Starting phenix.real_space_refine on Tue Apr 16 05:07:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t5h_8361/04_2024/5t5h_8361_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t5h_8361/04_2024/5t5h_8361.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t5h_8361/04_2024/5t5h_8361_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t5h_8361/04_2024/5t5h_8361_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t5h_8361/04_2024/5t5h_8361_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t5h_8361/04_2024/5t5h_8361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t5h_8361/04_2024/5t5h_8361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t5h_8361/04_2024/5t5h_8361_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t5h_8361/04_2024/5t5h_8361_trim_updated.pdb" } resolution = 2.54 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= 0.004 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 2884 5.49 5 Mg 105 5.21 5 S 187 5.16 5 C 54840 2.51 5 N 19822 2.21 5 O 27271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ARG 16": "NH1" <-> "NH2" Residue "L ARG 140": "NH1" <-> "NH2" Residue "L ARG 143": "NH1" <-> "NH2" Residue "L ARG 148": "NH1" <-> "NH2" Residue "N ARG 175": "NH1" <-> "NH2" Residue "P GLU 130": "OE1" <-> "OE2" Residue "Q ARG 54": "NH1" <-> "NH2" Residue "Q ARG 56": "NH1" <-> "NH2" Residue "Q ARG 65": "NH1" <-> "NH2" Residue "Q ARG 83": "NH1" <-> "NH2" Residue "Q ARG 188": "NH1" <-> "NH2" Residue "R ARG 127": "NH1" <-> "NH2" Residue "S ARG 119": "NH1" <-> "NH2" Residue "S ARG 156": "NH1" <-> "NH2" Residue "S ARG 162": "NH1" <-> "NH2" Residue "T ARG 81": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "X ARG 81": "NH1" <-> "NH2" Residue "a ARG 64": "NH1" <-> "NH2" Residue "a ARG 132": "NH1" <-> "NH2" Residue "b PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 26": "NH1" <-> "NH2" Residue "c ARG 41": "NH1" <-> "NH2" Residue "c ARG 124": "NH1" <-> "NH2" Residue "c ARG 127": "NH1" <-> "NH2" Residue "f ARG 169": "NH1" <-> "NH2" Residue "f ARG 347": "NH1" <-> "NH2" Residue "f ARG 355": "NH1" <-> "NH2" Residue "f ARG 394": "NH1" <-> "NH2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "k ARG 67": "NH1" <-> "NH2" Residue "k ARG 106": "NH1" <-> "NH2" Residue "l ARG 91": "NH1" <-> "NH2" Residue "m ARG 35": "NH1" <-> "NH2" Residue "m ARG 81": "NH1" <-> "NH2" Residue "o ARG 4": "NH1" <-> "NH2" Residue "r ARG 198": "NH1" <-> "NH2" Residue "r ARG 246": "NH1" <-> "NH2" Residue "r ARG 323": "NH1" <-> "NH2" Residue "t ARG 38": "NH1" <-> "NH2" Residue "t ARG 42": "NH1" <-> "NH2" Residue "t ARG 87": "NH1" <-> "NH2" Residue "v ARG 28": "NH1" <-> "NH2" Residue "v ARG 80": "NH1" <-> "NH2" Residue "v ARG 190": "NH1" <-> "NH2" Residue "w ARG 236": "NH1" <-> "NH2" Residue "x ARG 307": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 105112 Number of models: 1 Model: "" Number of chains: 74 Chain: "A" Number of atoms: 27441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 27441 Classifications: {'RNA': 1278} Modifications used: {'rna2p': 2, 'rna2p_pur': 132, 'rna2p_pyr': 55, 'rna3p': 21, 'rna3p_pur': 586, 'rna3p_pyr': 473} Link IDs: {'rna2p': 188, 'rna3p': 1089} Chain breaks: 30 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 19 Chain: "B" Number of atoms: 20110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 20110 Classifications: {'RNA': 941} Modifications used: {'rna2p': 3, 'rna2p_pur': 104, 'rna2p_pyr': 69, 'rna3p': 22, 'rna3p_pur': 384, 'rna3p_pyr': 353} Link IDs: {'rna2p': 175, 'rna3p': 765} Chain breaks: 16 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 21 Chain: "C" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3140 Classifications: {'RNA': 147} Modifications used: {'rna2p': 1, 'rna2p_pur': 12, 'rna2p_pyr': 11, 'rna3p': 5, 'rna3p_pur': 60, 'rna3p_pyr': 56} Link IDs: {'rna2p': 24, 'rna3p': 122} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2432 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 54, 'rna3p_pyr': 52} Link IDs: {'rna2p': 8, 'rna3p': 105} Chain breaks: 2 Chain: "E" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3110 Classifications: {'RNA': 146} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 3, 'rna3p_pur': 67, 'rna3p_pyr': 67} Link IDs: {'rna2p': 12, 'rna3p': 133} Chain breaks: 5 Chain: "F" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 965 Classifications: {'RNA': 46} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 11, 'rna3p_pur': 13, 'rna3p_pyr': 16} Link IDs: {'rna2p': 17, 'rna3p': 28} Chain breaks: 1 Chain: "G" Number of atoms: 2578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2578 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 5, 'rna3p': 1, 'rna3p_pur': 51, 'rna3p_pyr': 56} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1946 Classifications: {'RNA': 91} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 7, 'rna3p_pur': 46, 'rna3p_pyr': 36} Link IDs: {'rna2p': 9, 'rna3p': 81} Chain breaks: 4 Chain: "I" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1515 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 7, 'TRANS': 184} Chain: "L" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain breaks: 3 Chain: "N" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 13, 'TRANS': 158} Chain breaks: 1 Chain: "O" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1642 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1186 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 144} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "Q" Number of atoms: 1710 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1702 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Conformer: "B" Number of residues, atoms: 203, 1702 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} bond proxies already assigned to first conformer: 1732 Chain: "R" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1226 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 8, 'TRANS': 143} Chain: "S" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1449 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain: "T" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1273 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 3, 'TRANS': 146} Chain: "U" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1016 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain breaks: 1 Chain: "V" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 730 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain breaks: 2 Chain: "W" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 960 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "X" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 890 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain breaks: 1 Chain: "Y" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 519 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 6, 'TRANS': 54} Chain: "Z" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 919 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "a" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 877 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 2 Chain: "b" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1135 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "c" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 935 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain breaks: 1 Chain: "d" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 518 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "e" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 228} Chain: "f" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3189 Classifications: {'peptide': 397} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 378} Chain: "g" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain breaks: 1 Chain: "h" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1064 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 37} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain breaks: 4 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 85 Chain: "i" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 928 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "j" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 863 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "k" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 967 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain breaks: 1 Chain: "l" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1057 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 130} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "m" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "n" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 679 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'TRANS': 79} Chain: "o" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 669 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "p" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 432 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain breaks: 1 Chain: "q" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 456 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "r" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2513 Classifications: {'peptide': 325} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 309} Chain breaks: 1 Chain: "t" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 763 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "u" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1541 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 6, 'TRANS': 186} Chain breaks: 2 Chain: "v" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1037 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 122} Chain breaks: 1 Chain: "w" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1749 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 206} Chain: "x" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1690 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain breaks: 1 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Unusual residues: {' MG': 66} Classifications: {'undetermined': 66} Link IDs: {None: 65} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Unusual residues: {' MG': 32} Classifications: {'undetermined': 32} Link IDs: {None: 31} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 93528 SG CYS n 19 134.591 110.547 154.593 1.00 3.94 S ATOM 93556 SG CYS n 22 134.869 108.571 151.458 1.00 7.07 S ATOM 93662 SG CYS n 34 131.837 109.662 151.647 1.00 1.75 S ATOM 93678 SG CYS n 37 133.016 107.653 154.016 1.00 4.59 S ATOM 94370 SG CYS o 39 95.327 157.748 177.558 1.00 25.10 S ATOM 94393 SG CYS o 42 98.090 160.310 178.729 1.00 33.52 S ATOM 94519 SG CYS o 57 98.637 157.861 175.848 1.00 33.82 S ATOM 98235 SG CYS t 12 64.884 47.902 137.682 1.00 61.73 S ATOM 98272 SG CYS t 17 62.841 45.845 139.123 1.00120.00 S ATOM 98739 SG CYS t 74 62.879 49.186 140.989 1.00 74.59 S Time building chain proxies: 40.85, per 1000 atoms: 0.39 Number of scatterers: 105112 At special positions: 0 Unit cell: (201.685, 220.495, 236.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 187 16.00 P 2884 15.00 Mg 105 11.99 O 27271 8.00 N 19822 7.00 C 54840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 45.17 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 22 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 37 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 34 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 19 " pdb=" ZN o 101 " pdb="ZN ZN o 101 " - pdb=" SG CYS o 39 " pdb="ZN ZN o 101 " - pdb=" SG CYS o 57 " pdb="ZN ZN o 101 " - pdb=" SG CYS o 42 " pdb=" ZN t 101 " pdb="ZN ZN t 101 " - pdb=" SG CYS t 12 " pdb="ZN ZN t 101 " - pdb=" SG CYS t 74 " pdb="ZN ZN t 101 " - pdb=" SG CYS t 17 " Number of angles added : 6 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10038 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 204 helices and 57 sheets defined 44.1% alpha, 14.6% beta 762 base pairs and 1591 stacking pairs defined. Time for finding SS restraints: 54.26 Creating SS restraints... Processing helix chain 'I' and resid 7 through 13 removed outlier: 3.762A pdb=" N LYS I 11 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS I 12 " --> pdb=" O VAL I 8 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ARG I 13 " --> pdb=" O GLN I 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 7 through 13' Processing helix chain 'I' and resid 23 through 40 removed outlier: 3.574A pdb=" N LYS I 27 " --> pdb=" O ASN I 23 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE I 35 " --> pdb=" O LYS I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 55 removed outlier: 3.925A pdb=" N LYS I 46 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU I 53 " --> pdb=" O HIS I 49 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS I 54 " --> pdb=" O GLN I 50 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N SER I 55 " --> pdb=" O ARG I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 79 removed outlier: 4.867A pdb=" N TRP I 77 " --> pdb=" O ARG I 73 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU I 78 " --> pdb=" O LYS I 74 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLU I 79 " --> pdb=" O SER I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 124 removed outlier: 3.760A pdb=" N GLY I 124 " --> pdb=" O ILE I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 137 Processing helix chain 'I' and resid 149 through 154 removed outlier: 5.795A pdb=" N ARG I 153 " --> pdb=" O ARG I 149 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLU I 154 " --> pdb=" O LYS I 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 149 through 154' Processing helix chain 'I' and resid 155 through 160 removed outlier: 4.089A pdb=" N PHE I 159 " --> pdb=" O SER I 155 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY I 160 " --> pdb=" O VAL I 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 155 through 160' Processing helix chain 'I' and resid 175 through 181 removed outlier: 4.273A pdb=" N GLU I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG I 180 " --> pdb=" O ARG I 176 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN I 181 " --> pdb=" O GLY I 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 175 through 181' Processing helix chain 'L' and resid 141 through 147 removed outlier: 4.973A pdb=" N ALA L 145 " --> pdb=" O GLY L 141 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS L 146 " --> pdb=" O GLU L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 172 removed outlier: 3.744A pdb=" N HIS L 167 " --> pdb=" O GLU L 163 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP L 168 " --> pdb=" O GLU L 164 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE L 169 " --> pdb=" O ALA L 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 52 removed outlier: 3.588A pdb=" N LYS N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 89 Processing helix chain 'N' and resid 91 through 99 Proline residue: N 96 - end of helix Processing helix chain 'N' and resid 110 through 128 removed outlier: 3.705A pdb=" N SER N 126 " --> pdb=" O LYS N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 199 removed outlier: 3.835A pdb=" N LYS N 184 " --> pdb=" O GLU N 180 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ASN N 185 " --> pdb=" O GLU N 181 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL N 186 " --> pdb=" O ARG N 182 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N TYR N 187 " --> pdb=" O THR N 183 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LYS N 188 " --> pdb=" O LYS N 184 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL N 197 " --> pdb=" O ASN N 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 206 removed outlier: 3.735A pdb=" N ARG N 204 " --> pdb=" O PHE N 200 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA N 205 " --> pdb=" O GLY N 