 0.8420 (mmt90) cc_final: 0.8116 (mtp85) REVERT: 6 102 LYS cc_start: 0.8923 (tttt) cc_final: 0.8539 (ttpt) REVERT: 6 174 ARG cc_start: 0.8226 (mtm-85) cc_final: 0.7957 (mtm-85) REVERT: 6 178 ARG cc_start: 0.8792 (mtm-85) cc_final: 0.8569 (mtm110) REVERT: 9 15 LYS cc_start: 0.8394 (tptp) cc_final: 0.7938 (ttpp) REVERT: 9 78 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9238 (pp) REVERT: 9 118 TYR cc_start: 0.9347 (m-80) cc_final: 0.8975 (m-80) REVERT: A 4 MET cc_start: 0.8349 (mtm) cc_final: 0.8021 (tpt) REVERT: A 26 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7319 (mm-40) REVERT: A 58 VAL cc_start: 0.8901 (p) cc_final: 0.8591 (m) REVERT: H 55 LEU cc_start: 0.8917 (mt) cc_final: 0.8642 (mm) REVERT: H 67 SER cc_start: 0.8280 (t) cc_final: 0.8072 (m) REVERT: H 134 ARG cc_start: 0.9125 (mtp85) cc_final: 0.8792 (mtp85) REVERT: H 139 THR cc_start: 0.9116 (m) cc_final: 0.8895 (p) REVERT: J 1 MET cc_start: 0.4776 (tmt) cc_final: 0.3540 (mtp) REVERT: J 31 LEU cc_start: 0.8246 (tm) cc_final: 0.7981 (tp) REVERT: J 65 MET cc_start: 0.9176 (mmm) cc_final: 0.8947 (mmm) REVERT: J 99 MET cc_start: 0.4845 (mmt) cc_final: 0.4462 (tpt) REVERT: J 122 MET cc_start: 0.5022 (mtp) cc_final: 0.4413 (mtp) REVERT: K 6 MET cc_start: 0.8703 (ttp) cc_final: 0.8387 (tpt) REVERT: K 25 HIS cc_start: 0.7368 (m90) cc_final: 0.6978 (m-70) REVERT: L 14 LEU cc_start: 0.7760 (tp) cc_final: 0.7543 (tp) REVERT: L 106 TRP cc_start: 0.8023 (t60) cc_final: 0.7710 (t60) REVERT: L 157 TRP cc_start: 0.8495 (t-100) cc_final: 0.8239 (t-100) REVERT: L 251 THR cc_start: 0.8148 (m) cc_final: 0.7877 (m) REVERT: L 409 LEU cc_start: 0.7100 (tp) cc_final: 0.6794 (tp) REVERT: L 424 THR cc_start: 0.7790 (t) cc_final: 0.7303 (m) REVERT: L 477 ILE cc_start: 0.7831 (mt) cc_final: 0.7561 (pt) REVERT: L 544 MET cc_start: 0.4937 (tmm) cc_final: 0.4249 (mmp) REVERT: L 573 MET cc_start: 0.2043 (mmp) cc_final: 0.0551 (mpp) REVERT: M 47 ASP cc_start: 0.8204 (p0) cc_final: 0.7893 (p0) REVERT: M 190 TRP cc_start: 0.7734 (m100) cc_final: 0.7393 (m100) REVERT: M 195 MET cc_start: 0.8406 (tpt) cc_final: 0.8078 (tpp) REVERT: M 441 MET cc_start: 0.7240 (tpp) cc_final: 0.6757 (tpp) REVERT: N 11 MET cc_start: 0.7416 (mmp) cc_final: 0.7014 (mtt) REVERT: N 46 LYS cc_start: 0.9066 (ttmt) cc_final: 0.8612 (tttm) REVERT: N 167 TRP cc_start: 0.8191 (m-90) cc_final: 0.7866 (m100) REVERT: N 171 ASN cc_start: 0.8006 (t0) cc_final: 0.7662 (t0) REVERT: N 200 MET cc_start: 0.8641 (mmt) cc_final: 0.8428 (mmt) REVERT: N 268 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8416 (tp-100) REVERT: N 347 GLU cc_start: 0.6543 (mm-30) cc_final: 0.5862 (mm-30) REVERT: X 20 LYS cc_start: 0.6234 (mtmt) cc_final: 0.5874 (mmtt) REVERT: X 47 GLN cc_start: 0.7041 (tm-30) cc_final: 0.6828 (tp40) REVERT: X 71 MET cc_start: 0.3715 (mmt) cc_final: 0.3000 (pmm) REVERT: Y 35 CYS cc_start: 0.8745 (m) cc_final: 0.8446 (m) REVERT: Y 65 CYS cc_start: 0.8229 (t) cc_final: 0.7808 (t) REVERT: Y 103 GLN cc_start: 0.8520 (tt0) cc_final: 0.8242 (tt0) REVERT: Y 148 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8099 (pm20) REVERT: Z 74 THR cc_start: 0.7539 (p) cc_final: 0.7306 (p) REVERT: Z 110 LYS cc_start: 0.9090 (mtmt) cc_final: 0.8771 (mttm) REVERT: a 34 ASP cc_start: 0.6564 (t70) cc_final: 0.5886 (p0) REVERT: a 57 ASP cc_start: 0.8223 (t0) cc_final: 0.7944 (m-30) REVERT: a 61 PHE cc_start: 0.8494 (m-80) cc_final: 0.8177 (m-80) REVERT: a 71 GLU cc_start: 0.8796 (tt0) cc_final: 0.8145 (mp0) REVERT: b 21 GLU cc_start: 0.8048 (pm20) cc_final: 0.7474 (tt0) REVERT: b 37 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8158 (mm-30) REVERT: b 78 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6858 (pm20) REVERT: c 31 LYS cc_start: 0.8813 (mttt) cc_final: 0.8435 (tptp) REVERT: c 62 ARG cc_start: 0.8571 (mmt90) cc_final: 0.8333 (ttm170) REVERT: c 80 SER cc_start: 0.9117 (p) cc_final: 0.8835 (t) REVERT: c 85 THR cc_start: 0.9332 (m) cc_final: 0.9107 (t) REVERT: d 78 LYS cc_start: 0.8680 (mttm) cc_final: 0.8347 (mtmm) REVERT: d 291 ASP cc_start: 0.7990 (m-30) cc_final: 0.7739 (m-30) REVERT: e 25 ARG cc_start: 0.8518 (mmt-90) cc_final: 0.7848 (mtm180) REVERT: e 26 SER cc_start: 0.8434 (m) cc_final: 0.8033 (t) REVERT: e 34 ASP cc_start: 0.8764 (m-30) cc_final: 0.8553 (m-30) REVERT: e 41 VAL cc_start: 0.8452 (t) cc_final: 0.8214 (m) REVERT: e 47 ASN cc_start: 0.8764 (m110) cc_final: 0.8444 (m110) REVERT: e 84 ASP cc_start: 0.7478 (m-30) cc_final: 0.6941 (t0) REVERT: f 7 THR cc_start: 0.8351 (t) cc_final: 0.8033 (m) REVERT: f 8 THR cc_start: 0.8424 (p) cc_final: 0.8189 (t) REVERT: f 84 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8469 (mt-10) REVERT: g 35 TYR cc_start: 0.9269 (t80) cc_final: 0.9038 (t80) REVERT: g 41 GLU cc_start: 0.8929 (tp30) cc_final: 0.8654 (tp30) REVERT: g 63 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7638 (ttt90) REVERT: g 79 ASP cc_start: 0.8123 (m-30) cc_final: 0.7791 (m-30) REVERT: g 93 ILE cc_start: 0.9202 (mt) cc_final: 0.8965 (pt) REVERT: h 61 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8322 (mt-10) REVERT: i 21 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7500 (mpt180) REVERT: i 53 LYS cc_start: 0.8956 (mmtm) cc_final: 0.8524 (mtmm) REVERT: i 82 VAL cc_start: 0.9456 (t) cc_final: 0.9198 (m) REVERT: i 128 SER cc_start: 0.9330 (t) cc_final: 0.9103 (p) REVERT: i 141 SER cc_start: 0.8973 (p) cc_final: 0.8727 (m) REVERT: j 65 ILE cc_start: 0.8454 (pp) cc_final: 0.8176 (pt) REVERT: j 69 LYS cc_start: 0.7062 (mtmp) cc_final: 0.6715 (mtpp) REVERT: j 74 GLN cc_start: 0.8111 (tp40) cc_final: 0.7460 (tp40) REVERT: j 75 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7912 (tp30) REVERT: j 82 ASP cc_start: 0.7884 (m-30) cc_final: 0.7507 (t0) REVERT: k 112 LEU cc_start: 0.8546 (mt) cc_final: 0.8282 (mt) REVERT: k 129 TYR cc_start: 0.6319 (m-80) cc_final: 0.6074 (m-80) REVERT: k 183 ILE cc_start: 0.5260 (mt) cc_final: 0.4981 (mm) REVERT: k 193 LYS cc_start: 0.7021 (mttt) cc_final: 0.6466 (tttp) REVERT: k 204 ASN cc_start: 0.6763 (m-40) cc_final: 0.6295 (m-40) REVERT: k 250 ASP cc_start: 0.5914 (p0) cc_final: 0.5475 (m-30) REVERT: k 252 ASP cc_start: 0.6982 (p0) cc_final: 0.6731 (m-30) REVERT: l 14 ASP cc_start: 0.9086 (p0) cc_final: 0.8859 (p0) REVERT: l 64 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8256 (tp30) REVERT: m 54 VAL cc_start: 0.8999 (t) cc_final: 0.8719 (p) REVERT: n 68 LYS cc_start: 0.6852 (tttt) cc_final: 0.6370 (ttpt) REVERT: o 25 LYS cc_start: 0.8364 (mttt) cc_final: 0.8076 (mtmt) REVERT: o 112 VAL cc_start: 0.8360 (t) cc_final: 0.7966 (t) REVERT: p 110 ARG cc_start: 0.7959 (tmm160) cc_final: 0.7748 (mtt-85) REVERT: q 6 LYS cc_start: 0.8582 (tptm) cc_final: 0.8137 (tttt) REVERT: q 84 GLN cc_start: 0.8318 (tp40) cc_final: 0.7821 (tm-30) REVERT: q 89 ASN cc_start: 0.8983 (m-40) cc_final: 0.8388 (t0) REVERT: q 91 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7439 (tm-30) REVERT: q 95 THR cc_start: 0.8854 (t) cc_final: 0.8550 (p) REVERT: q 107 GLU cc_start: 0.8235 (tt0) cc_final: 0.8012 (tp30) REVERT: q 122 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8067 (mm-30) REVERT: r 69 PHE cc_start: 0.8446 (t80) cc_final: 0.7328 (m-10) REVERT: r 119 MET cc_start: 0.6941 (mtm) cc_final: 0.6613 (pmm) REVERT: s 54 GLN cc_start: 0.6311 (mt0) cc_final: 0.5634 (mm-40) REVERT: s 94 TYR cc_start: 0.7764 (t80) cc_final: 0.7529 (t80) REVERT: s 109 GLN cc_start: 0.7768 (mt0) cc_final: 0.7288 (tm-30) REVERT: t 33 ARG cc_start: 0.6710 (mmm160) cc_final: 0.6499 (mmt-90) REVERT: v 29 MET cc_start: 0.5501 (ptm) cc_final: 0.5179 (tpt) REVERT: v 71 LEU cc_start: 0.7165 (tp) cc_final: 0.6866 (tp) REVERT: v 157 GLU cc_start: 0.5163 (mm-30) cc_final: 0.4527 (tp30) REVERT: w 82 ASP cc_start: 0.8731 (t0) cc_final: 0.8514 (t0) REVERT: z 14 VAL cc_start: 0.8834 (t) cc_final: 0.8532 (m) outliers start: 6 outliers final: 2 residues processed: 2140 average time/residue: 0.7050 time to fit residues: 2468.0069 Evaluate side-chains 1378 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1374 time to evaluate : 5.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 92 ILE Chi-restraints excluded: chain 6 residue 54 CYS Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain k residue 96 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 671 optimal weight: 0.0980 chunk 602 optimal weight: 6.9990 chunk 334 optimal weight: 30.0000 chunk 205 optimal weight: 7.9990 chunk 406 optimal weight: 6.9990 chunk 321 optimal weight: 10.0000 chunk 623 optimal weight: 30.0000 chunk 241 optimal weight: 1.9990 chunk 378 optimal weight: 8.9990 chunk 463 optimal weight: 6.9990 chunk 721 optimal weight: 0.6980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 148 ASN 1 373 ASN 1 437 HIS 3 365 ASN 3 392 ASN ** 3 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 150 HIS 4 252 ASN 5 15 ASN ** 5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 160 HIS 5 200 ASN 9 65 HIS ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN H 235 ASN H 284 GLN K 25 HIS K 83 ASN L 210 ASN L 248 HIS L 270 ASN L 442 ASN M 26 ASN M 43 ASN M 82 HIS M 169 ASN M 279 GLN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 333 ASN M 424 ASN ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 ASN V 7 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 54 GLN Z 55 HIS Z 133 GLN c 44 ASN d 67 GLN d 87 HIS d 89 ASN d 115 GLN f 72 GLN g 50 GLN g 69 ASN g 125 HIS h 8 GLN h 12 ASN ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 180 GLN k 294 GLN ** k 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 GLN l 97 HIS m 61 ASN o 59 HIS p 32 GLN p 116 GLN q 53 ASN ** r 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 11 HIS t 13 GLN t 17 GLN ** t 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 140 GLN v 87 ASN w 57 ASN w 103 HIS y 13 HIS Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.266 68996 Z= 0.540 Angle : 1.590 51.175 93232 Z= 1.025 Chirality : 0.305 6.410 10101 Planarity : 0.005 0.058 11630 Dihedral : 13.226 162.360 10501 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.45 % Favored : 96.54 % Rotamer: Outliers : 1.87 % Allowed : 9.14 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.09), residues: 8036 helix: -0.48 (0.07), residues: 4267 sheet: -1.96 (0.23), residues: 411 loop : -1.72 (0.10), residues: 3358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 106 HIS 0.008 0.001 HIS r 82 PHE 0.031 0.002 PHE N 292 TYR 0.033 0.002 TYR M 406 ARG 0.008 0.001 ARG p 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1628 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1495 time to evaluate : 5.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 337 MET cc_start: 0.8699 (mtm) cc_final: 0.8474 (mtt) REVERT: 1 357 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8101 (mm-30) REVERT: 1 376 MET cc_start: 0.8853 (mmt) cc_final: 0.8633 (mmt) REVERT: 1 385 ARG cc_start: 0.8435 (ptt90) cc_final: 0.8123 (ptp90) REVERT: 1 432 ARG cc_start: 0.7890 (ptt-90) cc_final: 0.7392 (tmm-80) REVERT: 2 98 TYR cc_start: 0.8871 (m-80) cc_final: 0.8419 (m-80) REVERT: 2 153 MET cc_start: 0.8250 (ppp) cc_final: 0.8019 (ppp) REVERT: 2 160 TYR cc_start: 0.8647 (m-80) cc_final: 0.8419 (m-80) REVERT: 2 170 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7677 (mt-10) REVERT: 2 174 ASP cc_start: 0.8238 (m-30) cc_final: 0.7867 (m-30) REVERT: 2 204 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8376 (mt-10) REVERT: 3 82 ASN cc_start: 0.9019 (t0) cc_final: 0.8643 (m-40) REVERT: 3 131 LEU cc_start: 0.9093 (mt) cc_final: 0.8782 (tt) REVERT: 3 196 SER cc_start: 0.9210 (p) cc_final: 0.8789 (t) REVERT: 3 420 ASP cc_start: 0.8302 (m-30) cc_final: 0.8003 (t0) REVERT: 3 537 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8722 (mm) REVERT: 3 539 LYS cc_start: 0.8177 (tptt) cc_final: 0.7291 (ptpt) REVERT: 3 654 GLN cc_start: 0.7386 (tp-100) cc_final: 0.7107 (mp10) REVERT: 4 182 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8431 (tm-30) REVERT: 4 290 ARG cc_start: 0.8496 (mtp180) cc_final: 0.8292 (ttm-80) REVERT: 4 403 ASP cc_start: 0.8347 (t70) cc_final: 0.8036 (m-30) REVERT: 4 407 LYS cc_start: 0.8475 (mtpm) cc_final: 0.8079 (ptmt) REVERT: 5 108 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8903 (mtpp) REVERT: 5 125 LYS cc_start: 0.9233 (mmtm) cc_final: 0.8888 (mtpt) REVERT: 6 44 SER cc_start: 0.8900 (t) cc_final: 0.8669 (t) REVERT: 6 81 ARG cc_start: 0.8360 (mmt90) cc_final: 0.8107 (mtp85) REVERT: 6 102 LYS cc_start: 0.8922 (tttt) cc_final: 0.8576 (ttpt) REVERT: 6 174 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7931 (mtm-85) REVERT: 6 178 ARG cc_start: 0.8781 (mtm-85) cc_final: 0.8529 (mtm110) REVERT: 9 15 LYS cc_start: 0.8510 (tptp) cc_final: 0.7963 (ttpp) REVERT: A 4 MET cc_start: 0.8393 (mtm) cc_final: 0.8076 (tpt) REVERT: A 26 GLN cc_start: 0.7502 (mm-40) cc_final: 0.7226 (mm-40) REVERT: A 58 VAL cc_start: 0.8752 (p) cc_final: 0.8410 (m) REVERT: H 139 THR cc_start: 0.9050 (m) cc_final: 0.8816 (p) REVERT: J 1 MET cc_start: 0.4558 (tmt) cc_final: 0.3287 (mtp) REVERT: K 6 MET cc_start: 0.8762 (ttp) cc_final: 0.8450 (tpt) REVERT: L 48 MET cc_start: 0.6992 (tpt) cc_final: 0.6272 (ttp) REVERT: L 145 GLU cc_start: 0.8215 (mm-30) cc_final: 0.8005 (mm-30) REVERT: L 237 MET cc_start: 0.8755 (mmm) cc_final: 0.8547 (mmm) REVERT: L 370 THR cc_start: 0.8532 (m) cc_final: 0.8331 (p) REVERT: L 413 LEU cc_start: 0.7274 (mm) cc_final: 0.6406 (tt) REVERT: L 477 ILE cc_start: 0.7915 (mt) cc_final: 0.7576 (pt) REVERT: L 544 MET cc_start: 0.5148 (tmm) cc_final: 0.4341 (mmp) REVERT: L 573 MET cc_start: 0.2212 (mmp) cc_final: 0.1466 (tpp) REVERT: N 11 MET cc_start: 0.7276 (mmp) cc_final: 0.6985 (mtt) REVERT: N 46 LYS cc_start: 0.9007 (ttmt) cc_final: 0.8647 (tttm) REVERT: N 167 TRP cc_start: 0.8282 (m-90) cc_final: 0.7978 (m100) REVERT: N 171 ASN cc_start: 0.7947 (t0) cc_final: 0.7635 (t0) REVERT: N 265 MET cc_start: 0.9112 (mmm) cc_final: 0.8850 (mmt) REVERT: N 268 GLN cc_start: 0.9067 (tm-30) cc_final: 0.8516 (tm-30) REVERT: N 323 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7267 (mmp) REVERT: N 347 GLU cc_start: 0.6654 (mm-30) cc_final: 0.5977 (mm-30) REVERT: W 49 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: W 107 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8144 (tt0) REVERT: X 20 LYS cc_start: 0.6050 (mtmt) cc_final: 0.5670 (mmtp) REVERT: X 71 MET cc_start: 0.3656 (mmt) cc_final: 0.2930 (pmm) REVERT: Y 47 TRP cc_start: 0.8187 (OUTLIER) cc_final: 0.7285 (m-90) REVERT: Y 109 CYS cc_start: 0.9144 (t) cc_final: 0.8777 (t) REVERT: Y 148 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8052 (pm20) REVERT: Z 110 LYS cc_start: 0.9022 (mtmt) cc_final: 0.8806 (mttp) REVERT: a 34 ASP cc_start: 0.6448 (t70) cc_final: 0.5825 (p0) REVERT: a 57 ASP cc_start: 0.8479 (t0) cc_final: 0.8131 (m-30) REVERT: a 71 GLU cc_start: 0.8819 (tt0) cc_final: 0.8165 (mp0) REVERT: b 21 GLU cc_start: 0.8072 (pm20) cc_final: 0.7492 (tt0) REVERT: b 37 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8161 (mm-30) REVERT: b 78 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6833 (pm20) REVERT: c 31 LYS cc_start: 0.8825 (mttt) cc_final: 0.8428 (tptp) REVERT: c 62 ARG cc_start: 0.8612 (mmt90) cc_final: 0.8313 (ttm170) REVERT: d 78 LYS cc_start: 0.8621 (mttm) cc_final: 0.8322 (mtmm) REVERT: d 251 ARG cc_start: 0.4664 (mmm160) cc_final: 0.4300 (ttm110) REVERT: e 25 ARG cc_start: 0.8255 (mmt-90) cc_final: 0.7841 (mtm180) REVERT: e 26 SER cc_start: 0.8191 (m) cc_final: 0.7986 (t) REVERT: e 34 ASP cc_start: 0.8692 (m-30) cc_final: 0.8222 (m-30) REVERT: e 37 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8190 (mp0) REVERT: e 84 ASP cc_start: 0.7323 (m-30) cc_final: 0.7109 (t0) REVERT: f 7 THR cc_start: 0.8192 (t) cc_final: 0.7924 (m) REVERT: f 8 THR cc_start: 0.8433 (p) cc_final: 0.8231 (t) REVERT: g 35 TYR cc_start: 0.9267 (t80) cc_final: 0.8938 (t80) REVERT: g 41 GLU cc_start: 0.8929 (tp30) cc_final: 0.8673 (tp30) REVERT: g 63 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7636 (ttm170) REVERT: g 79 ASP cc_start: 0.8157 (m-30) cc_final: 0.7852 (m-30) REVERT: g 93 ILE cc_start: 0.9192 (mt) cc_final: 0.8895 (pt) REVERT: i 21 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7465 (mpt180) REVERT: i 53 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8407 (mttm) REVERT: i 82 VAL cc_start: 0.9473 (t) cc_final: 0.9265 (m) REVERT: i 128 SER cc_start: 0.9335 (t) cc_final: 0.9046 (p) REVERT: i 131 ARG cc_start: 0.8500 (mpp80) cc_final: 0.8214 (mtt-85) REVERT: i 141 SER cc_start: 0.8936 (p) cc_final: 0.8674 (m) REVERT: j 74 GLN cc_start: 0.7964 (tp40) cc_final: 0.7351 (tp40) REVERT: j 75 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7894 (tp30) REVERT: j 82 ASP cc_start: 0.7853 (m-30) cc_final: 0.7463 (t0) REVERT: k 96 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6733 (tp) REVERT: k 129 TYR cc_start: 0.6367 (m-80) cc_final: 0.6022 (m-80) REVERT: k 183 ILE cc_start: 0.5369 (mt) cc_final: 0.5027 (mm) REVERT: k 193 LYS cc_start: 0.7010 (mttt) cc_final: 0.6395 (tttp) REVERT: k 200 GLN cc_start: 0.6252 (tp40) cc_final: 0.5881 (tp40) REVERT: k 204 ASN cc_start: 0.6604 (m-40) cc_final: 0.6332 (m-40) REVERT: k 236 GLU cc_start: 0.6344 (mm-30) cc_final: 0.5631 (tp30) REVERT: k 250 ASP cc_start: 0.5939 (p0) cc_final: 0.5471 (m-30) REVERT: k 252 ASP cc_start: 0.6923 (p0) cc_final: 0.6719 (m-30) REVERT: k 294 GLN cc_start: 0.8174 (tp40) cc_final: 0.7084 (pt0) REVERT: l 64 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8385 (tp30) REVERT: m 54 VAL cc_start: 0.9036 (t) cc_final: 0.8824 (p) REVERT: o 25 LYS cc_start: 0.8430 (mttt) cc_final: 0.8098 (mtmt) REVERT: p 119 LYS cc_start: 0.8251 (mmmm) cc_final: 0.7996 (mtpt) REVERT: q 6 LYS cc_start: 0.8428 (tptm) cc_final: 0.7928 (tttt) REVERT: q 7 GLN cc_start: 0.8552 (tt0) cc_final: 0.8149 (tt0) REVERT: q 89 ASN cc_start: 0.8984 (m-40) cc_final: 0.8374 (t0) REVERT: q 107 GLU cc_start: 0.8190 (tt0) cc_final: 0.7953 (tp30) REVERT: r 69 PHE cc_start: 0.8462 (t80) cc_final: 0.7476 (m-10) REVERT: r 119 MET cc_start: 0.6972 (mtm) cc_final: 0.6605 (pmm) REVERT: s 54 GLN cc_start: 0.6161 (mt0) cc_final: 0.5300 (mm-40) REVERT: s 88 TYR cc_start: 0.6699 (t80) cc_final: 0.6450 (t80) REVERT: s 109 GLN cc_start: 0.7672 (mt0) cc_final: 0.7234 (tm-30) REVERT: v 29 MET cc_start: 0.5425 (ptm) cc_final: 0.5220 (tpt) REVERT: w 82 ASP cc_start: 0.8799 (t0) cc_final: 0.8535 (t70) REVERT: w 109 GLU cc_start: 0.7296 (mp0) cc_final: 0.6959 (mm-30) REVERT: y 25 TYR cc_start: 0.7822 (t80) cc_final: 0.7547 (t80) REVERT: y 29 LYS cc_start: 0.8238 (tttp) cc_final: 0.7992 (ttpt) REVERT: z 14 VAL cc_start: 0.8426 (t) cc_final: 0.8090 (m) outliers start: 133 outliers final: 78 residues processed: 1564 average time/residue: 0.6888 time to fit residues: 1820.3912 Evaluate side-chains 1377 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1294 time to evaluate : 5.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 222 VAL Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 171 GLU Chi-restraints excluded: chain 2 residue 192 SER Chi-restraints excluded: chain 2 residue 199 LEU Chi-restraints excluded: chain 3 residue 360 SER Chi-restraints excluded: chain 3 residue 403 ASP Chi-restraints excluded: chain 3 residue 486 ASP Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 609 MET Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 669 LYS Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 414 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 423 SER Chi-restraints excluded: chain L residue 462 LEU Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain L residue 533 MET Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 152 ASP Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 323 MET Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain W residue 119 ASP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 47 TRP Chi-restraints excluded: chain Y residue 156 ASP Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 82 LEU Chi-restraints excluded: chain Z residue 133 GLN Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 158 GLU Chi-restraints excluded: chain e residue 23 CYS Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 136 GLU Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain m residue 64 ASP Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain q residue 143 THR Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain s residue 60 HIS Chi-restraints excluded: chain t residue 10 THR Chi-restraints excluded: chain u residue 34 PHE Chi-restraints excluded: chain v residue 70 ARG Chi-restraints excluded: chain v residue 80 ASP Chi-restraints excluded: chain w residue 44 SER Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 27 ASP Chi-restraints excluded: chain z residue 42 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 401 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 600 optimal weight: 3.9990 chunk 491 optimal weight: 30.0000 chunk 199 optimal weight: 0.2980 chunk 723 optimal weight: 40.0000 chunk 781 optimal weight: 20.0000 chunk 644 optimal weight: 50.0000 chunk 717 optimal weight: 20.0000 chunk 246 optimal weight: 9.9990 chunk 580 optimal weight: 5.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 356 HIS 1 437 HIS 3 36 GLN ** 3 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 15 ASN ** 5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 102 ASN ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 442 ASN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN Z 90 GLN Z 106 GLN c 44 ASN d 89 ASN f 70 GLN f 72 GLN g 69 ASN h 8 GLN i 91 HIS ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 96 HIS m 61 ASN p 32 GLN s 53 GLN ** t 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 17 GLN ** t 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 68996 Z= 0.535 Angle : 1.574 50.619 93232 Z= 1.016 Chirality : 0.311 6.394 10101 Planarity : 0.005 0.054 11630 Dihedral : 12.600 161.253 10496 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.57 % Allowed : 11.00 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: -0.94 (0.09), residues: 8036 helix: 0.15 (0.08), residues: 4251 sheet: -1.64 (0.24), residues: 410 loop : -1.43 (0.10), residues: 3375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 106 HIS 0.007 0.001 HIS 4 157 PHE 0.029 0.002 PHE N 292 TYR 0.029 0.002 TYR 9 118 ARG 0.019 0.001 ARG f 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1557 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1374 time to evaluate : 7.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 272 MET cc_start: 0.8235 (tpt) cc_final: 0.7965 (tpt) REVERT: 1 357 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8344 (mm-30) REVERT: 1 385 ARG cc_start: 0.8459 (ptt90) cc_final: 0.8090 (ptp90) REVERT: 1 393 TRP cc_start: 0.8976 (t-100) cc_final: 0.8588 (t-100) REVERT: 1 432 ARG cc_start: 0.7933 (ptt-90) cc_final: 0.7443 (tmm-80) REVERT: 2 98 TYR cc_start: 0.8872 (m-80) cc_final: 0.8413 (m-80) REVERT: 2 170 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7712 (mt-10) REVERT: 2 174 ASP cc_start: 0.8237 (m-30) cc_final: 0.7907 (m-30) REVERT: 2 204 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8329 (mt-10) REVERT: 3 82 ASN cc_start: 0.9101 (t0) cc_final: 0.8705 (m-40) REVERT: 3 131 LEU cc_start: 0.9111 (mt) cc_final: 0.8700 (tt) REVERT: 3 196 SER cc_start: 0.9218 (p) cc_final: 0.8876 (t) REVERT: 3 257 ASP cc_start: 0.8021 (m-30) cc_final: 0.7117 (t0) REVERT: 3 420 ASP cc_start: 0.8305 (m-30) cc_final: 0.8091 (t0) REVERT: 3 539 LYS cc_start: 0.8142 (tptt) cc_final: 0.7286 (ptpt) REVERT: 3 654 GLN cc_start: 0.7411 (tp-100) cc_final: 0.7176 (mp10) REVERT: 4 182 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8886 (tt0) REVERT: 4 241 ASP cc_start: 0.7514 (m-30) cc_final: 0.6743 (t0) REVERT: 4 290 ARG cc_start: 0.8574 (mtp180) cc_final: 0.8164 (ttm-80) REVERT: 4 326 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8338 (t70) REVERT: 4 403 ASP cc_start: 0.8345 (t70) cc_final: 0.8110 (m-30) REVERT: 4 407 LYS cc_start: 0.8479 (mtpm) cc_final: 0.8103 (ptmt) REVERT: 5 108 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8822 (mtpp) REVERT: 5 125 LYS cc_start: 0.9249 (mmtm) cc_final: 0.8900 (mtpt) REVERT: 6 81 ARG cc_start: 0.8316 (mmt90) cc_final: 0.8030 (mtp85) REVERT: 6 102 LYS cc_start: 0.8961 (tttt) cc_final: 0.8599 (ttpt) REVERT: 6 178 ARG cc_start: 0.8770 (mtm-85) cc_final: 0.8307 (ttp-110) REVERT: 9 15 LYS cc_start: 0.8469 (tptp) cc_final: 0.7934 (ttpp) REVERT: A 4 MET cc_start: 0.8435 (mtm) cc_final: 0.8140 (tpt) REVERT: A 26 GLN cc_start: 0.7389 (mm-40) cc_final: 0.7147 (mm-40) REVERT: A 58 VAL cc_start: 0.8768 (p) cc_final: 0.8439 (m) REVERT: H 139 THR cc_start: 0.9035 (m) cc_final: 0.8737 (p) REVERT: H 289 LEU cc_start: 0.9370 (tp) cc_final: 0.9049 (tp) REVERT: J 1 MET cc_start: 0.4561 (tmt) cc_final: 0.3346 (mtt) REVERT: J 31 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8059 (mp) REVERT: L 312 LEU cc_start: 0.8202 (tp) cc_final: 0.7873 (mp) REVERT: L 389 PHE cc_start: 0.7240 (t80) cc_final: 0.6947 (t80) REVERT: L 413 LEU cc_start: 0.7134 (mm) cc_final: 0.6549 (tp) REVERT: L 477 ILE cc_start: 0.7980 (mt) cc_final: 0.7669 (pt) REVERT: L 544 MET cc_start: 0.5306 (tmm) cc_final: 0.4484 (mmm) REVERT: L 573 MET cc_start: 0.2186 (mmp) cc_final: 0.1017 (tpt) REVERT: M 89 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8714 (tp) REVERT: M 207 MET cc_start: 0.8778 (tpt) cc_final: 0.8541 (tpt) REVERT: M 278 ARG cc_start: 0.7001 (mmm-85) cc_final: 0.6729 (mmm-85) REVERT: N 11 MET cc_start: 0.7317 (mmp) cc_final: 0.6938 (mtm) REVERT: N 46 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8635 (tttm) REVERT: N 167 TRP cc_start: 0.8309 (m-90) cc_final: 0.8003 (m100) REVERT: N 171 ASN cc_start: 0.7834 (t0) cc_final: 0.7606 (t0) REVERT: N 265 MET cc_start: 0.9124 (mmm) cc_final: 0.8920 (mmt) REVERT: N 268 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8551 (tm-30) REVERT: N 347 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6081 (mm-30) REVERT: V 89 TYR cc_start: 0.5775 (m-10) cc_final: 0.5500 (m-10) REVERT: W 49 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: W 107 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8177 (tt0) REVERT: X 20 LYS cc_start: 0.6082 (mtmt) cc_final: 0.5554 (mmtp) REVERT: X 71 MET cc_start: 0.3865 (mmt) cc_final: 0.2976 (pmm) REVERT: Y 47 TRP cc_start: 0.8247 (OUTLIER) cc_final: 0.7105 (m-90) REVERT: Y 72 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8361 (mm110) REVERT: Y 148 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8022 (pm20) REVERT: Z 27 ASN cc_start: 0.5334 (p0) cc_final: 0.5081 (p0) REVERT: Z 90 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: Z 110 LYS cc_start: 0.8967 (mtmt) cc_final: 0.8602 (mttm) REVERT: a 34 ASP cc_start: 0.6465 (t70) cc_final: 0.5821 (p0) REVERT: a 57 ASP cc_start: 0.8433 (t0) cc_final: 0.8107 (m-30) REVERT: a 71 GLU cc_start: 0.8824 (tt0) cc_final: 0.8154 (mp0) REVERT: b 21 GLU cc_start: 0.8065 (pm20) cc_final: 0.7573 (tt0) REVERT: b 37 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8177 (mm-30) REVERT: c 31 LYS cc_start: 0.8839 (mttt) cc_final: 0.8453 (tptp) REVERT: d 78 LYS cc_start: 0.8533 (mttm) cc_final: 0.8230 (mtmm) REVERT: d 251 ARG cc_start: 0.4605 (mmm160) cc_final: 0.4157 (ttm110) REVERT: d 285 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7855 (mt-10) REVERT: e 25 ARG cc_start: 0.8267 (mmt-90) cc_final: 0.7906 (mtm180) REVERT: e 26 SER cc_start: 0.8269 (m) cc_final: 0.8055 (t) REVERT: e 37 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8174 (mp0) REVERT: f 7 THR cc_start: 0.8054 (t) cc_final: 0.7797 (m) REVERT: f 8 THR cc_start: 0.8461 (p) cc_final: 0.8261 (t) REVERT: g 41 GLU cc_start: 0.8931 (tp30) cc_final: 0.8673 (tp30) REVERT: g 63 ARG cc_start: 0.8033 (ttm-80) cc_final: 0.7721 (ttm170) REVERT: g 79 ASP cc_start: 0.8174 (m-30) cc_final: 0.7868 (m-30) REVERT: g 93 ILE cc_start: 0.9199 (mt) cc_final: 0.8905 (pt) REVERT: g 110 GLU cc_start: 0.7522 (tp30) cc_final: 0.6951 (pp20) REVERT: h 61 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8341 (mt-10) REVERT: i 21 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7467 (mpt180) REVERT: i 53 LYS cc_start: 0.9019 (mmtm) cc_final: 0.8663 (mttp) REVERT: i 128 SER cc_start: 0.9336 (t) cc_final: 0.8936 (p) REVERT: i 131 ARG cc_start: 0.8521 (mpp80) cc_final: 0.8229 (mtt-85) REVERT: j 54 MET cc_start: 0.7469 (mmt) cc_final: 0.7056 (mmt) REVERT: j 74 GLN cc_start: 0.8002 (tp40) cc_final: 0.7656 (tp40) REVERT: j 75 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7971 (tp30) REVERT: j 82 ASP cc_start: 0.7805 (m-30) cc_final: 0.7401 (t0) REVERT: k 129 TYR cc_start: 0.6424 (m-80) cc_final: 0.6037 (m-80) REVERT: k 183 ILE cc_start: 0.5367 (mt) cc_final: 0.5042 (mm) REVERT: k 193 LYS cc_start: 0.7005 (mttt) cc_final: 0.6392 (tttp) REVERT: k 200 GLN cc_start: 0.6629 (tp40) cc_final: 0.6169 (tp40) REVERT: k 204 ASN cc_start: 0.6618 (m-40) cc_final: 0.6320 (m-40) REVERT: k 236 GLU cc_start: 0.6412 (mm-30) cc_final: 0.5898 (tp30) REVERT: k 250 ASP cc_start: 0.6038 (p0) cc_final: 0.5522 (m-30) REVERT: k 294 GLN cc_start: 0.8183 (tp40) cc_final: 0.7157 (pt0) REVERT: k 302 ARG cc_start: 0.6237 (mpt180) cc_final: 0.5812 (mpt180) REVERT: k 320 LYS cc_start: 0.5307 (mtmt) cc_final: 0.4738 (mttp) REVERT: l 104 ARG cc_start: 0.7148 (mtp85) cc_final: 0.5914 (mtp85) REVERT: m 54 VAL cc_start: 0.9115 (t) cc_final: 0.8907 (p) REVERT: n 68 LYS cc_start: 0.6983 (tttt) cc_final: 0.6427 (ttpt) REVERT: o 25 LYS cc_start: 0.8394 (mttt) cc_final: 0.8088 (mtmt) REVERT: p 119 LYS cc_start: 0.8274 (mmmm) cc_final: 0.8067 (mtpt) REVERT: q 6 LYS cc_start: 0.8411 (tptm) cc_final: 0.8007 (tttt) REVERT: q 85 MET cc_start: 0.8714 (mtm) cc_final: 0.8507 (mtp) REVERT: q 89 ASN cc_start: 0.8984 (m-40) cc_final: 0.8390 (t0) REVERT: q 107 GLU cc_start: 0.8198 (tt0) cc_final: 0.7953 (tp30) REVERT: r 69 PHE cc_start: 0.8442 (t80) cc_final: 0.7505 (m-10) REVERT: r 119 MET cc_start: 0.6992 (mtm) cc_final: 0.6623 (pmm) REVERT: s 54 GLN cc_start: 0.6080 (mt0) cc_final: 0.5230 (mm-40) REVERT: s 83 GLN cc_start: 0.7709 (tm-30) cc_final: 0.7416 (tm-30) REVERT: s 87 ASP cc_start: 0.7843 (m-30) cc_final: 0.7511 (m-30) REVERT: s 88 TYR cc_start: 0.6779 (t80) cc_final: 0.6520 (t80) REVERT: s 94 TYR cc_start: 0.7722 (t80) cc_final: 0.7391 (t80) REVERT: s 98 MET cc_start: 0.7368 (mmt) cc_final: 0.7082 (mtt) REVERT: s 109 GLN cc_start: 0.7588 (mt0) cc_final: 0.7194 (tm-30) REVERT: v 29 MET cc_start: 0.5465 (ptm) cc_final: 0.5223 (tpt) REVERT: v 70 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7365 (mmt90) REVERT: w 82 ASP cc_start: 0.8820 (t0) cc_final: 0.8532 (t70) REVERT: y 25 TYR cc_start: 0.7819 (t80) cc_final: 0.7605 (t80) REVERT: y 29 LYS cc_start: 0.8239 (tttp) cc_final: 0.8011 (ttpt) outliers start: 183 outliers final: 109 residues processed: 1483 average time/residue: 0.6587 time to fit residues: 1668.9841 Evaluate side-chains 1385 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1269 time to evaluate : 6.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 222 VAL Chi-restraints excluded: chain 1 residue 327 THR Chi-restraints excluded: chain 1 residue 356 HIS Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 171 GLU Chi-restraints excluded: chain 2 residue 199 LEU Chi-restraints excluded: chain 3 residue 403 ASP Chi-restraints excluded: chain 3 residue 486 ASP Chi-restraints excluded: chain 3 residue 587 VAL Chi-restraints excluded: chain 3 residue 609 MET Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 669 LYS Chi-restraints excluded: chain 4 residue 189 MET Chi-restraints excluded: chain 4 residue 222 ILE Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 326 ASP Chi-restraints excluded: chain 4 residue 414 VAL Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 9 residue 16 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 423 SER Chi-restraints excluded: chain L residue 462 LEU Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 256 PHE Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain Y residue 3 ILE Chi-restraints excluded: chain Y residue 47 TRP Chi-restraints excluded: chain Y residue 128 THR Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 156 ASP Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 82 LEU Chi-restraints excluded: chain Z residue 90 GLN Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 35 VAL Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 158 GLU Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain e residue 23 CYS Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 29 GLU Chi-restraints excluded: chain h residue 92 LYS Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 96 ASP Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 136 GLU Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain q residue 143 THR Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain s residue 60 HIS Chi-restraints excluded: chain s residue 84 HIS Chi-restraints excluded: chain t residue 10 THR Chi-restraints excluded: chain u residue 34 PHE Chi-restraints excluded: chain v residue 70 ARG Chi-restraints excluded: chain v residue 128 VAL Chi-restraints excluded: chain w residue 39 GLU Chi-restraints excluded: chain w residue 44 SER Chi-restraints excluded: chain w residue 75 THR Chi-restraints excluded: chain w residue 94 GLU Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain z residue 42 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 714 optimal weight: 5.9990 chunk 543 optimal weight: 20.0000 chunk 375 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 345 optimal weight: 30.0000 chunk 485 optimal weight: 0.4980 chunk 725 optimal weight: 30.0000 chunk 768 optimal weight: 0.4980 chunk 379 optimal weight: 1.9990 chunk 687 optimal weight: 30.0000 chunk 207 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 356 HIS ** 3 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 ASN ** 4 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 15 ASN ** 5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 442 ASN M 103 GLN ** M 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 399 ASN X 33 ASN ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN d 89 ASN ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 72 GLN g 69 ASN ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 309 ASN m 61 ASN p 32 GLN ** t 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 13 GLN ** t 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 68996 Z= 0.513 Angle : 1.561 50.640 93232 Z= 1.011 Chirality : 0.309 6.366 10101 Planarity : 0.004 0.047 11630 Dihedral : 12.108 161.383 10496 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.37 % Allowed : 12.12 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: -0.46 (0.09), residues: 8036 helix: 0.53 (0.08), residues: 4272 sheet: -1.35 (0.24), residues: 433 loop : -1.20 (0.11), residues: 3331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 106 HIS 0.021 0.001 HIS 1 356 PHE 0.028 0.001 PHE N 292 TYR 0.025 0.001 TYR 9 118 ARG 0.013 0.000 ARG f 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1539 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1370 time to evaluate : 5.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 272 MET cc_start: 0.8230 (tpt) cc_final: 0.7951 (tpt) REVERT: 1 385 ARG cc_start: 0.8450 (ptt90) cc_final: 0.8075 (ptp90) REVERT: 1 393 TRP cc_start: 0.8935 (t-100) cc_final: 0.8616 (t-100) REVERT: 1 432 ARG cc_start: 0.7949 (ptt-90) cc_final: 0.7448 (tmm-80) REVERT: 2 170 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7712 (mt-10) REVERT: 2 174 ASP cc_start: 0.8239 (m-30) cc_final: 0.7903 (m-30) REVERT: 2 204 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8183 (mp0) REVERT: 3 82 ASN cc_start: 0.9097 (t0) cc_final: 0.8724 (m-40) REVERT: 3 131 LEU cc_start: 0.9105 (mt) cc_final: 0.8689 (tt) REVERT: 3 196 SER cc_start: 0.9204 (p) cc_final: 0.8815 (t) REVERT: 3 539 LYS cc_start: 0.8057 (tptt) cc_final: 0.7263 (ptpt) REVERT: 4 66 MET cc_start: 0.9173 (mmm) cc_final: 0.8803 (mtp) REVERT: 4 182 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8849 (tt0) REVERT: 4 241 ASP cc_start: 0.7349 (m-30) cc_final: 0.6577 (t0) REVERT: 4 290 ARG cc_start: 0.8520 (mtp180) cc_final: 0.8086 (ttm-80) REVERT: 4 326 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8394 (t70) REVERT: 4 403 ASP cc_start: 0.8285 (t70) cc_final: 0.8028 (m-30) REVERT: 5 108 LYS cc_start: 0.9209 (mtpt) cc_final: 0.8805 (mtpp) REVERT: 5 125 LYS cc_start: 0.9215 (mmtm) cc_final: 0.8896 (mtpt) REVERT: 6 81 ARG cc_start: 0.8248 (mmt90) cc_final: 0.7967 (mtp85) REVERT: 6 102 LYS cc_start: 0.8953 (tttt) cc_final: 0.8585 (ttpt) REVERT: 6 178 ARG cc_start: 0.8733 (mtm-85) cc_final: 0.8218 (ttp-110) REVERT: 9 15 LYS cc_start: 0.8441 (tptp) cc_final: 0.7913 (ttpp) REVERT: A 4 MET cc_start: 0.8409 (mtm) cc_final: 0.8113 (tpt) REVERT: A 58 VAL cc_start: 0.8698 (p) cc_final: 0.8421 (m) REVERT: H 98 MET cc_start: 0.9033 (ptm) cc_final: 0.8811 (ptm) REVERT: H 139 THR cc_start: 0.8936 (m) cc_final: 0.8693 (p) REVERT: J 1 MET cc_start: 0.4486 (tmt) cc_final: 0.3198 (mtp) REVERT: J 31 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8078 (mp) REVERT: K 6 MET cc_start: 0.8691 (ttp) cc_final: 0.8437 (ttm) REVERT: L 28 LYS cc_start: 0.5982 (OUTLIER) cc_final: 0.5380 (mmtt) REVERT: L 261 ILE cc_start: 0.8805 (mt) cc_final: 0.8588 (mp) REVERT: L 312 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7801 (mp) REVERT: L 396 ILE cc_start: 0.6978 (tp) cc_final: 0.6460 (pt) REVERT: L 413 LEU cc_start: 0.7106 (mm) cc_final: 0.6600 (tp) REVERT: L 477 ILE cc_start: 0.8022 (mt) cc_final: 0.7771 (pt) REVERT: L 544 MET cc_start: 0.5290 (tmm) cc_final: 0.4420 (mmm) REVERT: L 573 MET cc_start: 0.2245 (mmp) cc_final: 0.1721 (tpp) REVERT: M 229 MET cc_start: 0.7415 (mtt) cc_final: 0.6929 (mtt) REVERT: M 278 ARG cc_start: 0.6928 (mmm-85) cc_final: 0.6679 (mmm-85) REVERT: N 11 MET cc_start: 0.7282 (mmp) cc_final: 0.6902 (mtm) REVERT: N 46 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8585 (tttm) REVERT: N 167 TRP cc_start: 0.8248 (m-90) cc_final: 0.7981 (m100) REVERT: N 265 MET cc_start: 0.9111 (mmm) cc_final: 0.8702 (mmt) REVERT: N 268 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8358 (tm-30) REVERT: N 347 GLU cc_start: 0.6629 (mm-30) cc_final: 0.6082 (mm-30) REVERT: W 49 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: W 107 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8186 (tt0) REVERT: X 20 LYS cc_start: 0.6179 (mtmt) cc_final: 0.5703 (mmtt) REVERT: X 37 MET cc_start: 0.5362 (mmt) cc_final: 0.5037 (mmt) REVERT: X 71 MET cc_start: 0.3776 (mmt) cc_final: 0.3030 (pmm) REVERT: X 84 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7895 (tttp) REVERT: Y 47 TRP cc_start: 0.8254 (OUTLIER) cc_final: 0.7367 (m-90) REVERT: Y 148 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7969 (pm20) REVERT: Z 27 ASN cc_start: 0.5327 (p0) cc_final: 0.5089 (p0) REVERT: Z 110 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8558 (mttm) REVERT: a 34 ASP cc_start: 0.6400 (t70) cc_final: 0.5774 (p0) REVERT: a 57 ASP cc_start: 0.8408 (t0) cc_final: 0.8099 (m-30) REVERT: a 71 GLU cc_start: 0.8772 (tt0) cc_final: 0.8106 (mp0) REVERT: b 21 GLU cc_start: 0.8117 (pm20) cc_final: 0.7577 (tt0) REVERT: b 37 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8168 (mm-30) REVERT: c 31 LYS cc_start: 0.8808 (mttt) cc_final: 0.8435 (tptp) REVERT: d 78 LYS cc_start: 0.8504 (mttm) cc_final: 0.8199 (mtmm) REVERT: d 251 ARG cc_start: 0.4673 (mmm160) cc_final: 0.4221 (ttm110) REVERT: d 285 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7927 (mt-10) REVERT: e 25 ARG cc_start: 0.8223 (mmt-90) cc_final: 0.7907 (mtm180) REVERT: e 26 SER cc_start: 0.8236 (m) cc_final: 0.8011 (t) REVERT: e 37 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8152 (mt-10) REVERT: f 7 THR cc_start: 0.7998 (t) cc_final: 0.7786 (m) REVERT: f 8 THR cc_start: 0.8489 (p) cc_final: 0.8267 (t) REVERT: g 41 GLU cc_start: 0.8920 (tp30) cc_final: 0.8656 (tp30) REVERT: g 63 ARG cc_start: 0.8002 (ttm-80) cc_final: 0.7726 (ttp-110) REVERT: g 79 ASP cc_start: 0.8150 (m-30) cc_final: 0.7888 (m-30) REVERT: g 93 ILE cc_start: 0.9180 (mt) cc_final: 0.8918 (pt) REVERT: g 110 GLU cc_start: 0.7521 (tp30) cc_final: 0.6984 (pp20) REVERT: h 61 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8357 (mt-10) REVERT: i 21 ARG cc_start: 0.8110 (ttm-80) cc_final: 0.7513 (mpt180) REVERT: i 53 LYS cc_start: 0.9019 (mmtm) cc_final: 0.8707 (mttp) REVERT: i 54 GLN cc_start: 0.8553 (mm-40) cc_final: 0.7989 (mt0) REVERT: i 128 SER cc_start: 0.9348 (t) cc_final: 0.8924 (p) REVERT: i 131 ARG cc_start: 0.8486 (mpp80) cc_final: 0.8209 (mtt-85) REVERT: j 54 MET cc_start: 0.7435 (mmt) cc_final: 0.7083 (mmt) REVERT: j 74 GLN cc_start: 0.8004 (tp40) cc_final: 0.7694 (tp40) REVERT: j 82 ASP cc_start: 0.7771 (m-30) cc_final: 0.7415 (t0) REVERT: k 129 TYR cc_start: 0.6403 (m-80) cc_final: 0.6010 (m-80) REVERT: k 183 ILE cc_start: 0.5381 (mt) cc_final: 0.5016 (mm) REVERT: k 193 LYS cc_start: 0.6903 (mttt) cc_final: 0.6341 (tttp) REVERT: k 200 GLN cc_start: 0.6695 (tp40) cc_final: 0.6361 (tp40) REVERT: k 204 ASN cc_start: 0.6647 (m-40) cc_final: 0.6317 (m-40) REVERT: k 236 GLU cc_start: 0.6422 (mm-30) cc_final: 0.5938 (tp30) REVERT: k 250 ASP cc_start: 0.6109 (p0) cc_final: 0.5565 (m-30) REVERT: k 294 GLN cc_start: 0.8144 (tp40) cc_final: 0.7113 (pt0) REVERT: k 320 LYS cc_start: 0.5195 (mtmt) cc_final: 0.4676 (tptm) REVERT: n 68 LYS cc_start: 0.6921 (tttt) cc_final: 0.6383 (ttpt) REVERT: o 25 LYS cc_start: 0.8372 (mttt) cc_final: 0.8067 (mtmt) REVERT: q 6 LYS cc_start: 0.8391 (tptm) cc_final: 0.7948 (tttt) REVERT: q 89 ASN cc_start: 0.9008 (m-40) cc_final: 0.8488 (t0) REVERT: q 91 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7422 (tm-30) REVERT: q 93 GLU cc_start: 0.8432 (tt0) cc_final: 0.8071 (tm-30) REVERT: q 107 GLU cc_start: 0.8203 (tt0) cc_final: 0.7858 (tp30) REVERT: q 122 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7974 (mm-30) REVERT: q 131 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: r 69 PHE cc_start: 0.8396 (t80) cc_final: 0.7395 (m-80) REVERT: r 119 MET cc_start: 0.7001 (mtm) cc_final: 0.6603 (pmm) REVERT: s 21 MET cc_start: 0.6498 (tmm) cc_final: 0.6152 (tmm) REVERT: s 38 MET cc_start: 0.6412 (mmm) cc_final: 0.6050 (mmm) REVERT: s 54 GLN cc_start: 0.6090 (mt0) cc_final: 0.5280 (mm-40) REVERT: s 94 TYR cc_start: 0.7732 (t80) cc_final: 0.7384 (t80) REVERT: s 98 MET cc_start: 0.7311 (mmt) cc_final: 0.7006 (mtt) REVERT: s 109 GLN cc_start: 0.7598 (mt0) cc_final: 0.7186 (tm-30) REVERT: w 82 ASP cc_start: 0.8758 (t0) cc_final: 0.8448 (t70) REVERT: x 44 ARG cc_start: 0.8525 (ttp80) cc_final: 0.8181 (ttp-170) REVERT: y 25 TYR cc_start: 0.7777 (t80) cc_final: 0.7559 (t80) REVERT: y 29 LYS cc_start: 0.8222 (tttp) cc_final: 0.8015 (ttpt) REVERT: z 14 VAL cc_start: 0.8465 (t) cc_final: 0.8227 (m) outliers start: 169 outliers final: 97 residues processed: 1462 average time/residue: 0.6575 time to fit residues: 1625.0102 Evaluate side-chains 1362 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1257 time to evaluate : 5.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 327 THR Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 360 SER Chi-restraints excluded: chain 3 residue 403 ASP Chi-restraints excluded: chain 3 residue 486 ASP Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 609 MET Chi-restraints excluded: chain 3 residue 651 LEU Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 669 LYS Chi-restraints excluded: chain 4 residue 67 GLU Chi-restraints excluded: chain 4 residue 222 ILE Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 326 ASP Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 9 residue 16 SER Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 57 PHE Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 423 SER Chi-restraints excluded: chain L residue 462 LEU Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain M residue 38 SER Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 256 PHE Chi-restraints excluded: chain M residue 338 HIS Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 119 ASP Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 47 GLN Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain Y residue 47 TRP Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 82 LEU Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain d residue 158 GLU Chi-restraints excluded: chain d residue 170 ASP Chi-restraints excluded: chain e residue 23 CYS Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 29 GLU Chi-restraints excluded: chain h residue 92 LYS Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain k residue 252 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain m residue 64 ASP Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain n residue 61 SER Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain p residue 60 GLU Chi-restraints excluded: chain q residue 131 GLU Chi-restraints excluded: chain q residue 143 THR Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain s residue 60 HIS Chi-restraints excluded: chain t residue 10 THR Chi-restraints excluded: chain t residue 138 GLN Chi-restraints excluded: chain t residue 162 LEU Chi-restraints excluded: chain u residue 34 PHE Chi-restraints excluded: chain v residue 128 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 39 GLU Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain z residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 639 optimal weight: 20.0000 chunk 436 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 572 optimal weight: 5.9990 chunk 317 optimal weight: 10.0000 chunk 655 optimal weight: 20.0000 chunk 531 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 392 optimal weight: 20.0000 chunk 689 optimal weight: 30.0000 chunk 193 optimal weight: 8.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 356 HIS 1 373 ASN 3 237 ASN 3 392 ASN ** 3 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 581 GLN 4 3 GLN ** 4 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 15 ASN ** 5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 156 ASN ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 321 GLN L 348 HIS L 442 ASN L 470 ASN M 138 ASN M 139 GLN M 319 HIS M 399 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 90 GLN ** b 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 89 ASN d 103 ASN ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 72 GLN g 50 GLN g 69 ASN ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 204 ASN l 44 HIS s 53 GLN ** t 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 13 GLN ** t 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 6 HIS ** y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.238 68996 Z= 0.615 Angle : 1.607 50.775 93232 Z= 1.030 Chirality : 0.311 6.394 10101 Planarity : 0.005 0.052 11630 Dihedral : 12.264 159.884 10496 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.34 % Allowed : 12.53 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: -0.50 (0.09), residues: 8036 helix: 0.46 (0.08), residues: 4294 sheet: -1.20 (0.25), residues: 411 loop : -1.20 (0.11), residues: 3331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP t 101 HIS 0.010 0.002 HIS i 59 PHE 0.030 0.002 PHE s 65 TYR 0.027 0.002 TYR 9 118 ARG 0.014 0.001 ARG f 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1530 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1292 time to evaluate : 5.