201 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG N 206 " --> pdb=" O ILE N 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 200 through 206' Processing helix chain 'O' and resid 33 through 48 removed outlier: 3.840A pdb=" N LEU O 46 " --> pdb=" O ALA O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 removed outlier: 3.733A pdb=" N LEU O 59 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR O 60 " --> pdb=" O CYS O 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 55 through 60' Processing helix chain 'O' and resid 64 through 79 removed outlier: 4.099A pdb=" N LYS O 78 " --> pdb=" O GLN O 74 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG O 79 " --> pdb=" O PHE O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 88 removed outlier: 3.653A pdb=" N GLY O 87 " --> pdb=" O ASN O 83 " (cutoff:3.500A) Proline residue: O 88 - end of helix No H-bonds generated for 'chain 'O' and resid 83 through 88' Processing helix chain 'O' and resid 93 through 107 removed outlier: 3.772A pdb=" N MET O 105 " --> pdb=" O THR O 101 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU O 106 " --> pdb=" O VAL O 102 " (cutoff:3.500A) Proline residue: O 107 - end of helix Processing helix chain 'O' and resid 110 through 121 removed outlier: 3.550A pdb=" N ARG O 118 " --> pdb=" O GLN O 114 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU O 120 " --> pdb=" O ALA O 116 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL O 121 " --> pdb=" O LEU O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 132 removed outlier: 5.306A pdb=" N ARG O 132 " --> pdb=" O THR O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 148 Processing helix chain 'O' and resid 156 through 165 removed outlier: 3.933A pdb=" N HIS O 163 " --> pdb=" O ASN O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 208 removed outlier: 3.528A pdb=" N LYS O 173 " --> pdb=" O SER O 169 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS O 188 " --> pdb=" O ALA O 184 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU O 191 " --> pdb=" O HIS O 187 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS O 192 " --> pdb=" O LYS O 188 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU O 193 " --> pdb=" O LYS O 189 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU O 205 " --> pdb=" O ARG O 201 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER O 206 " --> pdb=" O LYS O 202 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL O 208 " --> pdb=" O ALA O 204 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 220 removed outlier: 3.542A pdb=" N GLU O 214 " --> pdb=" O LYS O 210 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE O 219 " --> pdb=" O VAL O 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 57 removed outlier: 5.343A pdb=" N GLU P 57 " --> pdb=" O LEU P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 82 removed outlier: 4.148A pdb=" N ALA P 79 " --> pdb=" O LYS P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 90 removed outlier: 3.805A pdb=" N ALA P 89 " --> pdb=" O GLU P 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 105 removed outlier: 3.783A pdb=" N ILE P 96 " --> pdb=" O SER P 92 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG P 104 " --> pdb=" O ARG P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 133 removed outlier: 4.113A pdb=" N ALA P 116 " --> pdb=" O GLN P 112 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS P 133 " --> pdb=" O ASP P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 153 removed outlier: 3.544A pdb=" N GLN P 148 " --> pdb=" O LEU P 144 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS P 149 " --> pdb=" O LYS P 145 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN P 150 " --> pdb=" O LYS P 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 30 removed outlier: 3.574A pdb=" N TYR Q 22 " --> pdb=" O GLY Q 18 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP Q 27 " --> pdb=" O LEU Q 23 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS Q 29 " --> pdb=" O GLU Q 25 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS Q 30 " --> pdb=" O LEU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 50 removed outlier: 3.704A pdb=" N HIS Q 48 " --> pdb=" O TRP Q 44 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN Q 49 " --> pdb=" O GLU Q 45 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N HIS Q 50 " --> pdb=" O PHE Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 68 Processing helix chain 'Q' and resid 99 through 104 removed outlier: 5.098A pdb=" N GLY Q 104 " --> pdb=" O PRO Q 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 127 removed outlier: 3.882A pdb=" N GLY Q 127 " --> pdb=" O GLY Q 123 " (cutoff:3.500A) Processing helix chain 'Q' and resid 155 through 161 Processing helix chain 'Q' and resid 164 through 170 removed outlier: 4.463A pdb=" N VAL Q 168 " --> pdb=" O ILE Q 164 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN Q 169 " --> pdb=" O ASN Q 165 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ALA Q 170 " --> pdb=" O TRP Q 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 164 through 170' Processing helix chain 'Q' and resid 171 through 179 removed outlier: 5.703A pdb=" N ARG Q 175 " --> pdb=" O VAL Q 171 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLU Q 176 " --> pdb=" O HIS Q 172 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLN Q 177 " --> pdb=" O LYS Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 189 removed outlier: 3.588A pdb=" N ARG Q 188 " --> pdb=" O GLY Q 184 " (cutoff:3.500A) Processing helix chain 'Q' and resid 203 through 213 Processing helix chain 'R' and resid 25 through 38 removed outlier: 3.560A pdb=" N ASN R 34 " --> pdb=" O PHE R 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE R 36 " --> pdb=" O THR R 32 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN R 37 " --> pdb=" O ALA R 33 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLY R 38 " --> pdb=" O ASN R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 54 removed outlier: 3.516A pdb=" N ALA R 53 " --> pdb=" O ARG R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 77 removed outlier: 4.825A pdb=" N LYS R 74 " --> pdb=" O THR R 70 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TRP R 76 " --> pdb=" O GLN R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 106 removed outlier: 3.828A pdb=" N VAL R 88 " --> pdb=" O PRO R 84 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN R 97 " --> pdb=" O SER R 93 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS R 105 " --> pdb=" O ASN R 101 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY R 106 " --> pdb=" O ALA R 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 35 through 50 Processing helix chain 'S' and resid 100 through 116 Processing helix chain 'S' and resid 119 through 124 removed outlier: 5.062A pdb=" N GLU S 124 " --> pdb=" O TYR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 138 through 146 removed outlier: 3.807A pdb=" N SER S 142 " --> pdb=" O ARG S 138 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU S 143 " --> pdb=" O LEU S 139 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR S 144 " --> pdb=" O SER S 140 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS S 145 " --> pdb=" O ILE S 141 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA S 146 " --> pdb=" O SER S 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 138 through 146' Processing helix chain 'T' and resid 4 through 16 removed outlier: 3.873A pdb=" N ALA T 8 " --> pdb=" O LEU T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 23 removed outlier: 5.568A pdb=" N TRP T 23 " --> pdb=" O ARG T 19 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 36 removed outlier: 4.415A pdb=" N ALA T 35 " --> pdb=" O GLU T 31 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASN T 36 " --> pdb=" O ILE T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 48 Processing helix chain 'T' and resid 60 through 73 removed outlier: 3.636A pdb=" N SER T 71 " --> pdb=" O LYS T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 82 removed outlier: 3.501A pdb=" N ARG T 81 " --> pdb=" O GLY T 77 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLU T 82 " --> pdb=" O ALA T 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 77 through 82' Processing helix chain 'T' and resid 84 through 113 Proline residue: T 90 - end of helix removed outlier: 6.310A pdb=" N GLU T 93 " --> pdb=" O MET T 89 " (cutoff:3.500A) Processing helix chain 'T' and resid 116 through 130 removed outlier: 4.158A pdb=" N ARG T 121 " --> pdb=" O ARG T 117 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS T 126 " --> pdb=" O GLU T 122 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS T 128 " --> pdb=" O TYR T 124 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY T 129 " --> pdb=" O VAL T 125 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN T 130 " --> pdb=" O LYS T 126 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 152 removed outlier: 3.575A pdb=" N LEU T 138 " --> pdb=" O ASN T 134 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS T 143 " --> pdb=" O MET T 139 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS T 146 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU T 148 " --> pdb=" O LYS T 144 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS T 149 " --> pdb=" O VAL T 145 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU T 152 " --> pdb=" O GLU T 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 16 removed outlier: 4.574A pdb=" N ALA U 16 " --> pdb=" O ARG U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 32 Processing helix chain 'U' and resid 54 through 59 removed outlier: 6.334A pdb=" N HIS U 58 " --> pdb=" O HIS U 54 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLY U 59 " --> pdb=" O LYS U 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 54 through 59' Processing helix chain 'U' and resid 92 through 97 removed outlier: 4.051A pdb=" N VAL U 96 " --> pdb=" O ARG U 92 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG U 97 " --> pdb=" O PHE U 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 92 through 97' Processing helix chain 'U' and resid 102 through 113 removed outlier: 3.554A pdb=" N LEU U 113 " --> pdb=" O GLN U 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 55 removed outlier: 3.906A pdb=" N PHE V 51 " --> pdb=" O PHE V 47 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN V 52 " --> pdb=" O GLU V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 102 removed outlier: 4.437A pdb=" N PHE V 90 " --> pdb=" O ARG V 86 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS V 91 " --> pdb=" O LYS V 87 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS V 100 " --> pdb=" O LYS V 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 73 removed outlier: 4.319A pdb=" N ARG W 73 " --> pdb=" O PRO W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 129 removed outlier: 4.181A pdb=" N LEU W 127 " --> pdb=" O GLU W 123 " (cutoff:3.500A) Proline residue: W 129 - end of helix Processing helix chain 'W' and resid 130 through 135 Processing helix chain 'X' and resid 110 through 116 removed outlier: 5.284A pdb=" N ARG X 116 " --> pdb=" O PHE X 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 130 removed outlier: 3.528A pdb=" N LYS X 127 " --> pdb=" O LYS X 123 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU X 129 " --> pdb=" O MET X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 155 Processing helix chain 'X' and resid 183 through 192 removed outlier: 3.548A pdb=" N THR X 187 " --> pdb=" O ASP X 183 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY X 192 " --> pdb=" O ALA X 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 47 removed outlier: 3.977A pdb=" N LYS Y 47 " --> pdb=" O MET Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 49 through 54 removed outlier: 4.161A pdb=" N VAL Y 53 " --> pdb=" O ASN Y 49 " (cutoff:3.500A) Proline residue: Y 54 - end of helix No H-bonds generated for 'chain 'Y' and resid 49 through 54' Processing helix chain 'Y' and resid 56 through 63 removed outlier: 3.701A pdb=" N ILE Y 62 " --> pdb=" O THR Y 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN Y 63 " --> pdb=" O TYR Y 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 19 removed outlier: 3.584A pdb=" N PHE Z 17 " --> pdb=" O ARG Z 13 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA Z 19 " --> pdb=" O ALA Z 15 " (cutoff:3.500A) Processing helix chain 'Z' and resid 20 through 29 removed outlier: 4.273A pdb=" N ILE Z 26 " --> pdb=" O HIS Z 22 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER Z 29 " --> pdb=" O ARG Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 33 through 41 removed outlier: 4.384A pdb=" N ASN Z 41 " --> pdb=" O ARG Z 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 97 through 102 removed outlier: 3.765A pdb=" N VAL Z 101 " --> pdb=" O HIS Z 97 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLU Z 102 " --> pdb=" O PRO Z 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 97 through 102' Processing helix chain 'Z' and resid 109 through 119 removed outlier: 3.638A pdb=" N LYS Z 119 " --> pdb=" O ILE Z 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 66 removed outlier: 4.199A pdb=" N ARG a 63 " --> pdb=" O ARG a 59 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARG a 64 " --> pdb=" O THR a 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG a 66 " --> pdb=" O GLN a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 75 through 80 removed outlier: 4.148A pdb=" N PHE a 79 " --> pdb=" O ASN a 75 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU a 80 " --> pdb=" O HIS a 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 75 through 80' Processing helix chain 'a' and resid 107 through 122 removed outlier: 3.742A pdb=" N LEU a 114 " --> pdb=" O LEU a 110 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N TYR a 119 " --> pdb=" O PHE a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 124 through 130 removed outlier: 3.553A pdb=" N PHE a 128 " --> pdb=" O ASN a 124 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ARG a 130 " --> pdb=" O TRP a 126 " (cutoff:3.500A) Processing helix chain 'b' and resid 6 through 12 removed outlier: 3.814A pdb=" N HIS b 10 " --> pdb=" O LYS b 6 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG b 12 " --> pdb=" O THR b 8 " (cutoff:3.500A) Processing helix chain 'b' and resid 41 through 49 Processing helix chain 'b' and resid 64 through 69 removed outlier: 3.957A pdb=" N LEU b 68 " --> pdb=" O LYS b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 83 removed outlier: 3.546A pdb=" N LEU b 78 " --> pdb=" O ASN b 74 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ALA b 79 " --> pdb=" O LEU b 75 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS b 80 " --> pdb=" O ASN b 76 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU b 81 " --> pdb=" O ASN b 77 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ALA b 83 " --> pdb=" O ALA b 79 " (cutoff:3.500A) Processing helix chain 'b' and resid 100 through 105 removed outlier: 4.033A pdb=" N ASN b 104 " --> pdb=" O ASP b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 138 removed outlier: 3.816A pdb=" N LYS b 132 " --> pdb=" O LYS b 128 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY b 138 " --> pdb=" O ILE b 134 " (cutoff:3.500A) Processing helix chain 'c' and resid 4 through 16 removed outlier: 3.606A pdb=" N LEU c 10 " --> pdb=" O ASP c 6 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLN c 14 " --> pdb=" O LEU c 10 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN c 15 " --> pdb=" O LEU c 11 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER c 16 " --> pdb=" O VAL c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 