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 385 ARG cc_start: 0.8460 (ptt90) cc_final: 0.8085 (ptp90) REVERT: 1 432 ARG cc_start: 0.8107 (ptt-90) cc_final: 0.7596 (tmm160) REVERT: 2 170 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7916 (mt-10) REVERT: 2 174 ASP cc_start: 0.8266 (m-30) cc_final: 0.8017 (m-30) REVERT: 2 204 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8219 (mp0) REVERT: 3 82 ASN cc_start: 0.9253 (t0) cc_final: 0.8821 (m-40) REVERT: 3 131 LEU cc_start: 0.9111 (mt) cc_final: 0.8705 (tt) REVERT: 3 196 SER cc_start: 0.9226 (p) cc_final: 0.8883 (t) REVERT: 3 257 ASP cc_start: 0.8163 (m-30) cc_final: 0.7289 (t0) REVERT: 4 182 GLU cc_start: 0.9342 (tm-30) cc_final: 0.9037 (tt0) REVERT: 4 241 ASP cc_start: 0.7849 (m-30) cc_final: 0.7636 (m-30) REVERT: 4 326 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8517 (t70) REVERT: 5 108 LYS cc_start: 0.9254 (mtpt) cc_final: 0.8851 (mtmm) REVERT: 5 125 LYS cc_start: 0.9315 (mmtm) cc_final: 0.8940 (mtpt) REVERT: 5 144 ASN cc_start: 0.8630 (t0) cc_final: 0.8352 (t0) REVERT: 6 50 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8223 (m-80) REVERT: 6 102 LYS cc_start: 0.9001 (tttt) cc_final: 0.8600 (ttpt) REVERT: 6 175 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.9009 (mp) REVERT: 6 178 ARG cc_start: 0.8761 (mtm-85) cc_final: 0.8333 (ttp-110) REVERT: 9 15 LYS cc_start: 0.8474 (tptp) cc_final: 0.8004 (ttpp) REVERT: 9 50 TYR cc_start: 0.9168 (t80) cc_final: 0.8925 (t80) REVERT: 9 78 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8983 (pp) REVERT: A 4 MET cc_start: 0.8432 (mtm) cc_final: 0.8094 (tpt) REVERT: A 26 GLN cc_start: 0.7080 (mm-40) cc_final: 0.6820 (mm-40) REVERT: A 33 LYS cc_start: 0.5945 (OUTLIER) cc_final: 0.5553 (mmtp) REVERT: A 58 VAL cc_start: 0.9078 (p) cc_final: 0.8740 (m) REVERT: H 139 THR cc_start: 0.9032 (m) cc_final: 0.8746 (p) REVERT: J 1 MET cc_start: 0.4556 (tmt) cc_final: 0.3269 (mtt) REVERT: J 31 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8179 (mp) REVERT: J 57 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8618 (m-80) REVERT: K 6 MET cc_start: 0.8703 (ttp) cc_final: 0.8439 (ttm) REVERT: L 312 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7880 (mp) REVERT: L 396 ILE cc_start: 0.7026 (tp) cc_final: 0.6527 (pt) REVERT: L 477 ILE cc_start: 0.7923 (mt) cc_final: 0.7664 (pt) REVERT: L 544 MET cc_start: 0.5628 (tmm) cc_final: 0.4633 (mmm) REVERT: L 573 MET cc_start: 0.2581 (mmp) cc_final: 0.0441 (mpp) REVERT: M 207 MET cc_start: 0.8771 (tpt) cc_final: 0.8434 (tpt) REVERT: M 229 MET cc_start: 0.7812 (mtt) cc_final: 0.7420 (mtt) REVERT: M 278 ARG cc_start: 0.7042 (mmm-85) cc_final: 0.6720 (mmm-85) REVERT: N 11 MET cc_start: 0.7371 (mmp) cc_final: 0.6938 (mtm) REVERT: N 45 MET cc_start: 0.8931 (mmm) cc_final: 0.8711 (mtt) REVERT: N 46 LYS cc_start: 0.9106 (ttmt) cc_final: 0.8678 (tttm) REVERT: N 96 MET cc_start: 0.8385 (ttt) cc_final: 0.8104 (mtp) REVERT: N 167 TRP cc_start: 0.8472 (m-90) cc_final: 0.8134 (m100) REVERT: N 268 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8617 (tm-30) REVERT: N 309 ASN cc_start: 0.5822 (t0) cc_final: 0.5390 (t0) REVERT: N 347 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6164 (mm-30) REVERT: X 14 ARG cc_start: 0.6751 (mmm-85) cc_final: 0.5514 (mmm-85) REVERT: X 20 LYS cc_start: 0.6057 (mtmt) cc_final: 0.5662 (mmtt) REVERT: X 33 ASN cc_start: 0.5803 (t0) cc_final: 0.5545 (t0) REVERT: X 37 MET cc_start: 0.5476 (mmt) cc_final: 0.4972 (mmt) REVERT: X 71 MET cc_start: 0.4099 (mmt) cc_final: 0.3460 (pmm) REVERT: X 84 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8028 (tttm) REVERT: Y 47 TRP cc_start: 0.8339 (OUTLIER) cc_final: 0.7609 (m-90) REVERT: Y 148 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8002 (pm20) REVERT: Z 27 ASN cc_start: 0.5657 (p0) cc_final: 0.5409 (p0) REVERT: a 34 ASP cc_start: 0.6583 (t70) cc_final: 0.5888 (p0) REVERT: a 45 ASP cc_start: 0.8990 (t0) cc_final: 0.8754 (t0) REVERT: a 57 ASP cc_start: 0.8444 (t0) cc_final: 0.8125 (m-30) REVERT: a 71 GLU cc_start: 0.8944 (tt0) cc_final: 0.8226 (mp0) REVERT: b 21 GLU cc_start: 0.8052 (pm20) cc_final: 0.7616 (tt0) REVERT: b 37 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8185 (mm-30) REVERT: c 31 LYS cc_start: 0.8871 (mttt) cc_final: 0.8480 (tptp) REVERT: d 78 LYS cc_start: 0.8550 (mttm) cc_final: 0.8215 (mtmm) REVERT: d 119 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8168 (tm-30) REVERT: d 251 ARG cc_start: 0.4772 (mmm160) cc_final: 0.4158 (ttm110) REVERT: d 285 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7970 (mt-10) REVERT: e 25 ARG cc_start: 0.8338 (mmt-90) cc_final: 0.7879 (mtm-85) REVERT: e 37 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8122 (mt-10) REVERT: f 7 THR cc_start: 0.8065 (t) cc_final: 0.7804 (m) REVERT: f 8 THR cc_start: 0.8548 (p) cc_final: 0.8322 (t) REVERT: g 41 GLU cc_start: 0.8898 (tp30) cc_final: 0.8638 (tp30) REVERT: g 50 GLN cc_start: 0.8696 (mt0) cc_final: 0.8473 (mm-40) REVERT: g 63 ARG cc_start: 0.8047 (ttm-80) cc_final: 0.7664 (ttm170) REVERT: g 79 ASP cc_start: 0.8222 (m-30) cc_final: 0.7907 (m-30) REVERT: g 93 ILE cc_start: 0.9163 (mt) cc_final: 0.8899 (pt) REVERT: g 110 GLU cc_start: 0.7570 (tp30) cc_final: 0.7023 (pp20) REVERT: i 21 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7475 (mpt180) REVERT: i 53 LYS cc_start: 0.9064 (mmtm) cc_final: 0.8722 (mttp) REVERT: i 128 SER cc_start: 0.9363 (t) cc_final: 0.8850 (p) REVERT: j 54 MET cc_start: 0.7525 (mmt) cc_final: 0.7172 (mmt) REVERT: j 74 GLN cc_start: 0.7986 (tp40) cc_final: 0.7567 (tp40) REVERT: j 82 ASP cc_start: 0.7815 (m-30) cc_final: 0.7351 (t0) REVERT: k 129 TYR cc_start: 0.6493 (m-80) cc_final: 0.6110 (m-80) REVERT: k 183 ILE cc_start: 0.5301 (mt) cc_final: 0.4948 (mm) REVERT: k 193 LYS cc_start: 0.6991 (mttt) cc_final: 0.6421 (tttp) REVERT: k 236 GLU cc_start: 0.6395 (mm-30) cc_final: 0.6086 (tp30) REVERT: k 294 GLN cc_start: 0.8213 (tp40) cc_final: 0.7208 (pt0) REVERT: l 75 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8916 (tt) REVERT: n 68 LYS cc_start: 0.6962 (tttt) cc_final: 0.6425 (ttpt) REVERT: o 25 LYS cc_start: 0.8428 (mttt) cc_final: 0.8125 (mtmt) REVERT: q 6 LYS cc_start: 0.8619 (tptm) cc_final: 0.8191 (tttt) REVERT: q 89 ASN cc_start: 0.9035 (m-40) cc_final: 0.8424 (t0) REVERT: q 91 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7513 (tm-30) REVERT: q 93 GLU cc_start: 0.8561 (tt0) cc_final: 0.8219 (tm-30) REVERT: q 107 GLU cc_start: 0.8191 (tt0) cc_final: 0.7852 (tp30) REVERT: r 69 PHE cc_start: 0.8412 (t80) cc_final: 0.7483 (m-10) REVERT: r 119 MET cc_start: 0.7021 (mtm) cc_final: 0.6593 (pmm) REVERT: s 38 MET cc_start: 0.6607 (mmm) cc_final: 0.6137 (mmm) REVERT: s 54 GLN cc_start: 0.6222 (mt0) cc_final: 0.5380 (mm-40) REVERT: s 94 TYR cc_start: 0.7794 (t80) cc_final: 0.7545 (t80) REVERT: s 98 MET cc_start: 0.7411 (mmt) cc_final: 0.7047 (mtt) REVERT: s 109 GLN cc_start: 0.7665 (mt0) cc_final: 0.7252 (tm-30) REVERT: w 54 ASP cc_start: 0.7594 (m-30) cc_final: 0.7261 (m-30) REVERT: w 82 ASP cc_start: 0.8816 (t0) cc_final: 0.8508 (t70) outliers start: 238 outliers final: 161 residues processed: 1434 average time/residue: 0.6730 time to fit residues: 1615.9238 Evaluate side-chains 1390 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1218 time to evaluate : 5.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 174 ASP Chi-restraints excluded: chain 1 residue 264 ASN Chi-restraints excluded: chain 1 residue 318 ASP Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 192 SER Chi-restraints excluded: chain 2 residue 199 LEU Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 109 ASP Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 294 THR Chi-restraints excluded: chain 3 residue 360 SER Chi-restraints excluded: chain 3 residue 403 ASP Chi-restraints excluded: chain 3 residue 486 ASP Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 585 VAL Chi-restraints excluded: chain 3 residue 587 VAL Chi-restraints excluded: chain 3 residue 609 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 669 LYS Chi-restraints excluded: chain 4 residue 67 GLU Chi-restraints excluded: chain 4 residue 189 MET Chi-restraints excluded: chain 4 residue 208 MET Chi-restraints excluded: chain 4 residue 217 ASN Chi-restraints excluded: chain 4 residue 222 ILE Chi-restraints excluded: chain 4 residue 230 THR Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 326 ASP Chi-restraints excluded: chain 4 residue 365 THR Chi-restraints excluded: chain 4 residue 414 VAL Chi-restraints excluded: chain 5 residue 174 LEU Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 175 ILE Chi-restraints excluded: chain 9 residue 16 SER Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 57 PHE Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 195 THR Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 423 SER Chi-restraints excluded: chain L residue 462 LEU Chi-restraints excluded: chain L residue 479 GLN Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain L residue 575 THR Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 256 PHE Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 384 SER Chi-restraints excluded: chain M residue 391 ILE Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 248 LEU Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain V residue 87 LEU Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 98 SER Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain X residue 47 GLN Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain Y residue 17 VAL Chi-restraints excluded: chain Y residue 47 TRP Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 128 THR Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 153 VAL Chi-restraints excluded: chain Y residue 170 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain Z residue 161 ARG Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 26 VAL Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 89 ASN Chi-restraints excluded: chain d residue 158 GLU Chi-restraints excluded: chain d residue 290 THR Chi-restraints excluded: chain e residue 23 CYS Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 29 GLU Chi-restraints excluded: chain i residue 26 VAL Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 96 ASP Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 141 SER Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain n residue 61 SER Chi-restraints excluded: chain n residue 63 VAL Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain p residue 49 GLN Chi-restraints excluded: chain p residue 60 GLU Chi-restraints excluded: chain q residue 109 VAL Chi-restraints excluded: chain q residue 131 GLU Chi-restraints excluded: chain q residue 143 THR Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 60 HIS Chi-restraints excluded: chain s residue 84 HIS Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain t residue 10 THR Chi-restraints excluded: chain t residue 36 TYR Chi-restraints excluded: chain t residue 138 GLN Chi-restraints excluded: chain t residue 139 LEU Chi-restraints excluded: chain t residue 162 LEU Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 29 SER Chi-restraints excluded: chain u residue 34 PHE Chi-restraints excluded: chain v residue 128 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 39 GLU Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 27 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 258 optimal weight: 10.0000 chunk 692 optimal weight: 40.0000 chunk 151 optimal weight: 7.9990 chunk 451 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 769 optimal weight: 30.0000 chunk 638 optimal weight: 4.9990 chunk 356 optimal weight: 20.0000 chunk 63 optimal weight: 0.0970 chunk 254 optimal weight: 8.9990 chunk 403 optimal weight: 5.9990 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 356 HIS ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 15 ASN ** 5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 442 ASN L 470 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 89 ASN e 24 GLN g 69 ASN ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 204 ASN m 61 ASN q 84 GLN t 13 GLN ** t 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.239 68996 Z= 0.544 Angle : 1.579 50.727 93232 Z= 1.018 Chirality : 0.310 6.375 10101 Planarity : 0.004 0.053 11630 Dihedral : 12.056 160.323 10496 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.99 % Allowed : 13.49 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 8036 helix: 0.64 (0.08), residues: 4271 sheet: -1.16 (0.26), residues: 406 loop : -1.11 (0.11), residues: 3359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP t 101 HIS 0.006 0.001 HIS t 25 PHE 0.029 0.002 PHE N 292 TYR 0.028 0.002 TYR 9 118 ARG 0.011 0.000 ARG 4 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1486 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1273 time to evaluate : 5.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 272 MET cc_start: 0.8208 (tpt) cc_final: 0.7892 (tpp) REVERT: 1 385 ARG cc_start: 0.8455 (ptt90) cc_final: 0.8076 (ptp90) REVERT: 1 432 ARG cc_start: 0.8104 (ptt-90) cc_final: 0.7598 (tmm160) REVERT: 2 98 TYR cc_start: 0.8927 (m-80) cc_final: 0.8533 (m-80) REVERT: 2 170 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7916 (mt-10) REVERT: 2 174 ASP cc_start: 0.8223 (m-30) cc_final: 0.7965 (m-30) REVERT: 2 204 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8203 (mp0) REVERT: 3 82 ASN cc_start: 0.9247 (t0) cc_final: 0.8827 (m-40) REVERT: 3 131 LEU cc_start: 0.9115 (mt) cc_final: 0.8702 (tt) REVERT: 3 196 SER cc_start: 0.9211 (p) cc_final: 0.8879 (t) REVERT: 3 257 ASP cc_start: 0.8074 (m-30) cc_final: 0.7224 (t0) REVERT: 3 539 LYS cc_start: 0.8275 (tptt) cc_final: 0.7439 (ptpt) REVERT: 4 182 GLU cc_start: 0.9308 (tm-30) cc_final: 0.9003 (tt0) REVERT: 4 326 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8481 (t70) REVERT: 5 108 LYS cc_start: 0.9193 (mtpt) cc_final: 0.8792 (mtmm) REVERT: 5 125 LYS cc_start: 0.9257 (mmtm) cc_final: 0.8889 (mtpt) REVERT: 5 144 ASN cc_start: 0.8648 (t0) cc_final: 0.8355 (t0) REVERT: 6 50 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: 6 102 LYS cc_start: 0.8973 (tttt) cc_final: 0.8569 (ttpt) REVERT: 6 175 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8987 (mp) REVERT: 6 178 ARG cc_start: 0.8741 (mtm-85) cc_final: 0.8329 (ttp-110) REVERT: 9 15 LYS cc_start: 0.8647 (tptp) cc_final: 0.8009 (ttpp) REVERT: 9 78 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8984 (pp) REVERT: A 4 MET cc_start: 0.8386 (mtm) cc_final: 0.8077 (tpt) REVERT: A 33 LYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5556 (mmtp) REVERT: A 58 VAL cc_start: 0.8947 (p) cc_final: 0.8676 (m) REVERT: H 139 THR cc_start: 0.8988 (m) cc_final: 0.8694 (p) REVERT: J 1 MET cc_start: 0.4531 (tmt) cc_final: 0.3195 (mtt) REVERT: J 31 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8156 (mp) REVERT: J 57 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8552 (m-80) REVERT: L 82 MET cc_start: 0.7413 (mmm) cc_final: 0.7171 (mmp) REVERT: L 312 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7905 (mp) REVERT: L 396 ILE cc_start: 0.7001 (tp) cc_final: 0.6480 (pt) REVERT: L 477 ILE cc_start: 0.7934 (mt) cc_final: 0.7635 (pt) REVERT: L 544 MET cc_start: 0.5643 (tmm) cc_final: 0.4560 (mmm) REVERT: L 573 MET cc_start: 0.2615 (mmp) cc_final: 0.0542 (mpp) REVERT: M 190 TRP cc_start: 0.7595 (m100) cc_final: 0.7104 (m100) REVERT: M 278 ARG cc_start: 0.7035 (mmm-85) cc_final: 0.6675 (mmm-85) REVERT: N 11 MET cc_start: 0.7355 (mmp) cc_final: 0.6933 (mtm) REVERT: N 45 MET cc_start: 0.8850 (mmm) cc_final: 0.8603 (mtt) REVERT: N 46 LYS cc_start: 0.9107 (ttmt) cc_final: 0.8652 (tttm) REVERT: N 96 MET cc_start: 0.8327 (ttt) cc_final: 0.8024 (mtp) REVERT: N 167 TRP cc_start: 0.8433 (m-90) cc_final: 0.8080 (m100) REVERT: N 268 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8643 (tm-30) REVERT: N 309 ASN cc_start: 0.5790 (t0) cc_final: 0.5415 (t0) REVERT: X 20 LYS cc_start: 0.5990 (mtmt) cc_final: 0.5618 (mmtt) REVERT: X 33 ASN cc_start: 0.5914 (t0) cc_final: 0.5595 (t0) REVERT: X 37 MET cc_start: 0.5485 (mmt) cc_final: 0.5120 (mmt) REVERT: X 71 MET cc_start: 0.3788 (mmt) cc_final: 0.3351 (pmm) REVERT: Y 43 MET cc_start: 0.8454 (mmm) cc_final: 0.7826 (mmm) REVERT: Y 47 TRP cc_start: 0.8264 (OUTLIER) cc_final: 0.7731 (m-90) REVERT: Y 148 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7986 (pm20) REVERT: Z 27 ASN