43 through 48 removed outlier: 5.720A pdb=" N THR c 48 " --> pdb=" O GLY c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 88 through 99 removed outlier: 4.208A pdb=" N SER c 92 " --> pdb=" O ALA c 88 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA c 97 " --> pdb=" O LYS c 93 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL c 98 " --> pdb=" O ALA c 94 " (cutoff:3.500A) Processing helix chain 'c' and resid 100 through 128 removed outlier: 4.760A pdb=" N SER c 104 " --> pdb=" O PRO c 100 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE c 105 " --> pdb=" O ASP c 101 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG c 108 " --> pdb=" O SER c 104 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA c 114 " --> pdb=" O ALA c 110 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS c 128 " --> pdb=" O ARG c 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 20 removed outlier: 4.822A pdb=" N ASN d 19 " --> pdb=" O LYS d 15 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY d 20 " --> pdb=" O ASN d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 31 removed outlier: 4.695A pdb=" N HIS d 30 " --> pdb=" O PRO d 26 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN d 31 " --> pdb=" O MET d 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 26 through 31' Processing helix chain 'd' and resid 37 through 68 removed outlier: 4.866A pdb=" N ALA d 68 " --> pdb=" O ALA d 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 13 removed outlier: 4.160A pdb=" N GLY e 11 " --> pdb=" O THR e 7 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN e 12 " --> pdb=" O CYS e 8 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY e 13 " --> pdb=" O ARG e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 33 through 39 Processing helix chain 'e' and resid 103 through 108 removed outlier: 5.545A pdb=" N THR e 108 " --> pdb=" O LEU e 104 " (cutoff:3.500A) Processing helix chain 'e' and resid 181 through 193 removed outlier: 3.529A pdb=" N TYR e 187 " --> pdb=" O GLY e 183 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG e 188 " --> pdb=" O ASN e 184 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE e 189 " --> pdb=" O SER e 185 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY e 191 " --> pdb=" O TYR e 187 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS e 192 " --> pdb=" O ARG e 188 " (cutoff:3.500A) Processing helix chain 'e' and resid 200 through 205 removed outlier: 4.912A pdb=" N ASN e 205 " --> pdb=" O GLY e 201 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 18 removed outlier: 5.003A pdb=" N LEU f 17 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Proline residue: f 18 - end of helix No H-bonds generated for 'chain 'f' and resid 13 through 18' Processing helix chain 'f' and resid 111 through 120 removed outlier: 3.813A pdb=" N ARG f 117 " --> pdb=" O GLU f 113 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE f 118 " --> pdb=" O PHE f 114 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR f 119 " --> pdb=" O ARG f 115 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N LYS f 120 " --> pdb=" O ARG f 116 " (cutoff:3.500A) Processing helix chain 'f' and resid 130 through 140 removed outlier: 3.786A pdb=" N ARG f 138 " --> pdb=" O LYS f 134 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR f 139 " --> pdb=" O GLN f 135 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N THR f 140 " --> pdb=" O PHE f 136 " (cutoff:3.500A) Processing helix chain 'f' and resid 141 through 156 Processing helix chain 'f' and resid 167 through 172 Processing helix chain 'f' and resid 192 through 204 Processing helix chain 'f' and resid 209 through 214 removed outlier: 3.829A pdb=" N ILE f 213 " --> pdb=" O ARG f 209 " (cutoff:3.500A) Processing helix chain 'f' and resid 233 through 238 Processing helix chain 'f' and resid 293 through 298 Proline residue: f 298 - end of helix Processing helix chain 'f' and resid 354 through 359 removed outlier: 3.919A pdb=" N GLU f 359 " --> pdb=" O ARG f 355 " (cutoff:3.500A) Processing helix chain 'f' and resid 379 through 388 Processing helix chain 'f' and resid 390 through 403 removed outlier: 4.307A pdb=" N GLU f 399 " --> pdb=" O ILE f 395 " (cutoff:3.500A) Processing helix chain 'g' and resid 14 through 23 removed outlier: 4.464A pdb=" N LEU g 18 " --> pdb=" O THR g 14 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS g 21 " --> pdb=" O GLN g 17 " (cutoff:3.500A) Processing helix chain 'g' and resid 29 through 39 removed outlier: 5.241A pdb=" N LYS g 34 " --> pdb=" O LYS g 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 51 through 66 removed outlier: 3.596A pdb=" N THR g 63 " --> pdb=" O GLU g 59 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS g 66 " --> pdb=" O CYS g 62 " (cutoff:3.500A) Processing helix chain 'h' and resid 15 through 42 removed outlier: 3.724A pdb=" N LYS h 28 " --> pdb=" O ILE h 24 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP h 31 " --> pdb=" O ARG h 27 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG h 37 " --> pdb=" O ARG h 33 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL h 38 " --> pdb=" O ARG h 34 " (cutoff:3.500A) Processing helix chain 'h' and resid 91 through 97 removed outlier: 3.826A pdb=" N LEU h 95 " --> pdb=" O HIS h 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 100 through 121 removed outlier: 4.842A pdb=" N ALA h 105 " --> pdb=" O PHE h 101 " (cutoff:3.500A) Proline residue: h 106 - end of helix removed outlier: 3.566A pdb=" N ARG h 118 " --> pdb=" O ALA h 114 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU h 119 " --> pdb=" O PHE h 115 " (cutoff:3.500A) Processing helix chain 'h' and resid 128 through 137 removed outlier: 3.611A pdb=" N TYR h 134 " --> pdb=" O SER h 130 " (cutoff:3.500A) Processing helix chain 'i' and resid 22 through 27 removed outlier: 3.792A pdb=" N PHE i 26 " --> pdb=" O LYS i 22 " (cutoff:3.500A) Proline residue: i 27 - end of helix No H-bonds generated for 'chain 'i' and resid 22 through 27' Processing helix chain 'i' and resid 41 through 46 Processing helix chain 'i' and resid 79 through 88 removed outlier: 4.026A pdb=" N LEU i 83 " --> pdb=" O ASN i 79 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR i 84 " --> pdb=" O VAL i 80 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET i 85 " --> pdb=" O GLN i 81 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU i 86 " --> pdb=" O ASP i 82 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N MET i 88 " --> pdb=" O TYR i 84 " (cutoff:3.500A) Processing helix chain 'i' and resid 102 through 117 removed outlier: 3.771A pdb=" N ALA i 108 " --> pdb=" O LYS i 104 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU i 115 " --> pdb=" O ARG i 111 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP i 117 " --> pdb=" O ALA i 113 " (cutoff:3.500A) Processing helix chain 'j' and resid 61 through 69 removed outlier: 3.767A pdb=" N ARG j 66 " --> pdb=" O HIS j 62 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU j 67 " --> pdb=" O THR j 63 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N SER j 69 " --> pdb=" O ALA j 65 " (cutoff:3.500A) Processing helix chain 'j' and resid 70 through 75 removed outlier: 3.984A pdb=" N SER j 74 " --> pdb=" O ARG j 70 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N THR j 75 " --> pdb=" O HIS j 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 70 through 75' Processing helix chain 'j' and resid 84 through 107 removed outlier: 3.554A pdb=" N ARG j 91 " --> pdb=" O GLN j 87 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG j 106 " --> pdb=" O ARG j 102 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA j 107 " --> pdb=" O ILE j 103 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 13 removed outlier: 3.512A pdb=" N ARG k 11 " --> pdb=" O ILE k 7 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS k 13 " --> pdb=" O ASP k 9 " (cutoff:3.500A) Processing helix chain 'k' and resid 14 through 38 removed outlier: 3.570A pdb=" N GLU k 24 " --> pdb=" O LYS k 20 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE k 25 " --> pdb=" O GLN k 21 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN k 31 " --> pdb=" O LYS k 27 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN k 37 " --> pdb=" O ARG k 33 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU k 38 " --> pdb=" O VAL k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 75 removed outlier: 4.796A pdb=" N LEU k 50 " --> pdb=" O GLY k 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER k 54 " --> pdb=" O LEU k 50 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN k 66 " --> pdb=" O LEU k 62 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG k 67 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS k 72 " --> pdb=" O GLU k 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 76 through 81 removed outlier: 4.291A pdb=" N LEU k 81 " --> pdb=" O ARG k 77 " (cutoff:3.500A) Processing helix chain 'k' and resid 84 through 89 Proline residue: k 89 - end of helix Processing helix chain 'k' and resid 92 through 98 Processing helix chain 'k' and resid 100 through 107 removed outlier: 5.190A pdb=" N ARG k 106 " --> pdb=" O ASN k 102 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS k 107 " --> pdb=" O GLU k 103 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 119 removed outlier: 3.869A pdb=" N PHE k 118 " --> pdb=" O MET k 114 " (cutoff:3.500A) Proline residue: k 119 - end of helix Processing helix chain 'l' and resid 14 through 25 removed outlier: 3.730A pdb=" N LYS l 18 " --> pdb=" O ASN l 14 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS l 24 " --> pdb=" O GLN l 20 " (cutoff:3.500A) Processing helix chain 'l' and resid 68 through 76 removed outlier: 3.947A pdb=" N TRP l 74 " --> pdb=" O GLU l 70 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL l 76 " --> pdb=" O ALA l 72 " (cutoff:3.500A) Processing helix chain 'l' and resid 94 through 99 Proline residue: l 99 - end of helix No H-bonds generated for 'chain 'l' and resid 94 through 99' Processing helix chain 'm' and resid 39 through 46 removed outlier: 4.192A pdb=" N TYR m 43 " --> pdb=" O SER m 39 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA m 44 " --> pdb=" O ASN m 40 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU m 45 " --> pdb=" O ASP m 41 " (cutoff:3.500A) Proline residue: m 46 - end of helix No H-bonds generated for 'chain 'm' and resid 39 through 46' Processing helix chain 'm' and resid 47 through 62 removed outlier: 3.552A pdb=" N LEU m 60 " --> pdb=" O ILE m 56 " (cutoff:3.500A) Processing helix chain 'm' and resid 64 through 77 removed outlier: 3.685A pdb=" N LEU m 73 " --> pdb=" O ARG m 69 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL m 76 " --> pdb=" O GLU m 72 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY m 77 " --> pdb=" O LEU m 73 " (cutoff:3.500A) Processing helix chain 'm' and resid 78 through 91 removed outlier: 4.345A pdb=" N LYS m 88 " --> pdb=" O LYS m 84 " (cutoff:3.500A) Processing helix chain 'm' and resid 92 through 108 removed outlier: 3.570A pdb=" N GLU m 105 " --> pdb=" O ALA m 101 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 12 removed outlier: 3.995A pdb=" N GLY n 9 " --> pdb=" O THR n 5 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN n 10 " --> pdb=" O THR n 6 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG n 11 " --> pdb=" O SER n 7 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N HIS n 12 " --> pdb=" O MET n 8 " (cutoff:3.500A) Processing helix chain 'n' and resid 50 through 58 Processing helix chain 'n' and resid 64 through 77 removed outlier: 4.517A pdb=" N GLU n 69 " --> pdb=" O ARG n 65 " (cutoff:3.500A) Processing helix chain 'o' and resid 19 through 35 removed outlier: 3.846A pdb=" N LYS o 28 " --> pdb=" O LYS o 24 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU o 29 " --> pdb=" O ARG o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 73 through 87 removed outlier: 3.950A pdb=" N THR o 78 " --> pdb=" O PRO o 74 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL o 79 " --> pdb=" O ASN o 75 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER o 81 " --> pdb=" O SER o 77 " (cutoff:3.500A) Processing helix chain 'p' and resid 7 through 14 removed outlier: 3.774A pdb=" N PHE p 11 " --> pdb=" O ASN p 7 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA p 13 " --> pdb=" O LYS p 9 " (cutoff:3.500A) Processing helix chain 'p' and resid 49 through 59 removed outlier: 3.722A pdb=" N ALA p 53 " --> pdb=" O ASP p 49 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS p 55 " --> pdb=" O LYS p 51 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE p 56 " --> pdb=" O LYS p 52 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER p 59 " --> pdb=" O LYS p 55 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 21 removed outlier: 5.074A pdb=" N ARG q 21 " --> pdb=" O LEU q 17 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 30 removed outlier: 4.124A pdb=" N ARG q 28 " --> pdb=" O PRO q 24 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU q 29 " --> pdb=" O TYR q 25 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG q 30 " --> pdb=" O TRP q 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 24 through 30' Processing helix chain 'r' and resid 24 through 30 removed outlier: 4.276A pdb=" N THR r 28 " --> pdb=" O PRO r 24 " (cutoff:3.500A) Proline residue: r 30 - end of helix Processing helix chain 'r' and resid 32 through 49 removed outlier: 3.863A pdb=" N LYS r 45 " --> pdb=" O THR r 41 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN r 46 " --> pdb=" O ASN r 42 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER r 47 " --> pdb=" O MET r 43 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG r 48 " --> pdb=" O ALA r 44 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLN r 49 " --> pdb=" O LYS r 45 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 133 removed outlier: 4.048A pdb=" N VAL r 132 " --> pdb=" O ALA r 128 " (cutoff:3.500A) Proline residue: r 133 - end of helix Processing helix chain 'r' and resid 134 through 140 removed outlier: 3.947A pdb=" N GLY r 140 " --> pdb=" O VAL r 136 " (cutoff:3.500A) Processing helix chain 'r' and resid 155 through 160 removed outlier: 4.722A pdb=" N GLY r 159 " --> pdb=" O ASP r 155 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR r 160 " --> pdb=" O ALA r 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 155 through 160' Processing helix chain 'r' and resid 162 through 174 removed outlier: 3.561A pdb=" N ALA r 166 " --> pdb=" O LYS r 162 " (cutoff:3.500A) Processing helix chain 'r' and resid 175 through 186 removed outlier: 3.767A pdb=" N VAL r 182 " --> pdb=" O ASP r 178 " (cutoff:3.500A) Processing helix chain 'r' and resid 192 through 197 removed outlier: 3.806A pdb=" N ARG r 196 " --> pdb=" O ARG r 192 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN r 197 " --> pdb=" O GLY r 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 192 through 197' Processing helix chain 'r' and resid 217 through 223 removed outlier: 5.302A pdb=" N ASN r 221 " --> pdb=" O ARG r 217 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE r 222 " --> pdb=" O ALA r 218 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE r 223 " --> pdb=" O PHE r 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 217 through 223' Processing helix chain 'r' and resid 234 through 240 Proline residue: r 240 - end of helix Processing helix chain 'r' and resid 251 through 263 removed outlier: 3.810A pdb=" N LYS r 257 " --> pdb=" O GLY r 253 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU r 258 " --> pdb=" O ALA r 254 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP r 259 " --> pdb=" O PHE r 255 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER r 260 " --> pdb=" O GLU r 256 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE r 262 " --> pdb=" O LEU r 258 " (cutoff:3.500A) Processing helix chain 'r' and resid 286 through 293 removed outlier: 3.657A pdb=" N ILE r 290 " --> pdb=" O ASP r 286 " (cutoff:3.500A) Processing helix chain 'r' and resid 294 through 301 removed outlier: 4.483A pdb=" N VAL r 299 " --> pdb=" O GLU r 295 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU r 300 " --> pdb=" O VAL r 296 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS r 301 " --> pdb=" O ARG r 297 " (cutoff:3.500A) Processing helix chain 'r' and resid 322 through 331 Proline residue: r 331 - end of helix Processing helix chain 'r' and resid 332 through 341 removed outlier: 3.623A pdb=" N MET r 339 " --> pdb=" O LYS r 335 " (cutoff:3.500A) Processing helix chain 't' and resid 37 through 49 removed outlier: 3.750A pdb=" N ARG t 42 " --> pdb=" O ARG t 38 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLY t 49 " --> pdb=" O ARG t 45 " (cutoff:3.500A) Processing helix chain 'u' and resid 9 through 16 Processing helix chain 'u' and resid 20 through 26 removed outlier: 3.507A pdb=" N GLY u 26 " --> pdb=" O ARG u 22 " (cutoff:3.500A) Processing helix chain 'u' and resid 29 through 38 removed outlier: 3.561A pdb=" N GLN u 35 " --> pdb=" O GLN u 31 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU u 38 " --> pdb=" O ARG u 34 " (cutoff:3.500A) Processing helix chain 'u' and resid 79 through 87 removed outlier: 4.293A pdb=" N LEU u 83 " --> pdb=" O TYR u 79 " (cutoff:3.500A) Proline residue: u 84 - end of helix Processing helix chain 'u' and resid 94 through 113 removed outlier: 4.148A pdb=" N ALA u 100 " --> pdb=" O ALA u 96 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS u 112 " --> pdb=" O ARG u 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU u 113 " --> pdb=" O MET u 109 " (cutoff:3.500A) Processing helix chain 'u' and resid 163 through 176 removed outlier: 3.645A pdb=" N GLY u 167 " --> pdb=" O ALA u 163 " (cutoff:3.500A) Processing helix chain 'u' and resid 197 through 207 removed outlier: 3.995A pdb=" N ASP u 203 " --> pdb=" O LYS u 199 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG u 204 " --> pdb=" O ALA u 200 " (cutoff:3.500A) Processing helix chain 'u' and resid 208 through 214 removed outlier: 3.560A pdb=" N GLU u 212 " --> pdb=" O LEU u 208 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR u 213 " --> pdb=" O HIS u 209 " (cutoff:3.500A) Processing helix chain 'u' and resid 244 through 259 removed outlier: 4.148A pdb=" N MET u 248 " --> pdb=" O GLU u 244 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS u 250 " --> pdb=" O GLU u 246 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP u 259 " --> pdb=" O ALA u 255 " (cutoff:3.500A) Processing helix chain 'v' and resid 78 through 83 removed outlier: 3.950A pdb=" N ILE v 82 " --> pdb=" O ASP v 78 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE v 83 " --> pdb=" O SER v 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 78 through 83' Processing helix chain 'v' and resid 145 through 166 removed outlier: 3.571A pdb=" N ALA v 157 " --> pdb=" O LYS v 153 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA v 158 " --> pdb=" O LYS v 154 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP v 166 " --> pdb=" O ALA v 162 " (cutoff:3.500A) Processing helix chain 'v' and resid 168 through 179 removed outlier: 3.803A pdb=" N LYS v 172 " --> pdb=" O LEU v 168 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA v 173 " --> pdb=" O GLY v 169 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL v 179 " --> pdb=" O TYR v 175 " (cutoff:3.500A) Processing helix chain 'v' and resid 187 through 192 removed outlier: 4.797A pdb=" N ARG v 192 " --> pdb=" O PRO v 188 " (cutoff:3.500A) Processing helix chain 'v' and resid 95 through 100 removed outlier: 4.615A pdb=" N GLY v 98 " --> pdb=" O ASP v 95 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR v 100 " --> pdb=" O SER v 97 " (cutoff:3.500A) Processing helix chain 'w' and resid 28 through 73 removed outlier: 4.200A pdb=" N LYS w 34 " --> pdb=" O ILE w 30 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS w 41 " --> pdb=" O ARG w 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU w 65 " --> pdb=" O LYS w 61 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG w 66 " --> pdb=" O LEU w 62 " (cutoff:3.500A) Processing helix chain 'w' and resid 96 through 107 removed outlier: 3.636A pdb=" N GLN w 104 " --> pdb=" O ARG w 100 " (cutoff:3.500A) Processing helix chain 'w' and resid 120 through 131 removed outlier: 3.883A pdb=" N ALA w 129 " --> pdb=" O ASN w 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL w 130 " --> pdb=" O MET w 126 " (cutoff:3.500A) Processing helix chain 'w' and resid 140 through 150 Processing helix chain 'w' and resid 165 through 174 removed outlier: 3.632A pdb=" N ILE w 169 " --> pdb=" O ASN w 165 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN w 174 " --> pdb=" O GLU w 170 " (cutoff:3.500A) Processing helix chain 'w' and resid 180 through 190 Processing helix chain 'w' and resid 194 through 203 removed outlier: 3.821A pdb=" N GLY w 201 " --> pdb=" O GLU w 197 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N TRP w 203 " --> pdb=" O THR w 199 " (cutoff:3.500A) Processing helix chain 'w' and resid 232 through 242 removed outlier: 4.778A pdb=" N ARG w 236 " --> pdb=" O ALA w 232 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET w 241 " --> pdb=" O PHE w 237 " (cutoff:3.500A) Processing helix chain 'x' and resid 111 through 127 removed outlier: 3.628A pdb=" N ARG x 121 " --> pdb=" O GLN x 117 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN x 124 " --> pdb=" O LYS x 120 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG x 125 " --> pdb=" O ARG x 121 " (cutoff:3.500A) Processing helix chain 'x' and resid 130 through 139 removed outlier: 3.533A pdb=" N GLN x 135 " --> pdb=" O PRO x 131 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE x 136 " --> pdb=" O ALA x 132 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR x 137 " --> pdb=" O LEU x 133 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL x 139 " --> pdb=" O GLN x 135 " (cutoff:3.500A) Processing helix chain 'x' and resid 141 through 156 removed outlier: 3.628A pdb=" N GLU x 147 " --> pdb=" O SER x 143 " (cutoff:3.500A) Proline residue: x 156 - end of helix Processing helix chain 'x' and resid 159 through 168 removed outlier: 3.762A pdb=" N GLN x 165 " --> pdb=" O ARG x 161 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE x 168 " --> pdb=" O ARG x 164 " (cutoff:3.500A) Processing helix chain 'x' and resid 192 through 203 removed outlier: 3.521A pdb=" N ARG x 198 " --> pdb=" O GLN x 194 " (cutoff:3.500A) Processing helix chain 'x' and resid 216 through 231 removed outlier: 4.586A pdb=" N VAL x 220 " --> pdb=" O PRO x 216 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TRP x 222 " --> pdb=" O GLU x 218 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N MET x 223 " --> pdb=" O LEU x 219 " (cutoff:3.500A) Proline residue: x 224 - end of helix Processing helix chain 'x' and resid 239 through 248 Processing helix chain 'x' and resid 261 through 280 removed outlier: 5.059A pdb=" N ALA x 266 " --> pdb=" O ALA x 262 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ALA x 267 " --> pdb=" O GLU x 263 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU x 271 " --> pdb=" O ALA x 267 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA x 277 " --> pdb=" O ARG x 273 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG x 278 " --> pdb=" O SER x 274 " (cutoff:3.500A) Processing helix chain 'x' and resid 282 through 289 removed outlier: 4.081A pdb=" N ARG x 288 " --> pdb=" O ASP x 284 " (cutoff:3.500A) Processing helix chain 'x' and resid 296 through 310 removed outlier: 3.672A pdb=" N ALA x 301 " --> pdb=" O LEU x 297 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU x 302 " --> pdb=" O ARG x 298 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'I' and resid 106 through 109 removed outlier: 5.348A pdb=" N ARG I 106 " --> pdb=" O PRO I 85 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'L' and resid 73 through 78 removed outlier: 4.468A pdb=" N VAL L 73 " --> pdb=" O ILE L 27 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE L 27 " --> pdb=" O VAL L 73 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N CYS L 75 " --> pdb=" O LEU L 25 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU L 25 " --> pdb=" O CYS L 75 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS L 22 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N CYS L 24 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR L 134 " --> pdb=" O CYS L 24 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLY L 106 " --> pdb=" O LEU L 137 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'N' and resid 60 through 64 Processing sheet with id= 4, first strand: chain 'O' and resid 24 through 28 Processing sheet with id= 5, first strand: chain 'P' and resid 11 through 15 removed outlier: 4.370A pdb=" N ARG P 11 " --> pdb=" O VAL P 27 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ARG P 23 " --> pdb=" O ILE P 15 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'P' and resid 28 through 31 removed outlier: 3.649A pdb=" N ASP P 29 " --> pdb=" O LEU P 37 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG P 35 " --> pdb=" O ILE P 31 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'Q' and resid 51 through 55 removed outlier: 6.464A pdb=" N THR Q 51 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL Q 77 " --> pdb=" O LEU Q 55 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLY Q 74 " --> pdb=" O ASP Q 152 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL Q 149 " --> pdb=" O LEU Q 132 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'Q' and resid 133 through 137 removed outlier: 4.013A pdb=" N ASN Q 133 " --> pdb=" O VAL Q 149 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP Q 145 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'R' and resid 13 through 20 removed outlier: 6.256A pdb=" N LYS R 13 " --> pdb=" O GLN R 152 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE R 149 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'R' and resid 116 through 122 Processing sheet with id= 11, first strand: chain 'R' and resid 124 through 131 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'S' and resid 26 through 32 removed outlier: 6.080A pdb=" N VAL S 12 " --> pdb=" O LEU S 61 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG S 14 " --> pdb=" O ASP S 59 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'S' and resid 88 through 97 removed outlier: 4.879A pdb=" N SER S 84 " --> pdb=" O GLY S 88 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET S 92 " --> pdb=" O ILE S 80 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN S 75 " --> pdb=" O ILE S 131 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY S 127 " --> pdb=" O ASP S 79 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'S' and resid 8 through 11 removed outlier: 5.305A pdb=" N HIS S 8 " --> pdb=" O VAL S 66 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS S 64 " --> pdb=" O CYS S 10 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'U' and resid 72 through 79 removed outlier: 3.521A pdb=" N VAL U 91 " --> pdb=" O VAL U 72 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'V' and resid 68 through 72 removed outlier: 7.183A pdb=" N ASN V 75 " --> pdb=" O CYS V 30 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE V 28 " --> pdb=" O LEU V 77 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR V 81 " --> pdb=" O LYS V 24 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP V 115 " --> pdb=" O VAL V 25 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS V 27 " --> pdb=" O ASP V 115 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'W' and resid 34 through 38 removed outlier: 5.885A pdb=" N LYS W 34 " --> pdb=" O CYS W 27 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA W 23 " --> pdb=" O ILE W 38 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASN W 100 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE W 104 " --> pdb=" O ALA W 28 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN W 77 " --> pdb=" O VAL W 105 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP W 58 " --> pdb=" O ILE W 80 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'W' and resid 86 through 89 removed outlier: 3.978A pdb=" N THR W 93 " --> pdb=" O ARG W 89 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'W' and resid 81 through 84 removed outlier: 3.709A pdb=" N ARG W 84 " --> pdb=" O ASP W 99 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP W 99 " --> pdb=" O ARG W 84 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'X' and resid 132 through 137 removed outlier: 6.598A pdb=" N ASN X 132 " --> pdb=" O LEU X 178 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU X 171 " --> pdb=" O ARG X 167 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Y' and resid 3 through 6 removed outlier: 4.607A pdb=" N PHE Y 11 " --> pdb=" O CYS Y 6 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Y' and resid 18 through 22 Processing sheet with id= 23, first strand: chain 'Z' and resid 53 through 56 removed outlier: 3.730A pdb=" N ARG Z 63 " --> pdb=" O VAL Z 55 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Z' and resid 69 through 72 removed outlier: 3.502A pdb=" N VAL Z 76 " --> pdb=" O TYR Z 71 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Z' and resid 82 through 86 removed outlier: 6.095A pdb=" N VAL Z 82 " --> pdb=" O VAL Z 94 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR Z 90 " --> pdb=" O LYS Z 86 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'a' and resid 7 through 12 removed outlier: 4.126A pdb=" N LYS a 8 " --> pdb=" O ILE a 24 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS a 20 " --> pdb=" O VAL a 12 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'a' and resid 26 through 29 removed outlier: 4.370A pdb=" N GLN a 26 " --> pdb=" O LEU a 41 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR a 28 " --> pdb=" O HIS a 39 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'c' and resid 18 through 21 removed outlier: 6.627A pdb=" N PHE c 18 " --> pdb=" O SER c 29 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'c' and resid 49 through 55 removed outlier: 5.664A pdb=" N ILE c 60 " --> pdb=" O MET c 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA c 80 " --> pdb=" O VAL c 62 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'e' and resid 47 through 50 removed outlier: 4.132A pdb=" N THR e 47 " --> pdb=" O ARG e 60 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG e 60 " --> pdb=" O LYS e 46 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL e 44 " --> pdb=" O GLU e 62 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN e 86 " --> pdb=" O VAL e 45 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'e' and resid 110 through 114 removed outlier: 4.393A pdb=" N CYS e 111 " --> pdb=" O ILE e 136 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE e 135 " --> pdb=" O LYS e 149 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ARG e 147 " --> pdb=" O ILE e 137 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG e 145 " --> pdb=" O ASN e 140 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN e 140 " --> pdb=" O ARG e 145 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER e 138 " --> pdb=" O ARG e 147 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'e' and resid 58 through 64 Processing sheet with id= 33, first strand: chain 'e' and resid 145 through 150 removed outlier: 