cc_start: 0.5712 (p0) cc_final: 0.5509 (p0) REVERT: a 34 ASP cc_start: 0.6475 (t70) cc_final: 0.5745 (p0) REVERT: a 57 ASP cc_start: 0.8467 (t0) cc_final: 0.8154 (m-30) REVERT: a 71 GLU cc_start: 0.8875 (tt0) cc_final: 0.8150 (mp0) REVERT: b 21 GLU cc_start: 0.8058 (pm20) cc_final: 0.7638 (tt0) REVERT: b 37 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8168 (mm-30) REVERT: c 31 LYS cc_start: 0.8873 (mttt) cc_final: 0.8476 (tptp) REVERT: c 36 ARG cc_start: 0.8982 (ttt-90) cc_final: 0.8766 (ttt-90) REVERT: d 78 LYS cc_start: 0.8541 (mttm) cc_final: 0.8209 (mtmm) REVERT: d 119 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8135 (tm-30) REVERT: d 285 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7982 (mt-10) REVERT: e 25 ARG cc_start: 0.8327 (mmt-90) cc_final: 0.7894 (mtm180) REVERT: e 37 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8145 (mt-10) REVERT: f 7 THR cc_start: 0.8102 (t) cc_final: 0.7845 (m) REVERT: f 8 THR cc_start: 0.8513 (p) cc_final: 0.8270 (t) REVERT: f 91 ARG cc_start: 0.8903 (mtt90) cc_final: 0.8525 (mtt90) REVERT: g 79 ASP cc_start: 0.8189 (m-30) cc_final: 0.7897 (m-30) REVERT: g 93 ILE cc_start: 0.9223 (mt) cc_final: 0.8963 (pt) REVERT: h 24 GLN cc_start: 0.8251 (pt0) cc_final: 0.7961 (pm20) REVERT: i 21 ARG cc_start: 0.8102 (ttm-80) cc_final: 0.7464 (mpt180) REVERT: i 53 LYS cc_start: 0.9042 (mmtm) cc_final: 0.8708 (mttp) REVERT: i 128 SER cc_start: 0.9348 (t) cc_final: 0.8834 (p) REVERT: j 25 ILE cc_start: 0.6910 (mt) cc_final: 0.6559 (mm) REVERT: j 54 MET cc_start: 0.7516 (mmt) cc_final: 0.7300 (mmt) REVERT: j 74 GLN cc_start: 0.7975 (tp40) cc_final: 0.7464 (tp40) REVERT: j 82 ASP cc_start: 0.7806 (m-30) cc_final: 0.7331 (t0) REVERT: k 48 LEU cc_start: 0.6397 (mt) cc_final: 0.6180 (mt) REVERT: k 129 TYR cc_start: 0.6495 (m-80) cc_final: 0.6157 (m-80) REVERT: k 193 LYS cc_start: 0.6922 (mttt) cc_final: 0.6342 (tttp) REVERT: k 236 GLU cc_start: 0.6409 (mm-30) cc_final: 0.6115 (tp30) REVERT: k 250 ASP cc_start: 0.5951 (p0) cc_final: 0.5439 (m-30) REVERT: k 294 GLN cc_start: 0.8190 (tp40) cc_final: 0.7210 (pt0) REVERT: l 64 GLU cc_start: 0.8842 (tp30) cc_final: 0.8622 (tp30) REVERT: n 68 LYS cc_start: 0.6974 (tttt) cc_final: 0.6441 (ttpt) REVERT: o 25 LYS cc_start: 0.8430 (mttt) cc_final: 0.8135 (mtmt) REVERT: q 6 LYS cc_start: 0.8571 (tptm) cc_final: 0.8187 (tttt) REVERT: q 91 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7437 (tm-30) REVERT: q 93 GLU cc_start: 0.8526 (tt0) cc_final: 0.8136 (tm-30) REVERT: q 107 GLU cc_start: 0.8180 (tt0) cc_final: 0.7853 (tp30) REVERT: r 69 PHE cc_start: 0.8414 (t80) cc_final: 0.7520 (m-10) REVERT: r 119 MET cc_start: 0.6984 (mtm) cc_final: 0.6605 (pmm) REVERT: s 38 MET cc_start: 0.6533 (mmm) cc_final: 0.6068 (mmm) REVERT: s 54 GLN cc_start: 0.6104 (mt0) cc_final: 0.5301 (mm-40) REVERT: s 94 TYR cc_start: 0.7714 (t80) cc_final: 0.7430 (t80) REVERT: s 98 MET cc_start: 0.7315 (mmt) cc_final: 0.6964 (mtt) REVERT: s 109 GLN cc_start: 0.7648 (mt0) cc_final: 0.7230 (tm-30) REVERT: v 33 ASP cc_start: 0.4420 (m-30) cc_final: 0.3117 (t0) REVERT: w 82 ASP cc_start: 0.8784 (t0) cc_final: 0.8500 (t70) outliers start: 213 outliers final: 158 residues processed: 1396 average time/residue: 0.6525 time to fit residues: 1537.7958 Evaluate side-chains 1381 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1214 time to evaluate : 5.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 98 ASP Chi-restraints excluded: chain 1 residue 107 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 318 ASP Chi-restraints excluded: chain 1 residue 356 HIS Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 192 SER Chi-restraints excluded: chain 2 residue 199 LEU Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 109 ASP Chi-restraints excluded: chain 3 residue 294 THR Chi-restraints excluded: chain 3 residue 360 SER Chi-restraints excluded: chain 3 residue 403 ASP Chi-restraints excluded: chain 3 residue 486 ASP Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 585 VAL Chi-restraints excluded: chain 3 residue 587 VAL Chi-restraints excluded: chain 3 residue 609 MET Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 669 LYS Chi-restraints excluded: chain 4 residue 67 GLU Chi-restraints excluded: chain 4 residue 88 GLU Chi-restraints excluded: chain 4 residue 217 ASN Chi-restraints excluded: chain 4 residue 222 ILE Chi-restraints excluded: chain 4 residue 230 THR Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 326 ASP Chi-restraints excluded: chain 4 residue 403 ASP Chi-restraints excluded: chain 4 residue 414 VAL Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 84 ASP Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 175 ILE Chi-restraints excluded: chain 9 residue 16 SER Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 57 PHE Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 315 VAL Chi-restraints excluded: chain L residue 423 SER Chi-restraints excluded: chain L residue 445 GLU Chi-restraints excluded: chain L residue 462 LEU Chi-restraints excluded: chain L residue 479 GLN Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 256 PHE Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 338 HIS Chi-restraints excluded: chain M residue 398 LEU Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain Y residue 47 TRP Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 117 VAL Chi-restraints excluded: chain Y residue 152 GLU Chi-restraints excluded: chain Y residue 156 ASP Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 46 LEU Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 89 ASN Chi-restraints excluded: chain d residue 158 GLU Chi-restraints excluded: chain e residue 23 CYS Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain g residue 23 ASP Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 29 GLU Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain j residue 15 VAL Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain k residue 96 LEU Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain n residue 61 SER Chi-restraints excluded: chain n residue 87 LEU Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 107 LYS Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain p residue 49 GLN Chi-restraints excluded: chain p residue 60 GLU Chi-restraints excluded: chain q residue 131 GLU Chi-restraints excluded: chain q residue 143 THR Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 60 HIS Chi-restraints excluded: chain s residue 84 HIS Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain t residue 10 THR Chi-restraints excluded: chain t residue 36 TYR Chi-restraints excluded: chain t residue 88 THR Chi-restraints excluded: chain t residue 138 GLN Chi-restraints excluded: chain t residue 139 LEU Chi-restraints excluded: chain t residue 162 LEU Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 34 PHE Chi-restraints excluded: chain u residue 43 ASP Chi-restraints excluded: chain v residue 128 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 39 GLU Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 27 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 741 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 438 optimal weight: 7.9990 chunk 561 optimal weight: 20.0000 chunk 435 optimal weight: 50.0000 chunk 647 optimal weight: 40.0000 chunk 429 optimal weight: 7.9990 chunk 766 optimal weight: 2.9990 chunk 479 optimal weight: 9.9990 chunk 467 optimal weight: 0.3980 chunk 353 optimal weight: 4.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN L 200 GLN ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 442 ASN M 180 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 89 ASN g 69 ASN ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 61 ASN p 32 GLN p 116 GLN t 13 GLN ** t 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 50 HIS v 155 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.242 68996 Z= 0.524 Angle : 1.571 50.613 93232 Z= 1.015 Chirality : 0.310 6.360 10101 Planarity : 0.004 0.052 11630 Dihedral : 11.829 160.491 10496 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.83 % Allowed : 13.95 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: -0.10 (0.09), residues: 8036 helix: 0.79 (0.08), residues: 4280 sheet: -1.09 (0.26), residues: 396 loop : -1.00 (0.11), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP t 101 HIS 0.020 0.001 HIS 1 356 PHE 0.029 0.001 PHE N 292 TYR 0.027 0.001 TYR 9 118 ARG 0.011 0.000 ARG 4 305 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1485 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1283 time to evaluate : 5.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 272 MET cc_start: 0.8206 (tpt) cc_final: 0.7880 (tpp) REVERT: 1 357 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8299 (mm-30) REVERT: 1 385 ARG cc_start: 0.8441 (ptt90) cc_final: 0.8054 (ptp90) REVERT: 1 432 ARG cc_start: 0.8130 (ptt-90) cc_final: 0.7742 (ptm-80) REVERT: 2 98 TYR cc_start: 0.8895 (m-80) cc_final: 0.8510 (m-80) REVERT: 2 170 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7919 (mt-10) REVERT: 2 174 ASP cc_start: 0.8207 (m-30) cc_final: 0.7978 (m-30) REVERT: 2 204 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8128 (mp0) REVERT: 3 82 ASN cc_start: 0.9216 (t0) cc_final: 0.8807 (m-40) REVERT: 3 95 GLU cc_start: 0.9219 (tp30) cc_final: 0.8787 (tp30) REVERT: 3 131 LEU cc_start: 0.9107 (mt) cc_final: 0.8677 (tt) REVERT: 3 196 SER cc_start: 0.9198 (p) cc_final: 0.8828 (t) REVERT: 3 257 ASP cc_start: 0.8079 (m-30) cc_final: 0.7224 (t0) REVERT: 3 539 LYS cc_start: 0.8249 (tptt) cc_final: 0.7369 (ptpt) REVERT: 4 74 ARG cc_start: 0.7836 (mmt180) cc_final: 0.7499 (mmt-90) REVERT: 4 75 LYS cc_start: 0.8385 (tttm) cc_final: 0.8039 (mmmm) REVERT: 4 182 GLU cc_start: 0.9293 (tm-30) cc_final: 0.8980 (tt0) REVERT: 4 222 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8724 (mt) REVERT: 4 303 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8456 (mm-30) REVERT: 4 326 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8454 (t70) REVERT: 5 108 LYS cc_start: 0.9184 (mtpt) cc_final: 0.8919 (mtmm) REVERT: 5 125 LYS cc_start: 0.9245 (mmtm) cc_final: 0.8869 (mtpt) REVERT: 5 144 ASN cc_start: 0.8653 (t0) cc_final: 0.8355 (t0) REVERT: 6 50 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8184 (m-80) REVERT: 6 102 LYS cc_start: 0.8936 (tttt) cc_final: 0.8444 (ttpp) REVERT: 6 105 ASP cc_start: 0.9103 (m-30) cc_final: 0.8892 (m-30) REVERT: 6 175 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8999 (mp) REVERT: 6 178 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.8227 (ttp-110) REVERT: 9 15 LYS cc_start: 0.8653 (tptp) cc_final: 0.8010 (ttpp) REVERT: A 4 MET cc_start: 0.8395 (mtm) cc_final: 0.8098 (tpt) REVERT: A 23 TRP cc_start: 0.6136 (m100) cc_final: 0.5574 (m-90) REVERT: A 33 LYS cc_start: 0.5943 (OUTLIER) cc_final: 0.5606 (mmtp) REVERT: A 58 VAL cc_start: 0.8853 (p) cc_final: 0.8600 (m) REVERT: H 139 THR cc_start: 0.8955 (m) cc_final: 0.8661 (p) REVERT: J 1 MET cc_start: 0.4591 (tmt) cc_final: 0.3221 (mtt) REVERT: J 31 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8124 (mp) REVERT: J 57 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.8522 (m-80) REVERT: L 216 LEU cc_start: 0.8275 (mt) cc_final: 0.7820 (mp) REVERT: L 312 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7838 (mp) REVERT: L 396 ILE cc_start: 0.7005 (tp) cc_final: 0.6473 (pt) REVERT: L 544 MET cc_start: 0.5657 (tmm) cc_final: 0.4540 (mmm) REVERT: L 573 MET cc_start: 0.2639 (mmp) cc_final: 0.0569 (mpp) REVERT: M 190 TRP cc_start: 0.7667 (m100) cc_final: 0.7236 (m100) REVERT: M 207 MET cc_start: 0.8672 (tpt) cc_final: 0.8386 (tpt) REVERT: M 271 MET cc_start: 0.8111 (tpt) cc_final: 0.7804 (tpt) REVERT: M 278 ARG cc_start: 0.6994 (mmm-85) cc_final: 0.6586 (mmm-85) REVERT: N 11 MET cc_start: 0.7332 (mmp) cc_final: 0.6917 (mtm) REVERT: N 45 MET cc_start: 0.8846 (mmm) cc_final: 0.8561 (mtt) REVERT: N 46 LYS cc_start: 0.9096 (ttmt) cc_final: 0.8637 (tttm) REVERT: N 96 MET cc_start: 0.8297 (ttt) cc_final: 0.8028 (mtp) REVERT: N 167 TRP cc_start: 0.8404 (m-90) cc_final: 0.8082 (m100) REVERT: N 268 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8612 (tm-30) REVERT: X 20 LYS cc_start: 0.5922 (mtmt) cc_final: 0.5506 (mmtt) REVERT: X 37 MET cc_start: 0.5477 (mmt) cc_final: 0.5120 (mmt) REVERT: X 71 MET cc_start: 0.3775 (mmt) cc_final: 0.3372 (pmm) REVERT: Y 47 TRP cc_start: 0.8205 (OUTLIER) cc_final: 0.7741 (m-90) REVERT: Y 109 CYS cc_start: 0.9170 (t) cc_final: 0.8743 (t) REVERT: Y 148 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7994 (pm20) REVERT: a 34 ASP cc_start: 0.6052 (t70) cc_final: 0.5545 (p0) REVERT: a 45 ASP cc_start: 0.8993 (t70) cc_final: 0.8777 (t0) REVERT: a 57 ASP cc_start: 0.8447 (t0) cc_final: 0.8117 (m-30) REVERT: a 71 GLU cc_start: 0.8833 (tt0) cc_final: 0.8136 (mp0) REVERT: b 21 GLU cc_start: 0.8050 (pm20) cc_final: 0.7642 (tt0) REVERT: b 37 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8160 (mm-30) REVERT: b 80 LYS cc_start: 0.8578 (mtpt) cc_final: 0.8314 (ptpt) REVERT: c 31 LYS cc_start: 0.8855 (mttt) cc_final: 0.8476 (tptp) REVERT: c 36 ARG cc_start: 0.8957 (ttt-90) cc_final: 0.8751 (ttt-90) REVERT: d 78 LYS cc_start: 0.8532 (mttm) cc_final: 0.8191 (mtmm) REVERT: d 119 GLN cc_start: 0.8356 (tm-30) cc_final: 0.8078 (tm-30) REVERT: e 25 ARG cc_start: 0.8309 (mmt-90) cc_final: 0.7867 (mtm180) REVERT: e 37 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8166 (mt-10) REVERT: f 7 THR cc_start: 0.8054 (t) cc_final: 0.7815 (m) REVERT: f 8 THR cc_start: 0.8513 (p) cc_final: 0.8280 (t) REVERT: f 91 ARG cc_start: 0.8892 (mtt90) cc_final: 0.8435 (mtt90) REVERT: g 79 ASP cc_start: 0.8183 (m-30) cc_final: 0.7926 (m-30) REVERT: g 93 ILE cc_start: 0.9143 (mt) cc_final: 0.8729 (pt) REVERT: h 24 GLN cc_start: 0.8236 (pt0) cc_final: 0.7973 (pm20) REVERT: i 21 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7452 (mpt180) REVERT: i 53 LYS cc_start: 0.9006 (mmtm) cc_final: 0.8698 (mttp) REVERT: i 54 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8036 (mt0) REVERT: i 128 SER cc_start: 0.9342 (t) cc_final: 0.8863 (p) REVERT: j 22 TYR cc_start: 0.7701 (t80) cc_final: 0.7499 (t80) REVERT: j 25 ILE cc_start: 0.6762 (mt) cc_final: 0.6465 (mm) REVERT: j 54 MET cc_start: 0.7490 (mmt) cc_final: 0.7254 (mmt) REVERT: j 74 GLN cc_start: 0.7968 (tp40) cc_final: 0.7470 (tp40) REVERT: j 78 ASP cc_start: 0.7247 (m-30) cc_final: 0.6996 (m-30) REVERT: j 82 ASP cc_start: 0.7802 (m-30) cc_final: 0.7371 (t0) REVERT: k 48 LEU cc_start: 0.6364 (mt) cc_final: 0.6140 (mt) REVERT: k 129 TYR cc_start: 0.6520 (m-80) cc_final: 0.6156 (m-80) REVERT: k 193 LYS cc_start: 0.6880 (mttt) cc_final: 0.6335 (tptm) REVERT: k 214 MET cc_start: 0.5922 (mmm) cc_final: 0.5454 (tpp) REVERT: k 236 GLU cc_start: 0.6437 (mm-30) cc_final: 0.6132 (tp30) REVERT: k 250 ASP cc_start: 0.5904 (p0) cc_final: 0.5409 (m-30) REVERT: k 294 GLN cc_start: 0.8163 (tp40) cc_final: 0.7179 (pt0) REVERT: l 58 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: n 68 LYS cc_start: 0.7009 (tttt) cc_final: 0.6469 (ttpt) REVERT: o 25 LYS cc_start: 0.8431 (mttt) cc_final: 0.8144 (mtmt) REVERT: q 6 LYS cc_start: 0.8552 (tptm) cc_final: 0.8087 (tttt) REVERT: q 9 MET cc_start: 0.8782 (mmm) cc_final: 0.8483 (mmm) REVERT: q 91 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7413 (tm-30) REVERT: q 93 GLU cc_start: 0.8494 (tt0) cc_final: 0.8115 (tm-30) REVERT: q 107 GLU cc_start: 0.8242 (tt0) cc_final: 0.7934 (tp30) REVERT: r 69 PHE cc_start: 0.8416 (t80) cc_final: 0.7506 (m-10) REVERT: r 119 MET cc_start: 0.7022 (mtm) cc_final: 0.6618 (pmm) REVERT: s 38 MET cc_start: 0.6442 (mmm) cc_final: 0.6002 (mmm) REVERT: s 45 MET cc_start: 0.6584 (ttp) cc_final: 0.6316 (ttt) REVERT: s 54 GLN cc_start: 0.6077 (mt0) cc_final: 0.5279 (mm-40) REVERT: s 94 TYR cc_start: 0.7635 (t80) cc_final: 0.7400 (t80) REVERT: s 98 MET cc_start: 0.7309 (mmt) cc_final: 0.6942 (mtt) REVERT: s 109 GLN cc_start: 0.7703 (mt0) cc_final: 0.7229 (tm-30) REVERT: v 33 ASP cc_start: 0.4420 (m-30) cc_final: 0.3171 (t0) REVERT: w 82 ASP cc_start: 0.8786 (t0) cc_final: 0.8479 (t70) outliers start: 202 outliers final: 149 residues processed: 1394 average time/residue: 0.6363 time to fit residues: 1512.4487 Evaluate side-chains 1389 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1230 time to evaluate : 5.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 98 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 192 SER Chi-restraints excluded: chain 2 residue 199 LEU Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 109 ASP Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 294 THR Chi-restraints excluded: chain 3 residue 324 ASP Chi-restraints excluded: chain 3 residue 360 SER Chi-restraints excluded: chain 3 residue 403 ASP Chi-restraints excluded: chain 3 residue 486 ASP Chi-restraints excluded: chain 3 residue 517 ASN Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 587 VAL Chi-restraints excluded: chain 3 residue 609 MET Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 669 LYS Chi-restraints excluded: chain 4 residue 67 GLU Chi-restraints excluded: chain 4 residue 88 GLU Chi-restraints excluded: chain 4 residue 222 ILE Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 326 ASP Chi-restraints excluded: chain 4 residue 403 ASP Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 175 ILE Chi-restraints excluded: chain 9 residue 16 SER Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 57 PHE Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 227 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 423 SER Chi-restraints excluded: chain L residue 462 LEU Chi-restraints excluded: chain L residue 479 GLN Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 256 PHE Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 326 LEU Chi-restraints excluded: chain M residue 338 HIS Chi-restraints excluded: chain M residue 398 LEU Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 245 LEU Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain Y residue 47 TRP Chi-restraints excluded: chain Y residue 156 ASP Chi-restraints excluded: chain Y residue 170 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 158 GLU Chi-restraints excluded: chain d residue 290 THR Chi-restraints excluded: chain e residue 23 CYS Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain g residue 23 ASP Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 29 GLU Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain j residue 15 VAL Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain k residue 115 LEU Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain k residue 290 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain m residue 61 ASN Chi-restraints excluded: chain m residue 64 ASP Chi-restraints excluded: chain n residue 30 THR Chi-restraints excluded: chain n residue 61 SER Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 107 LYS Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain p residue 49 GLN Chi-restraints excluded: chain p residue 60 GLU Chi-restraints excluded: chain q residue 131 GLU Chi-restraints excluded: chain q residue 143 THR Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 60 HIS Chi-restraints excluded: chain s residue 84 HIS Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain t residue 10 THR Chi-restraints excluded: chain t residue 36 TYR Chi-restraints excluded: chain t residue 138 GLN Chi-restraints excluded: chain t residue 139 LEU Chi-restraints excluded: chain t residue 162 LEU Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 34 PHE Chi-restraints excluded: chain v residue 85 ILE Chi-restraints excluded: chain v residue 128 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 39 GLU Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain z residue 16 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 474 optimal weight: 20.0000 chunk 305 optimal weight: 0.9990 chunk 457 optimal weight: 8.9990 chunk 230 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 487 optimal weight: 4.9990 chunk 522 optimal weight: 5.9990 chunk 378 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 602 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 37 ASN ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 15 ASN ** 5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN L 199 GLN ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 442 ASN ** L 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 HIS M 180 GLN M 415 GLN N 172 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 89 ASN g 69 ASN ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 61 ASN t 13 GLN ** t 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 68996 Z= 0.523 Angle : 1.572 50.700 93232 Z= 1.015 Chirality : 0.310 6.353 10101 Planarity : 0.004 0.049 11630 Dihedral : 11.648 160.659 10494 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.79 % Allowed : 14.55 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.02 (0.10), residues: 8036 helix: 0.87 (0.08), residues: 4284 sheet: -1.01 (0.27), residues: 390 loop : -0.92 (0.11), residues: 3362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP t 101 HIS 0.005 0.001 HIS M 30 PHE 0.030 0.001 PHE s 65 TYR 0.028 0.001 TYR 9 50 ARG 0.011 0.000 ARG 4 305 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1259 time to evaluate : 5.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 272 MET cc_start: 0.8198 (tpt) cc_final: 0.7873 (tpp) REVERT: 1 357 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8355 (mm-30) REVERT: 1 385 ARG cc_start: 0.8433 (ptt90) cc_final: 0.8041 (ptp90) REVERT: 1 394 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7998 (mt-10) REVERT: 1 432 ARG cc_start: 0.8109 (ptt-90) cc_final: 0.7720 (ttt-90) REVERT: 2 98 TYR cc_start: 0.8879 (m-80) cc_final: 0.8505 (m-80) REVERT: 2 170 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7909 (mt-10) REVERT: 2 174 ASP cc_start: 0.8192 (m-30) cc_final: 0.7980 (m-30) REVERT: 2 204 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8079 (mp0) REVERT: 3 82 ASN cc_start: 0.9214 (t0) cc_final: 0.8807 (m-40) REVERT: 3 95 GLU cc_start: 0.9201 (tp30) cc_final: 0.8776 (tp30) REVERT: 3 131 LEU cc_start: 0.9106 (mt) cc_final: 0.8672 (tt) REVERT: 3 196 SER cc_start: 0.9186 (p) cc_final: 0.8816 (t) REVERT: 3 257 ASP cc_start: 0.8086 (m-30) cc_final: 0.7253 (t0) REVERT: 3 539 LYS cc_start: 0.8222 (tptt) cc_final: 0.7345 (ptpt) REVERT: 4 74 ARG cc_start: 0.7833 (mmt180) cc_final: 0.7593 (mmt180) REVERT: 4 75 LYS cc_start: 0.8373 (tttm) cc_final: 0.8006 (mmmm) REVERT: 4 182 GLU cc_start: 0.9279 (tm-30) cc_final: 0.8982 (tt0) REVERT: 4 326 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8483 (t70) REVERT: 4 352 TYR cc_start: 0.9236 (m-80) cc_final: 0.9008 (m-80) REVERT: 5 108 LYS cc_start: 0.9173 (mtpt) cc_final: 0.8895 (mtmm) REVERT: 5 125 LYS cc_start: 0.9268 (mmtm) cc_final: 0.8875 (mtpt) REVERT: 5 144 ASN cc_start: 0.8692 (t0) cc_final: 0.8399 (t0) REVERT: 6 50 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8124 (m-80) REVERT: 6 102 LYS cc_start: 0.8929 (tttt) cc_final: 0.8453 (ttpp) REVERT: 6 105 ASP cc_start: 0.9106 (m-30) cc_final: 0.8899 (m-30) REVERT: 6 175 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8984 (mp) REVERT: 6 178 ARG cc_start: 0.8693 (mtm-85) cc_final: 0.8229 (ttp-110) REVERT: 9 15 LYS cc_start: 0.8647 (tptp) cc_final: 0.8005 (ttpp) REVERT: 9 78 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.9040 (pp) REVERT: A 4 MET cc_start: 0.8362 (mtm) cc_final: 0.8072 (tpt) REVERT: A 23 TRP cc_start: 0.6170 (m100) cc_final: 0.5588 (m-90) REVERT: A 33 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5668 (mmtp) REVERT: A 58 VAL cc_start: 0.8850 (p) cc_final: 0.8617 (m) REVERT: H 139 THR cc_start: 0.8952 (m) cc_final: 0.8657 (p) REVERT: H 241 LEU cc_start: 0.9293 (tp) cc_final: 0.8754 (mp) REVERT: J 1 MET cc_start: 0.4695 (tmt) cc_final: 0.3210 (mtt) REVERT: J 31 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8130 (mp) REVERT: J 57 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8500 (m-80) REVERT: J 122 MET cc_start: 0.6173 (tpt) cc_final: 0.5001 (ptp) REVERT: L 179 ASP cc_start: 0.8367 (m-30) cc_final: 0.8094 (t0) REVERT: L 312 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7795 (mp) REVERT: L 396 ILE cc_start: 0.6972 (tp) cc_final: 0.6458 (pt) REVERT: L 442 ASN cc_start: 0.6941 (OUTLIER) cc_final: 0.6542 (t0) REVERT: L 544 MET cc_start: 0.5714 (tmm) cc_final: 0.4628 (mmm) REVERT: L 573 MET cc_start: 0.2562 (mmp) cc_final: 0.0503 (mpp) REVERT: M 207 MET cc_start: 0.8678 (tpt) cc_final: 0.8344 (tpt) REVERT: M 278 ARG cc_start: 0.6938 (mmm-85) cc_final: 0.6634 (mmm-85) REVERT: N 11 MET cc_start: 0.7333 (mmp) cc_final: 0.6926 (mtm) REVERT: N 44 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8399 (mtp) REVERT: N 45 MET cc_start: 0.8811 (mmm) cc_final: 0.8505 (mtt) REVERT: N 96 MET cc_start: 0.8289 (ttt) cc_final: 0.8022 (mtp) REVERT: N 167 TRP cc_start: 0.8386 (m-90) cc_final: 0.8089 (m100) REVERT: N 268 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8597 (tm-30) REVERT: N 295 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.7793 (mmt90) REVERT: X 14 ARG cc_start: 0.6863 (mmm-85) cc_final: 0.5880 (mmm-85) REVERT: X 20 LYS cc_start: 0.5827 (mtmt) cc_final: 0.5487 (mmtt) REVERT: X 37 MET cc_start: 0.5418 (mmt) cc_final: 0.5091 (mmt) REVERT: X 71 MET cc_start: 0.3699 (mmt) cc_final: 0.3332 (pmm) REVERT: Y 43 MET cc_start: 0.8403 (mmm) cc_final: 0.7764 (mmm) REVERT: Y 47 TRP cc_start: 0.8160 (OUTLIER) cc_final: 0.7762 (m-90) REVERT: Y 109 CYS cc_start: 0.9170 (t) cc_final: 0.8558 (t) REVERT: Y 148 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7959 (pm20) REVERT: a 34 ASP cc_start: 0.5988 (t70) cc_final: 0.5477 (p0) REVERT: a 45 ASP cc_start: 0.9020 (t70) cc_final: 0.8777 (t0) REVERT: a 57 ASP cc_start: 0.8415 (t0) cc_final: 0.8107 (m-30) REVERT: a 71 GLU cc_start: 0.8839 (tt0) cc_final: 0.8147 (mp0) REVERT: b 21 GLU cc_start: 0.8050 (pm20) cc_final: 0.7652 (tt0) REVERT: b 37 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8096 (mm-30) REVERT: b 80 LYS cc_start: 0.8578 (mtpt) cc_final: 0.8337 (ptpt) REVERT: c 31 LYS cc_start: 0.8881 (mttt) cc_final: 0.8497 (tptp) REVERT: c 36 ARG cc_start: 0.8952 (ttt-90) cc_final: 0.8718 (ttt-90) REVERT: d 78 LYS cc_start: 0.8529 (mttm) cc_final: 0.8186 (mtmm) REVERT: d 119 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8049 (tm-30) REVERT: e 25 ARG cc_start: 0.8258 (mmt-90) cc_final: 0.7838 (mtm180) REVERT: e 37 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8164 (mt-10) REVERT: f 7 THR cc_start: 0.8088 (t) cc_final: 0.7853 (m) REVERT: f 8 THR cc_start: 0.8521 (p) cc_final: 0.8289 (t) REVERT: f 91 ARG cc_start: 0.8886 (mtt90) cc_final: 0.8444 (mtt90) REVERT: g 79 ASP cc_start: 0.8217 (m-30) cc_final: 0.7958 (m-30) REVERT: g 93 ILE cc_start: 0.9156 (mt) cc_final: 0.8803 (pt) REVERT: h 24 GLN cc_start: 0.8181 (pt0) cc_final: 0.7933 (pm20) REVERT: i 21 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7494 (mpt180) REVERT: i 53 LYS cc_start: 0.9015 (mmtm) cc_final: 0.8699 (mttp) REVERT: i 54 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8030 (mt0) REVERT: i 104 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8679 (p) REVERT: i 128 SER cc_start: 0.9349 (t) cc_final: 0.8868 (p) REVERT: j 25 ILE cc_start: 0.6877 (mt) cc_final: 0.6501 (mm) REVERT: j 54 MET cc_start: 0.7496 (mmt) cc_final: 0.7295 (mmt) REVERT: j 74 GLN cc_start: 0.7943 (tp40) cc_final: 0.7442 (tp40) REVERT: j 82 ASP cc_start: 0.7788 (m-30) cc_final: 0.7354 (t0) REVERT: k 193 LYS cc_start: 0.6867 (mttt) cc_final: 0.6274 (tptm) REVERT: k 236 GLU cc_start: 0.6423 (mm-30) cc_final: 0.6130 (tp30) REVERT: k 250 ASP cc_start: 0.5912 (p0) cc_final: 0.5425 (m-30) REVERT: k 294 GLN cc_start: 0.8128 (tp40) cc_final: 0.7166 (pt0) REVERT: l 58 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: l 72 MET cc_start: 0.8297 (mmp) cc_final: 0.7891 (mmt) REVERT: n 68 LYS cc_start: 0.6997 (tttt) cc_final: 0.6467 (ttpt) REVERT: o 25 LYS cc_start: 0.8424 (mttt) cc_final: 0.8127 (mtmt) REVERT: q 6 LYS cc_start: 0.8557 (tptm) cc_final: 0.8115 (tttt) REVERT: q 9 MET cc_start: 0.8767 (mmm) cc_final: 0.8445 (mmm) REVERT: q 91 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7425 (tm-30) REVERT: q 93 GLU cc_start: 0.8476 (tt0) cc_final: 0.8091 (tm-30) REVERT: q 107 GLU cc_start: 0.8245 (tt0) cc_final: 0.7954 (tp30) REVERT: r 69 PHE cc_start: 0.8411 (t80) cc_final: 0.7529 (m-10) REVERT: r 119 MET cc_start: 0.7023 (mtm) cc_final: 0.6581 (pmm) REVERT: s 38 MET cc_start: 0.6412 (mmm) cc_final: 0.6014 (mmm) REVERT: s 45 MET cc_start: 0.6538 (ttp) cc_final: 0.6323 (ttt) REVERT: s 94 TYR cc_start: 0.7580 (t80) cc_final: 0.7364 (t80) REVERT: s 98 MET cc_start: 0.7285 (mmt) cc_final: 0.6952 (mtt) REVERT: s 109 GLN cc_start: 0.7739 (mt0) cc_final: 0.7265 (tm-30) REVERT: t 35 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7155 (ttmm) REVERT: v 33 ASP cc_start: 0.4399 (m-30) cc_final: 0.3113 (t0) REVERT: w 82 ASP cc_start: 0.8779 (t0) cc_final: 0.8458 (t70) outliers start: 199 outliers final: 157 residues processed: 1371 average time/residue: 0.6431 time to fit residues: 1503.2164 Evaluate side-chains 1385 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1214 time to evaluate : 5.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 98 ASP Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 356 HIS Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 192 SER Chi-restraints excluded: chain 2 residue 199 LEU Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 109 ASP Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 294 THR Chi-restraints excluded: chain 3 residue 324 ASP Chi-restraints excluded: chain 3 residue 360 SER Chi-restraints excluded: chain 3 residue 403 ASP Chi-restraints excluded: chain 3 residue 486 ASP Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 585 VAL Chi-restraints excluded: chain 3 residue 587 VAL Chi-restraints excluded: chain 3 residue 609 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 669 LYS Chi-restraints excluded: chain 4 residue 67 GLU Chi-restraints excluded: chain 4 residue 88 GLU Chi-restraints excluded: chain 4 residue 230 THR Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 326 ASP Chi-restraints excluded: chain 4 residue 403 ASP Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 175 ILE Chi-restraints excluded: chain 9 residue 16 SER Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 133 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 57 PHE Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 227 PHE Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 423 SER Chi-restraints excluded: chain L residue 442 ASN Chi-restraints excluded: chain L residue 462 LEU Chi-restraints excluded: chain L residue 479 GLN Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 256 PHE Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 338 HIS Chi-restraints excluded: chain M residue 398 LEU Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 44 MET Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 245 LEU Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain Y residue 47 TRP Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 128 THR Chi-restraints excluded: chain Y residue 156 ASP Chi-restraints excluded: chain Y residue 170 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 82 LEU Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain c residue 44 ASN Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 89 ASN Chi-restraints excluded: chain d residue 158 GLU Chi-restraints excluded: chain d residue 290 THR Chi-restraints excluded: chain e residue 23 CYS Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain g residue 23 ASP Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 29 GLU Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 141 SER Chi-restraints excluded: chain j residue 15 VAL Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain k residue 115 LEU Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain k residue 290 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 103 LEU Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain n residue 61 SER Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 107 LYS Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain p residue 60 GLU Chi-restraints excluded: chain q residue 131 GLU Chi-restraints excluded: chain q residue 143 THR Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 60 HIS Chi-restraints excluded: chain s residue 84 HIS Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain t residue 10 THR Chi-restraints excluded: chain t residue 35 LYS Chi-restraints excluded: chain t residue 36 TYR Chi-restraints excluded: chain t residue 139 LEU Chi-restraints excluded: chain t residue 162 LEU Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain v residue 128 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 39 GLU Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 27 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 697 optimal weight: 0.8980 chunk 734 optimal weight: 6.9990 chunk 669 optimal weight: 20.0000 chunk 714 optimal weight: 7.9990 chunk 733 optimal weight: 20.0000 chunk 429 optimal weight: 8.9990 chunk 311 optimal weight: 10.0000 chunk 560 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 645 optimal weight: 30.0000 chunk 675 optimal weight: 7.