4.256A pdb=" N GLN e 154 " --> pdb=" O LEU e 150 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'f' and resid 40 through 44 removed outlier: 7.921A pdb=" N LYS f 40 " --> pdb=" O GLY f 191 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY f 191 " --> pdb=" O LYS f 40 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN f 187 " --> pdb=" O THR f 44 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N HIS f 182 " --> pdb=" O THR f 166 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE f 160 " --> pdb=" O ILE f 188 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL f 163 " --> pdb=" O VAL f 87 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'f' and resid 53 through 60 removed outlier: 6.719A pdb=" N ILE f 78 " --> pdb=" O ALA f 51 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG f 341 " --> pdb=" O LYS f 50 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL f 342 " --> pdb=" O VAL f 225 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL f 225 " --> pdb=" O VAL f 342 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'f' and resid 98 through 102 removed outlier: 3.965A pdb=" N THR f 95 " --> pdb=" O GLY f 98 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY f 91 " --> pdb=" O ILE f 102 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'f' and resid 289 through 292 Processing sheet with id= 38, first strand: chain 'f' and resid 76 through 80 No H-bonds generated for sheet with id= 38 Processing sheet with id= 39, first strand: chain 'f' and resid 88 through 93 No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'f' and resid 217 through 221 removed outlier: 4.783A pdb=" N GLU f 218 " --> pdb=" O ILE f 287 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'g' and resid 24 through 28 removed outlier: 6.384A pdb=" N LYS g 24 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR g 95 " --> pdb=" O LYS g 24 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL g 91 " --> pdb=" O GLY g 28 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU g 43 " --> pdb=" O ILE g 94 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'h' and resid 124 through 127 removed outlier: 4.639A pdb=" N ASP h 124 " --> pdb=" O PHE h 166 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N HIS h 165 " --> pdb=" O GLU h 156 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG h 148 " --> pdb=" O VAL h 173 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE h 84 " --> pdb=" O ARG h 153 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N THR h 85 " --> pdb=" O THR h 186 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR h 186 " --> pdb=" O THR h 85 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU h 87 " --> pdb=" O LYS h 184 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'i' and resid 72 through 78 Processing sheet with id= 44, first strand: chain 'j' and resid 20 through 25 removed outlier: 4.636A pdb=" N ARG j 20 " --> pdb=" O ARG j 36 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'l' and resid 105 through 113 removed outlier: 4.398A pdb=" N LYS l 78 " --> pdb=" O VAL l 112 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG l 79 " --> pdb=" O TYR l 143 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL l 83 " --> pdb=" O ARG l 139 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG l 139 " --> pdb=" O VAL l 83 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS l 138 " --> pdb=" O LEU l 44 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL l 140 " --> pdb=" O ALA l 42 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LYS l 41 " --> pdb=" O GLU l 64 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'o' and resid 47 through 50 removed outlier: 6.181A pdb=" N ILE o 54 " --> pdb=" O LYS o 50 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLY o 53 " --> pdb=" O GLY o 66 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY o 66 " --> pdb=" O GLY o 53 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS o 62 " --> pdb=" O CYS o 57 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'p' and resid 2 through 5 removed outlier: 3.533A pdb=" N VAL p 47 " --> pdb=" O THR p 32 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'r' and resid 6 through 9 removed outlier: 3.965A pdb=" N GLY r 19 " --> pdb=" O VAL r 9 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'r' and resid 76 through 79 removed outlier: 3.789A pdb=" N ALA r 88 " --> pdb=" O ILE r 78 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'r' and resid 224 through 229 removed outlier: 5.247A pdb=" N PHE r 247 " --> pdb=" O GLY r 205 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 't' and resid 2 through 5 removed outlier: 3.668A pdb=" N TYR t 4 " --> pdb=" O GLU t 92 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 't' and resid 6 through 10 removed outlier: 6.765A pdb=" N LYS t 6 " --> pdb=" O VAL t 25 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL t 25 " --> pdb=" O LYS t 6 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE t 68 " --> pdb=" O LEU t 85 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU t 85 " --> pdb=" O ILE t 68 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'u' and resid 59 through 66 Processing sheet with id= 54, first strand: chain 'v' and resid 35 through 39 removed outlier: 4.128A pdb=" N THR v 35 " --> pdb=" O ILE v 51 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG v 47 " --> pdb=" O ILE v 39 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL v 62 " --> pdb=" O LEU v 52 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'w' and resid 133 through 138 removed outlier: 7.357A pdb=" N TYR w 133 " --> pdb=" O ILE w 89 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY w 137 " --> pdb=" O VAL w 85 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN w 113 " --> pdb=" O ARG w 88 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE w 112 " --> pdb=" O LEU w 207 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'w' and resid 152 through 155 removed outlier: 6.702A pdb=" N GLY w 152 " --> pdb=" O ILE w 163 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'x' and resid 232 through 238 1531 hydrogen bonds defined for protein. 4550 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1846 hydrogen bonds 2954 hydrogen bond angles 0 basepair planarities 762 basepair parallelities 1591 stacking parallelities Total time for adding SS restraints: 94.60 Time building geometry restraints manager: 48.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 9198 1.27 - 1.41: 37302 1.41 - 1.54: 60449 1.54 - 1.68: 5751 1.68 - 1.82: 304 Bond restraints: 113004 Sorted by residual: bond pdb=" P A2M A1674 " pdb=" O5' A2M A1674 " ideal model delta sigma weight residual 1.647 1.530 0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" CA PHE b 16 " pdb=" C PHE b 16 " ideal model delta sigma weight residual 1.523 1.454 0.068 1.23e-02 6.61e+03 3.10e+01 bond pdb=" P A2M A1071 " pdb=" O5' A2M A1071 " ideal model delta sigma weight residual 1.647 1.538 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" P A2M A 775 " pdb=" O5' A2M A 775 " ideal model delta sigma weight residual 1.647 1.539 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" P A2M B 482 " pdb=" O5' A2M B 482 " ideal model delta sigma weight residual 1.647 1.541 0.106 2.00e-02 2.50e+03 2.83e+01 ... (remaining 112999 not shown) Histogram of bond angle deviations from ideal: 82.87 - 98.47: 33 98.47 - 114.07: 87099 114.07 - 129.67: 76647 129.67 - 145.28: 2501 145.28 - 160.88: 21 Bond angle restraints: 166301 Sorted by residual: angle pdb=" O ARG Q 40 " pdb=" C ARG Q 40 " pdb=" CA BARG Q 40 " ideal model delta sigma weight residual 120.55 141.32 -20.77 1.06e+00 8.90e-01 3.84e+02 angle pdb=" O ARG Q 40 " pdb=" C ARG Q 40 " pdb=" CA AARG Q 40 " ideal model delta sigma weight residual 120.55 140.91 -20.36 1.06e+00 8.90e-01 3.69e+02 angle pdb=" C1' OMG A1075 " pdb=" N9 OMG A1075 " pdb=" C8 OMG A1075 " ideal model delta sigma weight residual 142.82 89.78 53.04 3.00e+00 1.11e-01 3.13e+02 angle pdb=" C1' OMG A1075 " pdb=" N9 OMG A1075 " pdb=" C4 OMG A1075 " ideal model delta sigma weight residual 108.29 160.88 -52.59 3.00e+00 1.11e-01 3.07e+02 angle pdb=" C1' OMG B1492 " pdb=" N9 OMG B1492 " pdb=" C4 OMG B1492 " ideal model delta sigma weight residual 108.29 158.08 -49.79 3.00e+00 1.11e-01 2.75e+02 ... (remaining 166296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 63502 35.91 - 71.82: 7013 71.82 - 107.74: 850 107.74 - 143.65: 36 143.65 - 179.56: 57 Dihedral angle restraints: 71458 sinusoidal: 55944 harmonic: 15514 Sorted by residual: dihedral pdb=" C5' A A 442 " pdb=" C4' A A 442 " pdb=" C3' A A 442 " pdb=" O3' A A 442 " ideal model delta sinusoidal sigma weight residual 147.00 78.01 68.99 1 8.00e+00 1.56e-02 9.62e+01 dihedral pdb=" C4' A A 442 " pdb=" C3' A A 442 " pdb=" C2' A A 442 " pdb=" C1' A A 442 " ideal model delta sinusoidal sigma weight residual -35.00 31.44 -66.44 1 8.00e+00 1.56e-02 9.00e+01 dihedral pdb=" O4' U B 678 " pdb=" C1' U B 678 " pdb=" N1 U B 678 " pdb=" C2 U B 678 " ideal model delta sinusoidal sigma weight residual -160.00 15.38 -175.38 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 71455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.402: 20518 0.402 - 0.804: 7 0.804 - 1.205: 0 1.205 - 1.607: 0 1.607 - 2.009: 1 Chirality restraints: 20526 Sorted by residual: chirality pdb=" P A A1579 " pdb=" OP1 A A1579 " pdb=" OP2 A A1579 " pdb=" O5' A A1579 " both_signs ideal model delta sigma weight residual True 2.41 0.40 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CA BARG Q 40 " pdb=" N ARG Q 40 " pdb=" C ARG Q 40 " pdb=" CB BARG Q 40 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" C3' A2M A 794 " pdb=" C4' A2M A 794 " pdb=" O3' A2M A 794 " pdb=" C2' A2M A 794 " both_signs ideal model delta sigma weight residual False -2.56 -1.99 -0.57 2.00e-01 2.50e+01 8.10e+00 ... (remaining 20523 not shown) Planarity restraints: 10405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG B1107 " 0.133 2.00e-02 2.50e+03 6.91e-01 1.07e+04 pdb=" C4' 7MG B1107 " 0.485 2.00e-02 2.50e+03 pdb=" O4' 7MG B1107 " 0.698 2.00e-02 2.50e+03 pdb=" C3' 7MG B1107 " -0.576 2.00e-02 2.50e+03 pdb=" O3' 7MG B1107 " -0.796 2.00e-02 2.50e+03 pdb=" C2' 7MG B1107 " -0.111 2.00e-02 2.50e+03 pdb=" O2' 7MG B1107 " 1.140 2.00e-02 2.50e+03 pdb=" C1' 7MG B1107 " 0.149 2.00e-02 2.50e+03 pdb=" N9 7MG B1107 " -1.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG B1138 " 0.091 2.00e-02 2.50e+03 6.46e-01 9.39e+03 pdb=" C4' 7MG B1138 " 0.487 2.00e-02 2.50e+03 pdb=" O4' 7MG B1138 " 0.736 2.00e-02 2.50e+03 pdb=" C3' 7MG B1138 " -0.571 2.00e-02 2.50e+03 pdb=" O3' 7MG B1138 " -0.694 2.00e-02 2.50e+03 pdb=" C2' 7MG B1138 " -0.177 2.00e-02 2.50e+03 pdb=" O2' 7MG B1138 " 1.004 2.00e-02 2.50e+03 pdb=" C1' 7MG B1138 " 0.169 2.00e-02 2.50e+03 pdb=" N9 7MG B1138 " -1.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG B 657 " 0.097 2.00e-02 2.50e+03 6.45e-01 9.36e+03 pdb=" C4' 7MG B 657 " 0.425 2.00e-02 2.50e+03 pdb=" O4' 7MG B 657 " 0.627 2.00e-02 2.50e+03 pdb=" C3' 7MG B 657 " -0.628 2.00e-02 2.50e+03 pdb=" O3' 7MG B 657 " -0.734 2.00e-02 2.50e+03 pdb=" C2' 7MG B 657 " -0.114 2.00e-02 2.50e+03 pdb=" O2' 7MG B 657 " 1.089 2.00e-02 2.50e+03 pdb=" C1' 7MG B 657 " 0.227 2.00e-02 2.50e+03 pdb=" N9 7MG B 657 " -0.989 2.00e-02 2.50e+03 ... (remaining 10402 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.65: 8 1.65 - 2.46: 1142 2.46 - 3.28: 119582 3.28 - 4.09: 361341 4.09 - 4.90: 556965 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1039038 Sorted by model distance: nonbonded pdb=" CH2 TRP P 139 " pdb=" OG SER l 27 " model vdw 0.838 3.340 nonbonded pdb=" CH2 TRP P 139 " pdb=" CB SER l 27 " model vdw 1.046 3.740 nonbonded pdb=" OP1 U B1629 " pdb=" CD ARG f 138 " model vdw 1.073 3.440 nonbonded pdb=" OP1 A B1593 " pdb=" NH1 ARG f 148 " model vdw 1.173 2.520 nonbonded pdb=" O2 U B1644 " pdb=" NH2 ARG f 209 " model vdw 1.215 2.520 ... (remaining 1039033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 7.390 Check model and map are aligned: 1.150 Set scattering table: 0.720 Process input model: 329.720 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.320 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: 0.030 Load rotamer database and sin/cos tables:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 354.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.117 113004 Z= 0.782 Angle : 1.446 53.043 166301 Z= 0.752 Chirality : 0.059 2.009 20526 Planarity : 0.037 0.691 10405 Dihedral : 23.282 179.559 61420 Min Nonbonded Distance : 0.838 Molprobity Statistics. All-atom Clashscore : 36.80 Ramachandran Plot: Outliers : 1.22 % Allowed : 5.36 % Favored : 93.42 % Rotamer: Outliers : 0.69 % Allowed : 1.88 % Favored : 97.43 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.59 % 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: -2.36 (0.11), residues: 5247 helix: -3.65 (0.07), residues: 1753 sheet: -3.00 (0.17), residues: 708 loop : 0.58 (0.13), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.005 TRP O 166 HIS 0.022 0.004 HIS b 25 PHE 0.061 0.004 PHE R 60 TYR 0.071 0.004 TYR w 227 ARG 0.026 0.003 ARG n 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1417 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1387 time to evaluate : 5.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 180 ARG cc_start: 0.7766 (ttp-170) cc_final: 0.7333 (ttm-80) REVERT: P 82 LYS cc_start: 0.6846 (mtmm) cc_final: 0.6208 (mtmm) REVERT: P 91 LYS cc_start: 0.7787 (pttp) cc_final: 0.7552 (tttm) REVERT: Q 101 LYS cc_start: 0.7847 (tttp) cc_final: 0.7521 (tptp) REVERT: S 30 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6400 (tp30) REVERT: S 128 VAL cc_start: 0.8367 (t) cc_final: 0.8133 (p) REVERT: S 141 ILE cc_start: 0.7404 (pp) cc_final: 0.7171 (pp) REVERT: T 85 ARG cc_start: 0.7870 (ttp-170) cc_final: 0.7544 (ttt90) REVERT: V 95 LYS cc_start: 0.8484 (mtmt) cc_final: 0.7964 (mtpt) REVERT: V 101 LYS cc_start: 0.7374 (mmtm) cc_final: 0.7031 (mmtp) REVERT: W 111 MET cc_start: 0.7804 (ptm) cc_final: 0.7295 (ttm) REVERT: X 127 LYS cc_start: 0.8186 (mttm) cc_final: 0.7939 (mtmm) REVERT: X 163 ASN cc_start: 0.7930 (p0) cc_final: 0.7651 (p0) REVERT: f 69 LYS cc_start: 0.5984 (OUTLIER) cc_final: 0.5493 (tmtt) REVERT: f 185 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7685 (mt-10) REVERT: f 296 MET cc_start: 0.8042 (mtm) cc_final: 0.7810 (mtt) REVERT: f 343 ILE cc_start: 0.6980 (pt) cc_final: 0.6568 (pt) REVERT: f 359 GLU cc_start: 0.7667 (tt0) cc_final: 0.7239 (tp30) REVERT: i 50 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8384 (mm110) REVERT: j 20 ARG cc_start: 0.7901 (mmt180) cc_final: 0.7689 (mmt90) REVERT: j 30 ARG cc_start: 0.7745 (mtp-110) cc_final: 0.7456 (mtt90) REVERT: l 69 LYS cc_start: 0.8215 (tttp) cc_final: 0.8013 (ttpt) REVERT: r 85 THR cc_start: 0.8421 (p) cc_final: 0.7912 (t) REVERT: t 24 LYS cc_start: 0.7390 (tptp) cc_final: 0.7185 (tmtt) REVERT: u 68 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7797 (mttp) REVERT: u 202 ARG cc_start: 0.5576 (ttt-90) cc_final: 0.5147 (tpp80) REVERT: w 175 ASN cc_start: 0.7750 (t0) cc_final: 0.7501 (t160) REVERT: x 300 ARG cc_start: 0.7094 (tpp-160) cc_final: 0.6500 (ttm110) outliers start: 30 outliers final: 8 residues processed: 1410 average time/residue: 2.2018 time to fit residues: 4069.4685 Evaluate side-chains 952 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 943 time to evaluate : 5.