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 36 GLN ** 3 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 284 GLN L 199 GLN ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 442 ASN ** L 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 89 ASN g 69 ASN ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 61 ASN p 32 GLN t 13 GLN ** t 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 13 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.239 68996 Z= 0.558 Angle : 1.590 50.744 93232 Z= 1.022 Chirality : 0.310 6.366 10101 Planarity : 0.005 0.127 11630 Dihedral : 11.690 160.289 10494 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.92 % Allowed : 14.83 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: -0.07 (0.09), residues: 8036 helix: 0.80 (0.08), residues: 4280 sheet: -1.01 (0.27), residues: 387 loop : -0.98 (0.11), residues: 3369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP t 101 HIS 0.007 0.001 HIS o 59 PHE 0.031 0.002 PHE s 65 TYR 0.029 0.002 TYR 9 118 ARG 0.012 0.000 ARG 4 305 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1443 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1235 time to evaluate : 5.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 272 MET cc_start: 0.8210 (tpt) cc_final: 0.7871 (tpp) REVERT: 1 385 ARG cc_start: 0.8444 (ptt90) cc_final: 0.8051 (ptp90) REVERT: 1 394 GLU cc_start: 0.8238 (mt-10) cc_final: 0.8031 (mt-10) REVERT: 1 432 ARG cc_start: 0.8141 (ptt-90) cc_final: 0.7745 (ttt-90) REVERT: 2 170 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7903 (mt-10) REVERT: 2 174 ASP cc_start: 0.8226 (m-30) cc_final: 0.7997 (m-30) REVERT: 3 82 ASN cc_start: 0.9254 (t0) cc_final: 0.8831 (m-40) REVERT: 3 131 LEU cc_start: 0.9120 (mt) cc_final: 0.8696 (tt) REVERT: 3 196 SER cc_start: 0.9215 (p) cc_final: 0.8868 (t) REVERT: 3 257 ASP cc_start: 0.8116 (m-30) cc_final: 0.7306 (t0) REVERT: 3 539 LYS cc_start: 0.8226 (tptt) cc_final: 0.7352 (ptpt) REVERT: 4 182 GLU cc_start: 0.9316 (tm-30) cc_final: 0.9003 (tt0) REVERT: 4 326 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8491 (t70) REVERT: 4 352 TYR cc_start: 0.9289 (m-80) cc_final: 0.9073 (m-80) REVERT: 5 108 LYS cc_start: 0.9191 (mtpt) cc_final: 0.8778 (mtmm) REVERT: 5 125 LYS cc_start: 0.9301 (mmtm) cc_final: 0.8839 (mtpt) REVERT: 5 144 ASN cc_start: 0.8726 (t0) cc_final: 0.8438 (t0) REVERT: 6 50 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8214 (m-80) REVERT: 6 102 LYS cc_start: 0.8950 (tttt) cc_final: 0.8460 (ttpp) REVERT: 6 175 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8998 (mp) REVERT: 6 178 ARG cc_start: 0.8722 (mtm-85) cc_final: 0.8306 (ttp-110) REVERT: 9 15 LYS cc_start: 0.8656 (tptp) cc_final: 0.8012 (ttpp) REVERT: 9 78 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.9015 (pp) REVERT: 9 133 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8562 (mt-10) REVERT: A 4 MET cc_start: 0.8393 (mtm) cc_final: 0.8100 (tpt) REVERT: A 23 TRP cc_start: 0.6190 (m100) cc_final: 0.5605 (m-90) REVERT: A 33 LYS cc_start: 0.5972 (OUTLIER) cc_final: 0.5625 (mmtp) REVERT: A 58 VAL cc_start: 0.8962 (p) cc_final: 0.8717 (m) REVERT: H 139 THR cc_start: 0.8992 (m) cc_final: 0.8689 (p) REVERT: H 241 LEU cc_start: 0.9340 (tp) cc_final: 0.8842 (mp) REVERT: J 1 MET cc_start: 0.4738 (tmt) cc_final: 0.3256 (mtt) REVERT: J 31 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8140 (mp) REVERT: J 57 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: J 65 MET cc_start: 0.9064 (mmm) cc_final: 0.8823 (mmm) REVERT: J 122 MET cc_start: 0.5977 (tpt) cc_final: 0.4941 (ptm) REVERT: J 127 ILE cc_start: 0.4359 (OUTLIER) cc_final: 0.3922 (mt) REVERT: J 170 GLU cc_start: 0.7805 (tp30) cc_final: 0.7591 (tp30) REVERT: L 312 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7808 (mp) REVERT: L 396 ILE cc_start: 0.6945 (tp) cc_final: 0.6425 (pt) REVERT: L 442 ASN cc_start: 0.7164 (OUTLIER) cc_final: 0.6714 (t0) REVERT: L 544 MET cc_start: 0.5759 (tmm) cc_final: 0.4669 (mmm) REVERT: L 573 MET cc_start: 0.2663 (mmp) cc_final: 0.0660 (mpp) REVERT: M 207 MET cc_start: 0.8691 (tpt) cc_final: 0.8360 (tpt) REVERT: M 278 ARG cc_start: 0.6840 (mmm-85) cc_final: 0.6272 (mmm-85) REVERT: N 11 MET cc_start: 0.7388 (mmp) cc_final: 0.6956 (mtm) REVERT: N 44 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8414 (mtp) REVERT: N 45 MET cc_start: 0.8889 (mmm) cc_final: 0.8549 (mtt) REVERT: N 46 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8679 (tttm) REVERT: N 96 MET cc_start: 0.8323 (ttt) cc_final: 0.8051 (mtp) REVERT: N 167 TRP cc_start: 0.8457 (m-90) cc_final: 0.8139 (m100) REVERT: N 268 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8410 (tt0) REVERT: X 14 ARG cc_start: 0.6761 (mmm-85) cc_final: 0.5773 (mmm-85) REVERT: X 20 LYS cc_start: 0.5875 (mtmt) cc_final: 0.5512 (mmtt) REVERT: X 37 MET cc_start: 0.5463 (mmt) cc_final: 0.5151 (mmt) REVERT: X 71 MET cc_start: 0.3940 (mmt) cc_final: 0.3682 (mtm) REVERT: Y 43 MET cc_start: 0.8454 (mmm) cc_final: 0.7875 (mmm) REVERT: Y 47 TRP cc_start: 0.8258 (OUTLIER) cc_final: 0.7793 (m-90) REVERT: Y 109 CYS cc_start: 0.9107 (t) cc_final: 0.8670 (t) REVERT: Y 148 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7964 (pm20) REVERT: Z 110 LYS cc_start: 0.9055 (mtmt) cc_final: 0.8723 (mttp) REVERT: a 34 ASP cc_start: 0.5987 (t70) cc_final: 0.5461 (p0) REVERT: a 45 ASP cc_start: 0.9015 (t70) cc_final: 0.8766 (t0) REVERT: a 57 ASP cc_start: 0.8408 (t0) cc_final: 0.8089 (m-30) REVERT: a 71 GLU cc_start: 0.8894 (tt0) cc_final: 0.8173 (mp0) REVERT: b 21 GLU cc_start: 0.8038 (pm20) cc_final: 0.7648 (tt0) REVERT: b 37 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8092 (mm-30) REVERT: b 80 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8360 (ptpt) REVERT: c 31 LYS cc_start: 0.8888 (mttt) cc_final: 0.8506 (tptp) REVERT: c 36 ARG cc_start: 0.8989 (ttt-90) cc_final: 0.8734 (ttt-90) REVERT: d 78 LYS cc_start: 0.8549 (mttm) cc_final: 0.8210 (mtmm) REVERT: d 119 GLN cc_start: 0.8379 (tm-30) cc_final: 0.7766 (tm-30) REVERT: e 25 ARG cc_start: 0.8251 (mmt-90) cc_final: 0.7824 (mtm180) REVERT: e 37 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8180 (mt-10) REVERT: f 7 THR cc_start: 0.8104 (t) cc_final: 0.7861 (m) REVERT: f 8 THR cc_start: 0.8531 (p) cc_final: 0.8305 (t) REVERT: f 91 ARG cc_start: 0.8946 (mtt90) cc_final: 0.8406 (mtt90) REVERT: g 79 ASP cc_start: 0.8244 (m-30) cc_final: 0.7956 (m-30) REVERT: g 93 ILE cc_start: 0.9188 (mt) cc_final: 0.8843 (pt) REVERT: h 24 GLN cc_start: 0.8386 (pt0) cc_final: 0.8035 (pm20) REVERT: i 21 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7580 (mpt180) REVERT: i 53 LYS cc_start: 0.9004 (mmtm) cc_final: 0.8674 (mttp) REVERT: i 104 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8709 (p) REVERT: i 128 SER cc_start: 0.9344 (t) cc_final: 0.8843 (p) REVERT: j 22 TYR cc_start: 0.7823 (t80) cc_final: 0.7511 (t80) REVERT: j 54 MET cc_start: 0.7508 (mmt) cc_final: 0.7246 (mmt) REVERT: j 74 GLN cc_start: 0.7911 (tp40) cc_final: 0.7465 (tp40) REVERT: j 78 ASP cc_start: 0.7152 (m-30) cc_final: 0.6907 (m-30) REVERT: j 82 ASP cc_start: 0.7792 (m-30) cc_final: 0.7357 (t0) REVERT: k 193 LYS cc_start: 0.6914 (mttt) cc_final: 0.6286 (tptm) REVERT: k 236 GLU cc_start: 0.6390 (mm-30) cc_final: 0.6126 (tp30) REVERT: k 294 GLN cc_start: 0.8142 (tp40) cc_final: 0.7178 (pt0) REVERT: l 58 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: n 68 LYS cc_start: 0.7028 (tttt) cc_final: 0.6493 (ttpt) REVERT: o 25 LYS cc_start: 0.8433 (mttt) cc_final: 0.8167 (mtmt) REVERT: o 100 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8282 (t0) REVERT: q 6 LYS cc_start: 0.8617 (tptm) cc_final: 0.8160 (tttt) REVERT: q 89 ASN cc_start: 0.8998 (m-40) cc_final: 0.8762 (m-40) REVERT: q 91 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7494 (tm-30) REVERT: q 93 GLU cc_start: 0.8527 (tt0) cc_final: 0.8103 (tm-30) REVERT: q 107 GLU cc_start: 0.8268 (tt0) cc_final: 0.7985 (tp30) REVERT: r 69 PHE cc_start: 0.8395 (t80) cc_final: 0.7524 (m-10) REVERT: r 119 MET cc_start: 0.7036 (mtm) cc_final: 0.6568 (pmm) REVERT: s 38 MET cc_start: 0.6399 (mmm) cc_final: 0.5989 (mmm) REVERT: s 94 TYR cc_start: 0.7600 (t80) cc_final: 0.7237 (t80) REVERT: s 98 MET cc_start: 0.7277 (mmt) cc_final: 0.6943 (mtt) REVERT: s 109 GLN cc_start: 0.7710 (mt0) cc_final: 0.7237 (tm-30) REVERT: v 33 ASP cc_start: 0.4421 (m-30) cc_final: 0.3211 (t0) REVERT: v 70 ARG cc_start: 0.7523 (mtt-85) cc_final: 0.7306 (mmt90) REVERT: v 82 ASP cc_start: 0.7935 (p0) cc_final: 0.7619 (p0) REVERT: v 126 GLN cc_start: 0.6821 (mm110) cc_final: 0.6600 (tm-30) REVERT: w 82 ASP cc_start: 0.8767 (t0) cc_final: 0.8455 (t70) outliers start: 208 outliers final: 163 residues processed: 1355 average time/residue: 0.6509 time to fit residues: 1497.6634 Evaluate side-chains 1394 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1215 time to evaluate : 7.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 356 HIS Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 192 SER Chi-restraints excluded: chain 2 residue 199 LEU Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 109 ASP Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 294 THR Chi-restraints excluded: chain 3 residue 324 ASP Chi-restraints excluded: chain 3 residue 360 SER Chi-restraints excluded: chain 3 residue 403 ASP Chi-restraints excluded: chain 3 residue 486 ASP Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 585 VAL Chi-restraints excluded: chain 3 residue 587 VAL Chi-restraints excluded: chain 3 residue 609 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 669 LYS Chi-restraints excluded: chain 4 residue 67 GLU Chi-restraints excluded: chain 4 residue 88 GLU Chi-restraints excluded: chain 4 residue 217 ASN Chi-restraints excluded: chain 4 residue 222 ILE Chi-restraints excluded: chain 4 residue 230 THR Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 326 ASP Chi-restraints excluded: chain 4 residue 403 ASP Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 175 ILE Chi-restraints excluded: chain 9 residue 16 SER Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 133 GLU Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 57 PHE Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 286 LEU Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 423 SER Chi-restraints excluded: chain L residue 442 ASN Chi-restraints excluded: chain L residue 462 LEU Chi-restraints excluded: chain L residue 479 GLN Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 256 PHE Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 280 THR Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 338 HIS Chi-restraints excluded: chain M residue 398 LEU Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 44 MET Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 245 LEU Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain Y residue 17 VAL Chi-restraints excluded: chain Y residue 47 TRP Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 128 THR Chi-restraints excluded: chain Y residue 170 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 82 LEU Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain Z residue 161 ARG Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 89 ASN Chi-restraints excluded: chain d residue 158 GLU Chi-restraints excluded: chain d residue 290 THR Chi-restraints excluded: chain e residue 23 CYS Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain g residue 23 ASP Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 141 SER Chi-restraints excluded: chain j residue 15 VAL Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain k residue 290 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 103 LEU Chi-restraints excluded: chain m residue 64 ASP Chi-restraints excluded: chain n residue 61 SER Chi-restraints excluded: chain o residue 31 LEU Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 107 LYS Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain p residue 60 GLU Chi-restraints excluded: chain q residue 131 GLU Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 60 HIS Chi-restraints excluded: chain s residue 84 HIS Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain t residue 10 THR Chi-restraints excluded: chain t residue 36 TYR Chi-restraints excluded: chain t residue 88 THR Chi-restraints excluded: chain t residue 138 GLN Chi-restraints excluded: chain t residue 139 LEU Chi-restraints excluded: chain t residue 162 LEU Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 34 PHE Chi-restraints excluded: chain v residue 85 ILE Chi-restraints excluded: chain v residue 128 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 39 GLU Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 27 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 711 optimal weight: 40.0000 chunk 468 optimal weight: 20.0000 chunk 755 optimal weight: 6.9990 chunk 460 optimal weight: 9.9990 chunk 358 optimal weight: 10.0000 chunk 524 optimal weight: 0.4980 chunk 792 optimal weight: 9.9990 chunk 728 optimal weight: 30.0000 chunk 630 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 487 optimal weight: 20.0000 overall best weight: 4.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 373 ASN ** 2 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 ASN ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 442 ASN ** L 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN M 138 ASN M 180 GLN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 89 ASN g 69 ASN ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 13 GLN ** t 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.240 68996 Z= 0.542 Angle : 1.586 50.731 93232 Z= 1.020 Chirality : 0.310 6.359 10101 Planarity : 0.004 0.074 11630 Dihedral : 11.611 160.394 10494 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.69 % Allowed : 15.16 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: -0.02 (0.09), residues: 8036 helix: 0.83 (0.08), residues: 4284 sheet: -0.99 (0.27), residues: 385 loop : -0.93 (0.11), residues: 3367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP t 101 HIS 0.006 0.001 HIS o 59 PHE 0.030 0.002 PHE s 65 TYR 0.034 0.002 TYR 9 40 ARG 0.012 0.000 ARG 4 305 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16072 Ramachandran restraints generated. 8036 Oldfield, 0 Emsley, 8036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1428 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1236 time to evaluate : 5.