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 20 CYS Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain Y residue 28 SER Chi-restraints excluded: chain f residue 65 SER Chi-restraints excluded: chain f residue 69 LYS Chi-restraints excluded: chain g residue 42 LYS Chi-restraints excluded: chain g residue 95 THR Chi-restraints excluded: chain h residue 84 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 681 optimal weight: 5.9990 chunk 611 optimal weight: 5.9990 chunk 339 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 412 optimal weight: 5.9990 chunk 326 optimal weight: 5.9990 chunk 632 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 384 optimal weight: 8.9990 chunk 470 optimal weight: 6.9990 chunk 732 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 38 GLN I 45 ASN ** I 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN N 33 GLN N 108 ASN ** O 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 ASN O 143 GLN P 5 ASN P 112 GLN P 131 ASN Q 113 ASN R 28 ASN ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 116 HIS R 118 GLN R 121 GLN R 147 GLN R 152 GLN S 107 GLN S 116 HIS S 121 HIS ** S 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 3 HIS ** U 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 77 ASN U 107 GLN V 58 ASN X 83 GLN X 131 ASN X 156 GLN X 189 ASN Z 78 HIS Z 97 HIS Z 100 ASN ** a 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 60 HIS b 104 ASN b 144 GLN c 34 ASN d 9 ASN d 16 ASN d 19 ASN d 30 HIS e 17 GLN e 38 HIS ** e 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 115 ASN ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 GLN f 135 GLN f 173 ASN ** f 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 216 GLN f 229 HIS f 279 HIS f 289 GLN ** f 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 385 GLN h 125 ASN h 137 HIS ** i 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 89 GLN ** j 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 51 HIS l 57 ASN l 116 HIS m 40 ASN n 10 GLN ** n 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 93 ASN r 183 ASN t 73 GLN t 76 ASN ** t 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 17 GLN u 184 ASN v 58 ASN ** v 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 157 ASN w 165 ASN w 194 HIS Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 113004 Z= 0.347 Angle : 1.027 26.410 166301 Z= 0.545 Chirality : 0.047 2.050 20526 Planarity : 0.011 0.148 10405 Dihedral : 24.966 179.551 50317 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.58 % Favored : 96.23 % Rotamer: Outliers : 5.24 % Allowed : 13.50 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.11), residues: 5247 helix: -1.82 (0.10), residues: 1853 sheet: -2.57 (0.17), residues: 727 loop : -0.08 (0.12), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP P 139 HIS 0.013 0.002 HIS e 19 PHE 0.039 0.003 PHE a 115 TYR 0.029 0.003 TYR w 227 ARG 0.010 0.001 ARG i 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1066 time to evaluate : 4.942 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: I 27 LYS cc_start: 0.8087 (mttm) cc_final: 0.7810 (mttt) REVERT: I 180 ARG cc_start: 0.7625 (ttp-170) cc_final: 0.7181 (tpp-160) REVERT: N 78 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6889 (tmt90) REVERT: O 105 MET cc_start: 0.8585 (mtt) cc_final: 0.8354 (mtt) REVERT: P 57 GLU cc_start: 0.7583 (tt0) cc_final: 0.7349 (tt0) REVERT: P 82 LYS cc_start: 0.7155 (mtmm) cc_final: 0.6904 (pttt) REVERT: P 91 LYS cc_start: 0.7871 (pttp) cc_final: 0.7595 (tttm) REVERT: Q 39 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7759 (mp10) REVERT: Q 101 LYS cc_start: 0.7700 (tttp) cc_final: 0.7350 (tptp) REVERT: S 7 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7586 (mmt90) REVERT: S 30 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6523 (tp30) REVERT: S 128 VAL cc_start: 0.8249 (t) cc_final: 0.7988 (p) REVERT: S 129 LYS cc_start: 0.7474 (mtmt) cc_final: 0.7121 (ttmm) REVERT: T 20 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.7238 (t-170) REVERT: T 85 ARG cc_start: 0.7775 (ttp-170) cc_final: 0.7477 (ttt90) REVERT: T 86 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: T 114 LYS cc_start: 0.6657 (mtpt) cc_final: 0.6291 (mttt) REVERT: U 35 LYS cc_start: 0.8341 (ptpt) cc_final: 0.8139 (ptmt) REVERT: U 38 ASP cc_start: 0.7919 (m-30) cc_final: 0.7709 (m-30) REVERT: V 27 LYS cc_start: 0.7828 (mtpm) cc_final: 0.7579 (mttt) REVERT: V 100 LYS cc_start: 0.7675 (mmmm) cc_final: 0.7390 (mmmt) REVERT: X 113 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7933 (ttt180) REVERT: c 59 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.5524 (mpt180) REVERT: c 78 LYS cc_start: 0.7894 (ptmm) cc_final: 0.6744 (tppt) REVERT: f 113 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: f 185 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7801 (mt-10) REVERT: f 209 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7039 (mmm160) REVERT: f 296 MET cc_start: 0.8176 (mtm) cc_final: 0.7690 (mtt) REVERT: f 359 GLU cc_start: 0.7612 (tt0) cc_final: 0.7182 (tp30) REVERT: g 27 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6632 (tt) REVERT: h 84 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7747 (pp) REVERT: h 120 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7727 (mmt) REVERT: h 185 VAL cc_start: 0.7398 (t) cc_final: 0.7112 (m) REVERT: i 50 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8388 (mm110) REVERT: i 84 TYR cc_start: 0.7883 (m-80) cc_final: 0.7423 (m-80) REVERT: i 91 ARG cc_start: 0.7710 (mtp85) cc_final: 0.6859 (mmp80) REVERT: j 30 ARG cc_start: 0.7712 (mtp-110) cc_final: 0.7212 (mtt90) REVERT: k 72 LYS cc_start: 0.8185 (mtmt) cc_final: 0.7894 (mmtm) REVERT: l 82 TYR cc_start: 0.8977 (t80) cc_final: 0.8636 (t80) REVERT: l 114 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8352 (ptm160) REVERT: m 69 ARG cc_start: 0.6845 (ttt90) cc_final: 0.6397 (tpp80) REVERT: o 13 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7574 (ptt90) REVERT: q 13 TYR cc_start: 0.8761 (m-80) cc_final: 0.8201 (m-80) REVERT: q 19 GLN cc_start: 0.7984 (tt0) cc_final: 0.7716 (mt0) REVERT: r 16 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7377 (ptmt) REVERT: r 33 HIS cc_start: 0.7876 (t70) cc_final: 0.7412 (p-80) REVERT: r 187 GLU cc_start: 0.7506 (pm20) cc_final: 0.6531 (tp30) REVERT: r 203 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7301 (mtp180) REVERT: r 204 ARG cc_start: 0.7842 (mmt180) cc_final: 0.7563 (mmt180) REVERT: u 202 ARG cc_start: 0.5798 (ttt-90) cc_final: 0.5385 (tpp80) REVERT: x 102 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7186 (ptp90) REVERT: x 300 ARG cc_start: 0.7219 (tpp-160) cc_final: 0.6809 (ttm110) outliers start: 236 outliers final: 78 residues processed: 1173 average time/residue: 2.0449 time to fit residues: 3195.1884 Evaluate side-chains 1010 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 915 time to evaluate : 5.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain N residue 6 ASN Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain N residue 78 ARG Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain Q residue 39 GLN Chi-restraints excluded: chain Q residue 144 VAL Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain S residue 7 ARG Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain T residue 140 GLU Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 98 LYS Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain X residue 113 ARG Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 28 SER Chi-restraints excluded: chain Z residue 29 SER Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 39 THR Chi-restraints excluded: chain c residue 59 ARG Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 112 ILE Chi-restraints excluded: chain e residue 195 CYS Chi-restraints excluded: chain e residue 207 VAL Chi-restraints excluded: chain f residue 66 LYS Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 113 GLU Chi-restraints excluded: chain f residue 209 ARG Chi-restraints excluded: chain f residue 269 VAL Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 95 LEU Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain i residue 15 THR Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 32 SER Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 105 SER Chi-restraints excluded: chain k residue 20 LYS Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 69 SER Chi-restraints excluded: chain l residue 103 SER Chi-restraints excluded: chain l residue 114 ARG Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain m residue 20 ILE Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain p residue 23 VAL Chi-restraints excluded: chain r residue 8 SER Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 106 ILE Chi-restraints excluded: chain r residue 176 VAL Chi-restraints excluded: chain r residue 203 ARG Chi-restraints excluded: chain r residue 288 THR Chi-restraints excluded: chain r residue 317 THR Chi-restraints excluded: chain t residue 2 VAL Chi-restraints excluded: chain t residue 35 LEU Chi-restraints excluded: chain u residue 160 THR Chi-restraints excluded: chain u residue 256 ILE Chi-restraints excluded: chain v residue 62 VAL Chi-restraints excluded: chain v residue 103 ILE Chi-restraints excluded: chain v residue 154 LYS Chi-restraints excluded: chain w residue 89 ILE Chi-restraints excluded: chain w residue 180 CYS Chi-restraints excluded: chain x residue 102 ARG Chi-restraints excluded: chain x residue 238 LYS Chi-restraints excluded: chain x residue 253 THR Chi-restraints excluded: chain x residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 407 optimal weight: 7.9990 chunk 227 optimal weight: 20.0000 chunk 609 optimal weight: 0.5980 chunk 499 optimal weight: 3.9990 chunk 202 optimal weight: 30.0000 chunk 734 optimal weight: 8.9990 chunk 793 optimal weight: 5.9990 chunk 653 optimal weight: 0.5980 chunk 728 optimal weight: 5.9990 chunk 250 optimal weight: 20.0000 chunk 588 optimal weight: 0.8980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 38 GLN I 142 ASN ** I 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN N 108 ASN O 58 GLN O 68 ASN O 187 HIS P 5 ASN P 112 GLN P 131 ASN ** Q 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 GLN Q 177 GLN Q 192 HIS R 118 GLN ** S 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 77 ASN V 52 GLN X 83 GLN ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 100 ASN a 62 GLN ** a 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 ASN d 16 ASN d 50 ASN e 17 GLN e 100 ASN ** e 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 360 GLN ** f 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 385 GLN ** i 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 42 ASN r 183 ASN u 17 GLN ** v 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 117 GLN ** x 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 270 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 113004 Z= 0.192 Angle : 0.879 26.842 166301 Z= 0.486 Chirality : 0.040 2.024 20526 Planarity : 0.009 0.128 10405 Dihedral : 24.607 179.848 50305 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.32 % Favored : 96.61 % Rotamer: Outliers : 5.15 % Allowed : 16.64 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.11), residues: 5247 helix: -0.65 (0.11), residues: 1875 sheet: -2.16 (0.18), residues: 716 loop : -0.27 (0.12), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 44 HIS 0.011 0.001 HIS Q 187 PHE 0.032 0.002 PHE a 115 TYR 0.023 0.002 TYR R 139 ARG 0.014 0.001 ARG i 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1242 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1010 time to evaluate : 5.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 27 LYS cc_start: 0.8062 (mttm) cc_final: 0.7736 (mttt) REVERT: I 136 VAL cc_start: 0.7887 (p) cc_final: 0.7525 (m) REVERT: I 147 ARG cc_start: 0.8682 (mtt90) cc_final: 0.8454 (mtm180) REVERT: I 180 ARG cc_start: 0.7645 (ttp-170) cc_final: 0.7399 (ttm-80) REVERT: L 166 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.5896 (tpp) REVERT: O 74 GLN cc_start: 0.7965 (mt0) cc_final: 0.7722 (mt0) REVERT: O 103 ARG cc_start: 0.8301 (ttp80) cc_final: 0.8101 (ttp-170) REVERT: P 8 ARG cc_start: 0.7896 (ptt90) cc_final: 0.7623 (ppt170) REVERT: P 48 ARG cc_start: 0.7135 (ttm170) cc_final: 0.6932 (ttm110) REVERT: Q 22 TYR cc_start: 0.8647 (m-80) cc_final: 0.7839 (m-80) REVERT: R 14 SER cc_start: 0.8167 (OUTLIER) cc_final: 0.7878 (m) REVERT: R 111 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8403 (ttmm) REVERT: S 7 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7422 (mmm160) REVERT: S 129 LYS cc_start: 0.7129 (mtmt) cc_final: 0.6915 (ttmm) REVERT: T 20 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7358 (t-170) REVERT: T 85 ARG cc_start: 0.7649 (ttp-170) cc_final: 0.7355 (ttt90) REVERT: T 114 LYS cc_start: 0.6655 (mtpt) cc_final: 0.6202 (mtpp) REVERT: U 38 ASP cc_start: 0.7858 (m-30) cc_final: 0.7615 (m-30) REVERT: V 27 LYS cc_start: 0.7916 (mtpm) cc_final: 0.7711 (mttt) REVERT: V 92 TYR cc_start: 0.8328 (t80) cc_final: 0.8081 (t80) REVERT: V 100 LYS cc_start: 0.7674 (mmmm) cc_final: 0.7290 (mmmt) REVERT: W 111 MET cc_start: 0.7535 (ptm) cc_final: 0.7120 (ttm) REVERT: Z 112 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6385 (ttt90) REVERT: a 45 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7805 (mmm) REVERT: a 64 ARG cc_start: 0.7365 (ttt90) cc_final: 0.4920 (ttt180) REVERT: c 78 LYS cc_start: 0.8027 (ptmm) cc_final: 0.6849 (tppt) REVERT: e 76 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7641 (pmm) REVERT: e 112 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7689 (pp) REVERT: e 245 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7883 (ttt-90) REVERT: f 209 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7143 (mmm160) REVERT: f 296 MET cc_start: 0.8157 (mtm) cc_final: 0.7813 (mtt) REVERT: f 325 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8460 (mtt90) REVERT: f 356 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7739 (mtpt) REVERT: f 359 GLU cc_start: 0.7625 (tt0) cc_final: 0.7206 (tp30) REVERT: g 27 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6794 (tt) REVERT: h 84 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7666 (pp) REVERT: h 120 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7506 (mmt) REVERT: i 91 ARG cc_start: 0.7734 (mtp85) cc_final: 0.6800 (mmp80) REVERT: j 30 ARG cc_start: 0.7601 (mtp-110) cc_final: 0.7370 (mtm-85) REVERT: j 86 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: k 26 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7802 (mttt) REVERT: k 63 ASN cc_start: 0.8448 (m-40) cc_final: 0.8199 (m110) REVERT: k 72 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7929 (mtpp) REVERT: k 110 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7532 (ttt180) REVERT: l 82 TYR cc_start: 0.8923 (t80) cc_final: 0.8592 (t80) REVERT: l 114 ARG cc_start: 0.8407 (ptt90) cc_final: 0.8180 (ppp80) REVERT: o 13 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7576 (ptt90) REVERT: q 13 TYR cc_start: 0.8738 (m-80) cc_final: 0.8324 (m-80) REVERT: r 16 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6336 (tppt) REVERT: r 33 HIS cc_start: 0.7919 (t70) cc_final: 0.7434 (p-80) REVERT: r 203 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7299 (mtp180) REVERT: t 11 TYR cc_start: 0.7990 (t80) cc_final: 0.7573 (t80) REVERT: u 68 LYS cc_start: 0.8014 (mmmt) cc_final: 0.7688 (mttm) REVERT: u 202 ARG cc_start: 0.5669 (ttt-90) cc_final: 0.5358 (tpp-160) REVERT: v 103 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7318 (tp) REVERT: x 102 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.6418 (ptp90) REVERT: x 126 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7318 (tpp80) REVERT: x 154 LYS cc_start: 0.7549 (mtpt) cc_final: 0.7217 (mtmt) REVERT: x 161 ARG cc_start: 0.5541 (ttp80) cc_final: 0.5179 (tpp80) REVERT: x 272 ILE cc_start: 0.8145 (mt) cc_final: 0.7789 (mt) REVERT: x 300 ARG cc_start: 0.7247 (tpp-160) cc_final: 0.6967 (ttm110) outliers start: 232 outliers final: 78 residues processed: 1122 average time/residue: 2.0031 time to fit residues: 3012.7606 Evaluate side-chains 1001 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 899 time to evaluate : 5.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 166 MET Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 111 LYS Chi-restraints excluded: chain S residue 7 ARG Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 139 MET Chi-restraints excluded: chain T residue 140 GLU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain W residue 130 LYS Chi-restraints excluded: chain X residue 120 THR Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 163 ASN Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain X residue 185 LEU Chi-restraints excluded: chain Z residue 29 SER Chi-restraints excluded: chain Z residue 94 VAL Chi-restraints excluded: chain Z residue 112 ARG Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 45 MET Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 39 THR Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 76 MET Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 112 ILE Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 195 CYS Chi-restraints excluded: chain e residue 207 VAL Chi-restraints excluded: chain e residue 245 ARG Chi-restraints excluded: chain f residue 66 LYS Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 203 LEU Chi-restraints excluded: chain f residue 209 ARG Chi-restraints excluded: chain f residue 223 CYS Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 325 ARG Chi-restraints excluded: chain f residue 331 LEU Chi-restraints excluded: chain f residue 335 VAL Chi-restraints excluded: chain f residue 345 LEU Chi-restraints excluded: chain f residue 362 THR Chi-restraints excluded: chain f residue 384 SER Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 50 CYS Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 168 THR Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain i residue 15 THR Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 105 SER Chi-restraints excluded: chain j residue 86 GLU Chi-restraints excluded: chain k residue 26 LYS Chi-restraints excluded: chain k residue 69 SER Chi-restraints excluded: chain k residue 110 ARG Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 68 THR Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 147 SER Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 43 SER Chi-restraints excluded: chain n residue 77 HIS Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain p residue 23 VAL Chi-restraints excluded: chain r residue 8 SER Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 146 VAL Chi-restraints excluded: chain r residue 203 ARG Chi-restraints excluded: chain r residue 260 SER Chi-restraints excluded: chain r residue 288 THR Chi-restraints excluded: chain t residue 35 LEU Chi-restraints excluded: chain u residue 154 VAL Chi-restraints excluded: chain u residue 256 ILE Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 103 ILE Chi-restraints excluded: chain v residue 154 LYS Chi-restraints excluded: chain x residue 102 ARG Chi-restraints excluded: chain x residue 126 ARG Chi-restraints excluded: chain x residue 275 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 725 optimal weight: 20.0000 chunk 551 optimal weight: 10.0000 chunk 381 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 350 optimal weight: 8.9990 chunk 492 optimal weight: 20.0000 chunk 736 optimal weight: 10.0000 chunk 780 optimal weight: 0.7980 chunk 384 optimal weight: 10.0000 chunk 698 optimal weight: 0.8980 chunk 210 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN I 50 GLN ** I 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN N 23 GLN N 33 GLN O 20 HIS O 58 GLN P 112 GLN Q 50 HIS ** S 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 137 ASN ** U 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 GLN ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 100 ASN ** a 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 144 GLN c 20 GLN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 47 ASN d 16 ASN d 19 ASN e 17 GLN ** e 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 173 ASN ** f 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 326 ASN ** f 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 385 GLN ** i 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN ** n 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 HIS r 33 HIS r 183 ASN ** t 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 270 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 113004 Z= 0.260 Angle : 0.888 26.510 166301 Z= 0.486 Chirality : 0.042 2.029 20526 Planarity : 0.010 0.132 10405 Dihedral : 24.460 179.856 50304 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.53 % Rotamer: Outliers : 5.51 % Allowed : 18.87 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.84 (0.11), residues: 5247 helix: -0.19 (0.12), residues: 1879 sheet: -1.85 (0.18), residues: 697 loop : -0.30 (0.12), residues: 2671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 123 HIS 0.009 0.001 HIS Q 187 PHE 0.039 0.002 PHE a 115 TYR 0.026 0.002 TYR w 227 ARG 0.012 0.001 ARG r 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 922 time to evaluate : 5.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6724 (mmt-90) REVERT: I 27 LYS cc_start: 0.8082 (mttm) cc_final: 0.7805 (mtmt) REVERT: I 180 ARG cc_start: 0.7650 (ttp-170) cc_final: 0.7409 (ttm-80) REVERT: L 166 MET cc_start: 0.6107 (OUTLIER) cc_final: 0.5867 (tpp) REVERT: N 204 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7052 (mtm110) REVERT: O 86 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7934 (pp) REVERT: O 114 GLN cc_start: 0.8453 (mt0) cc_final: 0.8139 (mt0) REVERT: P 100 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6564 (tmm160) REVERT: P 107 ASP cc_start: 0.8411 (t70) cc_final: 0.8124 (t70) REVERT: Q 22 TYR cc_start: 0.8751 (m-80) cc_final: 0.7928 (m-80) REVERT: R 14 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7941 (m) REVERT: R 111 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8361 (ttmm) REVERT: R 141 CYS cc_start: 0.7577 (p) cc_final: 0.6194 (t) REVERT: S 7 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7305 (mmm160) REVERT: T 20 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.7195 (t-170) REVERT: T 85 ARG cc_start: 0.7705 (ttp-170) cc_final: 0.7382 (ttt90) REVERT: T 86 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7364 (tt0) REVERT: T 114 LYS cc_start: 0.6680 (mtpt) cc_final: 0.6338 (mtpt) REVERT: U 38 ASP cc_start: 0.7824 (m-30) cc_final: 0.7602 (m-30) REVERT: V 92 TYR cc_start: 0.8500 (t80) cc_final: 0.8247 (t80) REVERT: V 100 LYS cc_start: 0.7609 (mmmm) cc_final: 0.7239 (mmmt) REVERT: Y 7 GLU cc_start: 0.7966 (tp30) cc_final: 0.7737 (tp30) REVERT: Z 112 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.6233 (ttt90) REVERT: a 45 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7780 (mmm) REVERT: a 83 ARG cc_start: 0.7328 (ttp-110) cc_final: 0.7125 (ttp80) REVERT: a 125 ARG cc_start: 0.5807 (mmt90) cc_final: 0.5333 (mmp80) REVERT: a 130 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6657 (ptt-90) REVERT: c 78 LYS cc_start: 0.8102 (ptmm) cc_final: 0.6929 (tppt) REVERT: e 245 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7861 (ttt-90) REVERT: f 74 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: f 169 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7032 (mtt90) REVERT: f 209 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7263 (mmm160) REVERT: f 215 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8408 (pt0) REVERT: f 246 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7460 (ttmp) REVERT: f 296 MET cc_start: 0.8038 (mtm) cc_final: 0.7574 (mtt) REVERT: f 325 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8489 (mtt90) REVERT: f 345 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8002 (pt) REVERT: f 356 LYS cc_start: 0.8033 (ttmm) cc_final: 0.7811 (mtpt) REVERT: f 359 GLU cc_start: 0.7667 (tt0) cc_final: 0.7152 (tp30) REVERT: g 27 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6783 (tt) REVERT: h 79 ARG cc_start: 0.6444 (OUTLIER) cc_final: 0.5779 (mmt-90) REVERT: h 84 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7679 (pp) REVERT: i 91 ARG cc_start: 0.7873 (mtp85) cc_final: 0.6967 (mmp80) REVERT: k 26 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7814 (mttt) REVERT: k 72 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7945 (mttm) REVERT: l 82 TYR cc_start: 0.8926 (t80) cc_final: 0.8583 (t80) REVERT: l 114 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8264 (ppp80) REVERT: n 14 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8223 (ptm160) REVERT: o 13 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7564 (ptt90) REVERT: o 64 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8423 (ttp) REVERT: r 14 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.6020 (pm20) REVERT: r 16 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7265 (pttm) REVERT: r 33 HIS cc_start: 0.7793 (t-90) cc_final: 0.7445 (p-80) REVERT: r 203 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7325 (mtp180) REVERT: t 11 TYR cc_start: 0.8098 (t80) cc_final: 0.7353 (t80) REVERT: u 68 LYS cc_start: 0.8044 (mmmt) cc_final: 0.7687 (mttm) REVERT: u 202 ARG cc_start: 0.5741 (ttt-90) cc_final: 0.5353 (tpp-160) REVERT: w 66 ARG cc_start: 0.7932 (ptp-170) cc_final: 0.7678 (ptp-170) REVERT: x 102 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7173 (ptp90) REVERT: x 126 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.5197 (mtm180) REVERT: x 154 LYS cc_start: 0.7693 (mtpt) cc_final: 0.7237 (mtmt) REVERT: x 272 ILE cc_start: 0.8276 (mt) cc_final: 0.8067 (mt) REVERT: x 276 ASN cc_start: 0.7449 (p0) cc_final: 0.7136 (p0) REVERT: x 300 ARG cc_start: 0.7193 (tpp-160) cc_final: 0.6986 (ttm110) outliers start: 248 outliers final: 109 residues processed: 1058 average time/residue: 2.0394 time to fit residues: 2888.5518 Evaluate side-chains 997 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 854 time to evaluate : 4.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 166 MET Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 204 ARG Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 111 LYS Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain S residue 5 HIS Chi-restraints excluded: chain S residue 7 ARG Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 112 LEU Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 46 LYS Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 46 SER Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain X residue 88 HIS Chi-restraints excluded: chain X residue 120 THR Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 163 ASN Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Z residue 29 SER Chi-restraints excluded: chain Z residue 94 VAL Chi-restraints excluded: chain Z residue 112 ARG Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 45 MET Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain a residue 130 ARG Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 141 VAL Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 39 THR Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain d residue 13 SER Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 112 ILE Chi-restraints excluded: chain e residue 148 LEU Chi-restraints excluded: chain e residue 195 CYS Chi-restraints excluded: chain e residue 207 VAL Chi-restraints excluded: chain e residue 245 ARG Chi-restraints excluded: chain f residue 66 LYS Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 104 THR Chi-restraints excluded: chain f residue 169 ARG Chi-restraints excluded: chain f residue 209 ARG Chi-restraints excluded: chain f residue 215 GLN Chi-restraints excluded: chain f residue 246 LYS Chi-restraints excluded: chain f residue 269 VAL Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 325 ARG Chi-restraints excluded: chain f residue 331 LEU Chi-restraints excluded: chain f residue 345 LEU Chi-restraints excluded: chain f residue 362 THR Chi-restraints excluded: chain f residue 384 SER Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain h residue 79 ARG Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 154 LYS Chi-restraints excluded: chain h residue 168 THR Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain i residue 15 THR Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 32 SER Chi-restraints excluded: chain i residue 96 VAL Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 105 SER Chi-restraints excluded: chain j residue 33 MET Chi-restraints excluded: chain j residue 83 LEU Chi-restraints excluded: chain k residue 26 LYS Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 68 THR Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 114 ARG Chi-restraints excluded: chain l residue 147 SER Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain m residue 20 ILE Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 14 ARG Chi-restraints excluded: chain n residue 43 SER Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 64 MET Chi-restraints excluded: chain p residue 23 VAL Chi-restraints excluded: chain r residue 8 SER Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 17 VAL Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 106 ILE Chi-restraints excluded: chain r residue 146 VAL Chi-restraints excluded: chain r residue 203 ARG Chi-restraints excluded: chain r residue 260 SER Chi-restraints excluded: chain r residue 288 THR Chi-restraints excluded: chain t residue 2 VAL Chi-restraints excluded: chain t residue 35 LEU Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain u residue 154 VAL Chi-restraints excluded: chain u residue 160 THR Chi-restraints excluded: chain u residue 248 MET Chi-restraints excluded: chain u residue 256 ILE Chi-restraints excluded: chain v residue 27 LEU Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 62 VAL Chi-restraints excluded: chain v residue 78 ASP Chi-restraints excluded: chain v residue 154 LYS Chi-restraints excluded: chain w residue 127 LEU Chi-restraints excluded: chain w residue 208 SER Chi-restraints excluded: chain w residue 226 ASP Chi-restraints excluded: chain x residue 102 ARG Chi-restraints excluded: chain x residue 126 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 649 optimal weight: 10.0000 chunk 442 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 580 optimal weight: 10.0000 chunk 321 optimal weight: 2.9990 chunk 665 optimal weight: 1.9990 chunk 539 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 398 optimal weight: 8.9990 chunk 700 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN I 50 GLN ** I 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN N 194 HIS O 58 GLN O 129 ASN Q 50 HIS Q 133 ASN R 9 GLN S 122 ASN ** S 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 GLN Y 14 HIS ** a 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 34 ASN ** c 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 47 ASN d 16 ASN d 19 ASN d 51 ASN e 17 GLN e 19 HIS ** e 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 173 ASN ** f 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 378 GLN f 385 GLN ** i 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 40 ASN ** n 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 HIS r 183 ASN ** t 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 200 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 113004 Z= 0.290 Angle : 0.891 26.269 166301 Z= 0.487 Chirality : 0.043 2.016 20526 Planarity : 0.010 0.132 10405 Dihedral : 24.406 179.712 50304 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.62 % Favored : 96.30 % Rotamer: Outliers : 6.13 % Allowed : 19.51 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.75 (0.11), residues: 5247 helix: 0.03 (0.12), residues: 1892 sheet: -1.79 (0.18), residues: 693 loop : -0.37 (0.12), residues: 2662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 123 HIS 0.009 0.001 HIS Q 187 PHE 0.036 0.002 PHE a 115 TYR 0.026 0.002 TYR w 227 ARG 0.010 0.001 ARG t 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 927 time to evaluate : 5.