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 272 MET cc_start: 0.8197 (tpt) cc_final: 0.7863 (tpp) REVERT: 1 385 ARG cc_start: 0.8436 (ptt90) cc_final: 0.8044 (ptp90) REVERT: 1 394 GLU cc_start: 0.8225 (mt-10) cc_final: 0.8019 (mt-10) REVERT: 1 432 ARG cc_start: 0.8160 (ptt-90) cc_final: 0.7747 (ttt-90) REVERT: 2 170 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7897 (mt-10) REVERT: 2 174 ASP cc_start: 0.8213 (m-30) cc_final: 0.7990 (m-30) REVERT: 2 204 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8106 (mp0) REVERT: 3 82 ASN cc_start: 0.9246 (t0) cc_final: 0.8829 (m-40) REVERT: 3 95 GLU cc_start: 0.9220 (tp30) cc_final: 0.8804 (tp30) REVERT: 3 131 LEU cc_start: 0.9121 (mt) cc_final: 0.8683 (tt) REVERT: 3 196 SER cc_start: 0.9212 (p) cc_final: 0.8869 (t) REVERT: 3 257 ASP cc_start: 0.8152 (m-30) cc_final: 0.7305 (t0) REVERT: 3 539 LYS cc_start: 0.8249 (tptt) cc_final: 0.7354 (ptpt) REVERT: 4 182 GLU cc_start: 0.9312 (tm-30) cc_final: 0.8996 (tt0) REVERT: 4 326 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8494 (t70) REVERT: 4 352 TYR cc_start: 0.9268 (m-80) cc_final: 0.9053 (m-80) REVERT: 5 108 LYS cc_start: 0.9185 (mtpt) cc_final: 0.8770 (mtmm) REVERT: 5 125 LYS cc_start: 0.9292 (mmtm) cc_final: 0.8823 (mtpt) REVERT: 5 144 ASN cc_start: 0.8689 (t0) cc_final: 0.8421 (t0) REVERT: 6 50 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: 6 102 LYS cc_start: 0.8936 (tttt) cc_final: 0.8456 (ttpp) REVERT: 6 175 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8993 (mp) REVERT: 6 178 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8303 (ttp-110) REVERT: 9 15 LYS cc_start: 0.8651 (tptp) cc_final: 0.8017 (ttpp) REVERT: 9 78 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.9032 (pp) REVERT: 9 133 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8570 (mt-10) REVERT: A 4 MET cc_start: 0.8369 (mtm) cc_final: 0.8082 (tpt) REVERT: A 23 TRP cc_start: 0.6186 (m100) cc_final: 0.5601 (m-90) REVERT: A 33 LYS cc_start: 0.5944 (OUTLIER) cc_final: 0.5629 (mmtp) REVERT: A 58 VAL cc_start: 0.8964 (p) cc_final: 0.8722 (m) REVERT: A 109 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7689 (mmtm) REVERT: H 139 THR cc_start: 0.8979 (m) cc_final: 0.8674 (p) REVERT: H 241 LEU cc_start: 0.9311 (tp) cc_final: 0.8823 (mp) REVERT: J 1 MET cc_start: 0.4772 (tmt) cc_final: 0.3277 (mtt) REVERT: J 31 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8144 (mp) REVERT: J 57 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8511 (m-80) REVERT: J 122 MET cc_start: 0.5898 (tpt) cc_final: 0.4912 (ptm) REVERT: J 127 ILE cc_start: 0.4312 (OUTLIER) cc_final: 0.3850 (mt) REVERT: L 48 MET cc_start: 0.6884 (tpt) cc_final: 0.6224 (ttp) REVERT: L 312 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7791 (mp) REVERT: L 396 ILE cc_start: 0.6881 (tp) cc_final: 0.6376 (pt) REVERT: L 544 MET cc_start: 0.5738 (tmm) cc_final: 0.4643 (mmm) REVERT: L 573 MET cc_start: 0.2668 (mmp) cc_final: 0.0665 (mpp) REVERT: M 278 ARG cc_start: 0.6851 (mmm-85) cc_final: 0.6323 (mmm-85) REVERT: N 11 MET cc_start: 0.7375 (mmp) cc_final: 0.6950 (mtm) REVERT: N 44 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8501 (mtp) REVERT: N 45 MET cc_start: 0.8800 (mmm) cc_final: 0.8442 (mtt) REVERT: N 46 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8693 (tttm) REVERT: N 96 MET cc_start: 0.8354 (ttt) cc_final: 0.8077 (mtp) REVERT: N 167 TRP cc_start: 0.8446 (m-90) cc_final: 0.8138 (m100) REVERT: N 268 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8409 (tt0) REVERT: N 295 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.7741 (mmt90) REVERT: X 14 ARG cc_start: 0.6671 (mmm-85) cc_final: 0.5811 (mmm-85) REVERT: X 20 LYS cc_start: 0.5950 (mtmt) cc_final: 0.5530 (mmtt) REVERT: X 37 MET cc_start: 0.5396 (mmt) cc_final: 0.5167 (mmt) REVERT: X 71 MET cc_start: 0.4039 (mmt) cc_final: 0.3747 (mtm) REVERT: Y 43 MET cc_start: 0.8439 (mmm) cc_final: 0.7880 (mmm) REVERT: Y 47 TRP cc_start: 0.8252 (OUTLIER) cc_final: 0.7819 (m-90) REVERT: Y 109 CYS cc_start: 0.9095 (t) cc_final: 0.8669 (t) REVERT: Y 148 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7952 (pm20) REVERT: Z 110 LYS cc_start: 0.9056 (mtmt) cc_final: 0.8728 (mttp) REVERT: a 34 ASP cc_start: 0.5980 (t70) cc_final: 0.5456 (p0) REVERT: a 45 ASP cc_start: 0.9018 (t70) cc_final: 0.8774 (t0) REVERT: a 57 ASP cc_start: 0.8408 (t0) cc_final: 0.8090 (m-30) REVERT: a 71 GLU cc_start: 0.8872 (tt0) cc_final: 0.8160 (mp0) REVERT: b 21 GLU cc_start: 0.8047 (pm20) cc_final: 0.7645 (tt0) REVERT: b 37 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8086 (mm-30) REVERT: c 31 LYS cc_start: 0.8893 (mttt) cc_final: 0.8505 (tptp) REVERT: c 36 ARG cc_start: 0.8970 (ttt-90) cc_final: 0.8696 (ttt-90) REVERT: d 119 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7771 (tm-30) REVERT: e 25 ARG cc_start: 0.8262 (mmt-90) cc_final: 0.7846 (mtm180) REVERT: e 37 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8176 (mt-10) REVERT: f 7 THR cc_start: 0.8108 (t) cc_final: 0.7863 (m) REVERT: f 8 THR cc_start: 0.8537 (p) cc_final: 0.8314 (t) REVERT: f 91 ARG cc_start: 0.8944 (mtt90) cc_final: 0.8366 (mtt90) REVERT: g 79 ASP cc_start: 0.8242 (m-30) cc_final: 0.7954 (m-30) REVERT: g 93 ILE cc_start: 0.9185 (mt) cc_final: 0.8848 (pt) REVERT: h 24 GLN cc_start: 0.8399 (pt0) cc_final: 0.8031 (pm20) REVERT: i 21 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7561 (mpt180) REVERT: i 53 LYS cc_start: 0.9009 (mmtm) cc_final: 0.8691 (mttp) REVERT: i 104 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8705 (p) REVERT: i 128 SER cc_start: 0.9341 (t) cc_final: 0.8850 (p) REVERT: j 54 MET cc_start: 0.7497 (mmt) cc_final: 0.7287 (mmt) REVERT: j 74 GLN cc_start: 0.7917 (tp40) cc_final: 0.7480 (tp40) REVERT: j 82 ASP cc_start: 0.7778 (m-30) cc_final: 0.7365 (t0) REVERT: k 48 LEU cc_start: 0.6397 (mt) cc_final: 0.6178 (mt) REVERT: k 193 LYS cc_start: 0.6913 (mttt) cc_final: 0.6254 (tptm) REVERT: k 236 GLU cc_start: 0.6382 (mm-30) cc_final: 0.6127 (tp30) REVERT: k 250 ASP cc_start: 0.5863 (p0) cc_final: 0.5378 (m-30) REVERT: k 294 GLN cc_start: 0.8139 (tp40) cc_final: 0.7183 (pt0) REVERT: l 58 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: l 64 GLU cc_start: 0.8556 (tp30) cc_final: 0.8315 (tp30) REVERT: n 68 LYS cc_start: 0.7035 (tttt) cc_final: 0.6523 (ttpt) REVERT: o 25 LYS cc_start: 0.8427 (mttt) cc_final: 0.8163 (mtmt) REVERT: o 100 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8248 (t0) REVERT: q 6 LYS cc_start: 0.8610 (tptm) cc_final: 0.8153 (tttt) REVERT: q 9 MET cc_start: 0.8801 (mmm) cc_final: 0.8537 (mmm) REVERT: q 89 ASN cc_start: 0.9032 (m-40) cc_final: 0.8790 (m-40) REVERT: q 91 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7493 (tm-30) REVERT: q 93 GLU cc_start: 0.8494 (tt0) cc_final: 0.8084 (tm-30) REVERT: q 107 GLU cc_start: 0.8267 (tt0) cc_final: 0.8000 (tp30) REVERT: r 69 PHE cc_start: 0.8390 (t80) cc_final: 0.7539 (m-10) REVERT: r 119 MET cc_start: 0.7033 (mtm) cc_final: 0.6556 (pmm) REVERT: s 38 MET cc_start: 0.6309 (mmm) cc_final: 0.5969 (mmm) REVERT: s 94 TYR cc_start: 0.7600 (t80) cc_final: 0.7250 (t80) REVERT: s 98 MET cc_start: 0.7228 (mmt) cc_final: 0.6959 (mtt) REVERT: s 109 GLN cc_start: 0.7731 (mt0) cc_final: 0.7261 (tm-30) REVERT: t 35 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7122 (ttmm) REVERT: v 33 ASP cc_start: 0.4401 (m-30) cc_final: 0.3173 (t0) REVERT: v 70 ARG cc_start: 0.7472 (mtt-85) cc_final: 0.7259 (mmt90) REVERT: v 126 GLN cc_start: 0.6896 (mm110) cc_final: 0.6575 (tm-30) REVERT: w 82 ASP cc_start: 0.8747 (t0) cc_final: 0.8466 (t70) outliers start: 192 outliers final: 163 residues processed: 1348 average time/residue: 0.6523 time to fit residues: 1491.0283 Evaluate side-chains 1396 residues out of total 7126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1217 time to evaluate : 7.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 147 SER Chi-restraints excluded: chain 1 residue 356 HIS Chi-restraints excluded: chain 1 residue 363 THR Chi-restraints excluded: chain 2 residue 134 ASP Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 192 SER Chi-restraints excluded: chain 2 residue 199 LEU Chi-restraints excluded: chain 3 residue 13 VAL Chi-restraints excluded: chain 3 residue 109 ASP Chi-restraints excluded: chain 3 residue 190 MET Chi-restraints excluded: chain 3 residue 294 THR Chi-restraints excluded: chain 3 residue 324 ASP Chi-restraints excluded: chain 3 residue 360 SER Chi-restraints excluded: chain 3 residue 403 ASP Chi-restraints excluded: chain 3 residue 486 ASP Chi-restraints excluded: chain 3 residue 537 LEU Chi-restraints excluded: chain 3 residue 585 VAL Chi-restraints excluded: chain 3 residue 587 VAL Chi-restraints excluded: chain 3 residue 609 MET Chi-restraints excluded: chain 3 residue 615 THR Chi-restraints excluded: chain 3 residue 662 VAL Chi-restraints excluded: chain 3 residue 669 LYS Chi-restraints excluded: chain 4 residue 67 GLU Chi-restraints excluded: chain 4 residue 88 GLU Chi-restraints excluded: chain 4 residue 208 MET Chi-restraints excluded: chain 4 residue 217 ASN Chi-restraints excluded: chain 4 residue 230 THR Chi-restraints excluded: chain 4 residue 323 ILE Chi-restraints excluded: chain 4 residue 326 ASP Chi-restraints excluded: chain 4 residue 403 ASP Chi-restraints excluded: chain 4 residue 414 VAL Chi-restraints excluded: chain 6 residue 44 SER Chi-restraints excluded: chain 6 residue 50 PHE Chi-restraints excluded: chain 6 residue 75 VAL Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 175 ILE Chi-restraints excluded: chain 9 residue 16 SER Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 83 CYS Chi-restraints excluded: chain 9 residue 122 CYS Chi-restraints excluded: chain 9 residue 133 GLU Chi-restraints excluded: chain 9 residue 143 THR Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 171 GLN Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 259 PHE Chi-restraints excluded: chain H residue 314 ILE Chi-restraints excluded: chain J residue 2 MET Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 57 PHE Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain L residue 17 MET Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 227 PHE Chi-restraints excluded: chain L residue 290 MET Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 423 SER Chi-restraints excluded: chain L residue 462 LEU Chi-restraints excluded: chain L residue 479 GLN Chi-restraints excluded: chain L residue 508 THR Chi-restraints excluded: chain L residue 589 LEU Chi-restraints excluded: chain M residue 36 LEU Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 246 ILE Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 256 PHE Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 398 LEU Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 44 MET Chi-restraints excluded: chain N residue 79 MET Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 163 THR Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 245 LEU Chi-restraints excluded: chain N residue 261 MET Chi-restraints excluded: chain N residue 285 THR Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain X residue 18 VAL Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain Y residue 17 VAL Chi-restraints excluded: chain Y residue 47 TRP Chi-restraints excluded: chain Y residue 63 ASN Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 128 THR Chi-restraints excluded: chain Y residue 170 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 82 LEU Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 154 CYS Chi-restraints excluded: chain Z residue 161 ARG Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain d residue 30 LEU Chi-restraints excluded: chain d residue 89 ASN Chi-restraints excluded: chain d residue 158 GLU Chi-restraints excluded: chain d residue 290 THR Chi-restraints excluded: chain e residue 23 CYS Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 64 LEU Chi-restraints excluded: chain e residue 84 ASP Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain f residue 88 SER Chi-restraints excluded: chain g residue 23 ASP Chi-restraints excluded: chain g residue 100 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 45 SER Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain i residue 141 SER Chi-restraints excluded: chain j residue 15 VAL Chi-restraints excluded: chain j residue 23 ASP Chi-restraints excluded: chain j residue 46 ASP Chi-restraints excluded: chain k residue 199 LEU Chi-restraints excluded: chain k residue 234 VAL Chi-restraints excluded: chain k residue 290 ASP Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 75 LEU Chi-restraints excluded: chain l residue 103 LEU Chi-restraints excluded: chain n residue 61 SER Chi-restraints excluded: chain o residue 31 LEU Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 100 ASP Chi-restraints excluded: chain o residue 107 LYS Chi-restraints excluded: chain o residue 119 VAL Chi-restraints excluded: chain p residue 36 LEU Chi-restraints excluded: chain p residue 60 GLU Chi-restraints excluded: chain q residue 117 THR Chi-restraints excluded: chain q residue 131 GLU Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 75 LEU Chi-restraints excluded: chain r residue 102 ARG Chi-restraints excluded: chain r residue 116 ILE Chi-restraints excluded: chain s residue 60 HIS Chi-restraints excluded: chain s residue 84 HIS Chi-restraints excluded: chain s residue 89 CYS Chi-restraints excluded: chain t residue 10 THR Chi-restraints excluded: chain t residue 35 LYS Chi-restraints excluded: chain t residue 36 TYR Chi-restraints excluded: chain t residue 88 THR Chi-restraints excluded: chain t residue 138 GLN Chi-restraints excluded: chain t residue 139 LEU Chi-restraints excluded: chain t residue 162 LEU Chi-restraints excluded: chain u residue 22 VAL Chi-restraints excluded: chain u residue 34 PHE Chi-restraints excluded: chain v residue 128 VAL Chi-restraints excluded: chain v residue 145 ASP Chi-restraints excluded: chain w residue 39 GLU Chi-restraints excluded: chain w residue 110 SER Chi-restraints excluded: chain y residue 27 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 795 random chunks: chunk 386 optimal weight: 20.0000 chunk 500 optimal weight: 6.9990 chunk 671 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 581 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 631 optimal weight: 40.0000 chunk 264 optimal weight: 6.9990 chunk 648 optimal weight: 0.3980 chunk 79 optimal weight: 5.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 157 ASN ** 3 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 582 GLN ** 4 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 ASN ** L 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN M 144 ASN ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 89 ASN g 69 ASN j 74 GLN ** k 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 61 ASN p 32 GLN ** p 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 13 GLN ** t 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.117946 restraints weight = 111456.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.119470 restraints weight = 66071.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.119949 restraints weight = 41930.667| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.240 68996 Z= 0.530 Angle : 1.581 50.716 93232 Z= 1.018 Chirality : 0.310 6.353 10101 Planarity : 0.004 0.052 11630 Dihedral : 11.452 160.632 10494 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.65 % Allowed : 15.45 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.52 % 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: 0.06 (0.09), residues: 8036 helix: 0.89 (0.08), residues: 4285 sheet: -0.93 (0.27), residues: 390 loop : -0.90 (0.11), residues: 3361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP t 101 HIS 0.005 0.001 HIS o 59 PHE 0.030 0.001 PHE s 65 TYR 0.034 0.002 TYR 9 50 ARG 0.011 0.000 ARG 4 305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23979.08 seconds wall clock time: 417 minutes 54.45 seconds (25074.45 seconds total)