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.6721 (mmt-90) REVERT: I 180 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.7418 (ttm-80) REVERT: N 188 LYS cc_start: 0.7888 (mmpt) cc_final: 0.7671 (tptp) REVERT: N 204 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7059 (mtm110) REVERT: O 86 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7766 (pp) REVERT: O 103 ARG cc_start: 0.8334 (ttp80) cc_final: 0.8080 (ttp80) REVERT: O 106 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8131 (pp) REVERT: O 189 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6767 (tttp) REVERT: O 198 LYS cc_start: 0.7319 (mmmt) cc_final: 0.6996 (ttmt) REVERT: P 107 ASP cc_start: 0.8196 (t70) cc_final: 0.7957 (t70) REVERT: Q 102 THR cc_start: 0.8110 (p) cc_final: 0.7900 (p) REVERT: R 14 SER cc_start: 0.8280 (OUTLIER) cc_final: 0.7985 (m) REVERT: R 85 ARG cc_start: 0.7447 (ttt180) cc_final: 0.7046 (tmt170) REVERT: R 96 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7714 (mtpt) REVERT: R 111 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8407 (ttmm) REVERT: R 141 CYS cc_start: 0.7681 (p) cc_final: 0.6905 (t) REVERT: S 7 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7419 (mmm160) REVERT: T 20 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7284 (t-170) REVERT: T 85 ARG cc_start: 0.7773 (ttp-170) cc_final: 0.7439 (ttt90) REVERT: T 86 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7276 (tt0) REVERT: T 117 ARG cc_start: 0.6898 (ttm110) cc_final: 0.6477 (ttm-80) REVERT: U 38 ASP cc_start: 0.7869 (m-30) cc_final: 0.7646 (m-30) REVERT: V 92 TYR cc_start: 0.8509 (t80) cc_final: 0.8256 (t80) REVERT: V 100 LYS cc_start: 0.7772 (mmmm) cc_final: 0.7393 (mmmt) REVERT: Y 7 GLU cc_start: 0.8092 (tp30) cc_final: 0.7878 (tp30) REVERT: Y 51 ARG cc_start: 0.7891 (tpt-90) cc_final: 0.7646 (ttt180) REVERT: Z 112 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6464 (ttt90) REVERT: a 5 LYS cc_start: 0.6152 (OUTLIER) cc_final: 0.5881 (mttm) REVERT: a 45 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7726 (mmm) REVERT: a 125 ARG cc_start: 0.5933 (mmt90) cc_final: 0.5443 (mmp80) REVERT: a 130 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6666 (ptt-90) REVERT: c 78 LYS cc_start: 0.8026 (ptmm) cc_final: 0.6768 (tppt) REVERT: e 245 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7893 (ttt-90) REVERT: f 74 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: f 198 GLU cc_start: 0.7838 (tp30) cc_final: 0.7633 (mt-10) REVERT: f 209 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7183 (mmm160) REVERT: f 246 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7563 (ttmp) REVERT: f 296 MET cc_start: 0.8097 (mtm) cc_final: 0.7674 (mtt) REVERT: f 325 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8490 (mtt90) REVERT: f 345 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8111 (pt) REVERT: f 359 GLU cc_start: 0.7495 (tt0) cc_final: 0.7166 (tp30) REVERT: i 91 ARG cc_start: 0.7996 (mtp85) cc_final: 0.7123 (mmp80) REVERT: j 86 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7542 (mm-30) REVERT: j 89 ARG cc_start: 0.8548 (ttp80) cc_final: 0.8270 (tmm160) REVERT: k 72 LYS cc_start: 0.8269 (mtmt) cc_final: 0.7983 (mttm) REVERT: l 82 TYR cc_start: 0.8900 (t80) cc_final: 0.8621 (t80) REVERT: l 114 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8265 (ppp80) REVERT: n 14 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8256 (ptm160) REVERT: o 13 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7640 (ptt90) REVERT: r 14 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.6109 (pm20) REVERT: r 16 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7279 (pttm) REVERT: r 33 HIS cc_start: 0.7993 (t-90) cc_final: 0.7450 (p-80) REVERT: t 11 TYR cc_start: 0.8142 (t80) cc_final: 0.7398 (t80) REVERT: u 68 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7652 (mttm) REVERT: u 202 ARG cc_start: 0.5728 (ttt-90) cc_final: 0.5279 (tpp-160) REVERT: w 62 LEU cc_start: 0.8169 (tp) cc_final: 0.7878 (mt) REVERT: w 66 ARG cc_start: 0.7951 (ptp-170) cc_final: 0.7726 (ptp-170) REVERT: x 102 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7188 (ptp90) REVERT: x 126 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.5453 (mtm180) REVERT: x 272 ILE cc_start: 0.8371 (mt) cc_final: 0.8156 (mt) REVERT: x 276 ASN cc_start: 0.7419 (p0) cc_final: 0.7145 (p0) outliers start: 276 outliers final: 127 residues processed: 1079 average time/residue: 1.9747 time to fit residues: 2848.6503 Evaluate side-chains 1032 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 876 time to evaluate : 4.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 178 LYS Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 204 ARG Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 189 LYS Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 144 VAL Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 96 LYS Chi-restraints excluded: chain R residue 111 LYS Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain S residue 7 ARG Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain T residue 140 GLU Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 33 ASN Chi-restraints excluded: chain U residue 46 SER Chi-restraints excluded: chain U residue 84 THR Chi-restraints excluded: chain W residue 130 LYS Chi-restraints excluded: chain X residue 88 HIS Chi-restraints excluded: chain X residue 120 THR Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 161 LYS Chi-restraints excluded: chain X residue 163 ASN Chi-restraints excluded: chain X residue 185 LEU Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Z residue 29 SER Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 ARG Chi-restraints excluded: chain Z residue 94 VAL Chi-restraints excluded: chain Z residue 112 ARG Chi-restraints excluded: chain a residue 5 LYS Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 45 MET Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain a residue 130 ARG Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 141 VAL Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 39 THR Chi-restraints excluded: chain d residue 13 SER Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 24 LEU Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 112 ILE Chi-restraints excluded: chain e residue 134 CYS Chi-restraints excluded: chain e residue 148 LEU Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 195 CYS Chi-restraints excluded: chain e residue 207 VAL Chi-restraints excluded: chain e residue 245 ARG Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 104 THR Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 209 ARG Chi-restraints excluded: chain f residue 246 LYS Chi-restraints excluded: chain f residue 269 VAL Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 325 ARG Chi-restraints excluded: chain f residue 331 LEU Chi-restraints excluded: chain f residue 335 VAL Chi-restraints excluded: chain f residue 345 LEU Chi-restraints excluded: chain f residue 362 THR Chi-restraints excluded: chain f residue 384 SER Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 154 LYS Chi-restraints excluded: chain h residue 168 THR Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain i residue 15 THR Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 96 VAL Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 105 SER Chi-restraints excluded: chain i residue 121 ILE Chi-restraints excluded: chain j residue 33 MET Chi-restraints excluded: chain j residue 83 LEU Chi-restraints excluded: chain j residue 86 GLU Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 68 THR Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 114 ARG Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain m residue 20 ILE Chi-restraints excluded: chain m residue 69 ARG Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 14 ARG Chi-restraints excluded: chain n residue 43 SER Chi-restraints excluded: chain n residue 77 HIS Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain p residue 23 VAL Chi-restraints excluded: chain r residue 8 SER Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 23 LEU Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 106 ILE Chi-restraints excluded: chain r residue 146 VAL Chi-restraints excluded: chain r residue 260 SER Chi-restraints excluded: chain r residue 271 VAL Chi-restraints excluded: chain r residue 285 THR Chi-restraints excluded: chain r residue 288 THR Chi-restraints excluded: chain t residue 35 LEU Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain u residue 103 LEU Chi-restraints excluded: chain u residue 109 MET Chi-restraints excluded: chain u residue 154 VAL Chi-restraints excluded: chain u residue 160 THR Chi-restraints excluded: chain u residue 161 THR Chi-restraints excluded: chain u residue 248 MET Chi-restraints excluded: chain u residue 256 ILE Chi-restraints excluded: chain v residue 27 LEU Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 74 ILE Chi-restraints excluded: chain v residue 78 ASP Chi-restraints excluded: chain v residue 87 THR Chi-restraints excluded: chain v residue 154 LYS Chi-restraints excluded: chain w residue 89 ILE Chi-restraints excluded: chain w residue 118 ARG Chi-restraints excluded: chain w residue 226 ASP Chi-restraints excluded: chain x residue 102 ARG Chi-restraints excluded: chain x residue 126 ARG Chi-restraints excluded: chain x residue 251 THR Chi-restraints excluded: chain x residue 275 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 262 optimal weight: 20.0000 chunk 702 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 457 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 chunk 780 optimal weight: 20.0000 chunk 648 optimal weight: 3.9990 chunk 361 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 258 optimal weight: 20.0000 chunk 409 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN I 45 ASN I 50 GLN ** I 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN O 58 GLN Q 50 HIS Q 133 ASN R 9 GLN ** S 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 GLN X 156 GLN c 34 ASN c 47 ASN d 16 ASN d 19 ASN e 17 GLN ** e 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 217 GLN f 24 GLN f 173 ASN ** f 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 326 ASN f 385 GLN ** i 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 40 ASN ** n 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 HIS r 183 ASN ** t 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 310 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 113004 Z= 0.227 Angle : 0.866 26.384 166301 Z= 0.476 Chirality : 0.041 1.997 20526 Planarity : 0.009 0.129 10405 Dihedral : 24.362 179.455 50302 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.53 % Rotamer: Outliers : 5.20 % Allowed : 21.24 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.11), residues: 5247 helix: 0.22 (0.12), residues: 1889 sheet: -1.71 (0.18), residues: 705 loop : -0.34 (0.12), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP l 74 HIS 0.009 0.001 HIS S 5 PHE 0.033 0.002 PHE a 115 TYR 0.021 0.002 TYR N 187 ARG 0.011 0.001 ARG S 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 884 time to evaluate : 5.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6720 (mmt-90) REVERT: I 180 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7404 (ttm-80) REVERT: N 46 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7763 (tt) REVERT: N 93 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7616 (mtt-85) REVERT: N 188 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7209 (mttt) REVERT: N 204 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7414 (mtm110) REVERT: O 86 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7709 (pp) REVERT: O 103 ARG cc_start: 0.8323 (ttp80) cc_final: 0.8097 (ttp80) REVERT: O 106 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7922 (mp) REVERT: O 198 LYS cc_start: 0.7412 (mmmt) cc_final: 0.7152 (ttmt) REVERT: P 48 ARG cc_start: 0.6987 (ttm170) cc_final: 0.6723 (ttm110) REVERT: P 100 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6648 (tmm160) REVERT: R 14 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7937 (m) REVERT: R 18 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7859 (ptmt) REVERT: R 85 ARG cc_start: 0.7395 (ttt180) cc_final: 0.7023 (tmt170) REVERT: R 141 CYS cc_start: 0.7108 (p) cc_final: 0.6336 (t) REVERT: S 2 VAL cc_start: 0.7993 (m) cc_final: 0.7746 (p) REVERT: S 7 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7334 (mmm160) REVERT: S 149 LEU cc_start: 0.6367 (OUTLIER) cc_final: 0.6076 (OUTLIER) REVERT: T 20 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7194 (t-170) REVERT: T 85 ARG cc_start: 0.7752 (ttp-170) cc_final: 0.7421 (ttt90) REVERT: T 86 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: T 114 LYS cc_start: 0.6775 (OUTLIER) cc_final: 0.6519 (mttm) REVERT: T 117 ARG cc_start: 0.6827 (ttm110) cc_final: 0.6345 (ttm170) REVERT: U 38 ASP cc_start: 0.7836 (m-30) cc_final: 0.7606 (m-30) REVERT: U 57 TYR cc_start: 0.8776 (m-80) cc_final: 0.8482 (m-80) REVERT: V 92 TYR cc_start: 0.8454 (t80) cc_final: 0.8172 (t80) REVERT: V 100 LYS cc_start: 0.7778 (mmmm) cc_final: 0.7396 (mmmt) REVERT: Y 7 GLU cc_start: 0.8047 (tp30) cc_final: 0.7821 (tp30) REVERT: Z 54 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7815 (ttm-80) REVERT: Z 112 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6411 (ttt90) REVERT: a 5 LYS cc_start: 0.6134 (OUTLIER) cc_final: 0.5879 (mttm) REVERT: a 45 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7722 (mmm) REVERT: a 66 ARG cc_start: 0.6812 (tmt170) cc_final: 0.6372 (tmt170) REVERT: a 113 LYS cc_start: 0.7496 (mmmt) cc_final: 0.6905 (mmmt) REVERT: a 125 ARG cc_start: 0.5985 (mmt90) cc_final: 0.5474 (mmp80) REVERT: b 42 ARG cc_start: 0.8212 (ttm170) cc_final: 0.7940 (ttm170) REVERT: c 78 LYS cc_start: 0.8006 (ptmm) cc_final: 0.6791 (tppt) REVERT: e 49 GLU cc_start: 0.7941 (mp0) cc_final: 0.7650 (mp0) REVERT: e 245 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7852 (ttt-90) REVERT: f 74 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: f 246 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7550 (ttmp) REVERT: f 292 ARG cc_start: 0.8131 (mtm110) cc_final: 0.7842 (mtm110) REVERT: f 296 MET cc_start: 0.7949 (mtm) cc_final: 0.7513 (mtt) REVERT: f 325 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8466 (mtt90) REVERT: f 359 GLU cc_start: 0.7495 (tt0) cc_final: 0.7164 (tp30) REVERT: g 69 MET cc_start: 0.6254 (ttm) cc_final: 0.6030 (tpp) REVERT: i 91 ARG cc_start: 0.7996 (mtp85) cc_final: 0.7136 (mmp80) REVERT: j 86 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7519 (mm-30) REVERT: j 89 ARG cc_start: 0.8580 (ttp80) cc_final: 0.8319 (tmm160) REVERT: k 37 GLN cc_start: 0.7440 (mm110) cc_final: 0.7222 (mp10) REVERT: k 72 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7944 (mttm) REVERT: l 82 TYR cc_start: 0.8876 (t80) cc_final: 0.8625 (t80) REVERT: n 14 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8230 (ptm160) REVERT: o 13 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7580 (ptt90) REVERT: r 14 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.6196 (pm20) REVERT: r 33 HIS cc_start: 0.7984 (t-90) cc_final: 0.7451 (p-80) REVERT: t 11 TYR cc_start: 0.8083 (t80) cc_final: 0.7351 (t80) REVERT: u 68 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7706 (mttm) REVERT: u 202 ARG cc_start: 0.5716 (ttt-90) cc_final: 0.5245 (tpp-160) REVERT: v 35 THR cc_start: 0.7871 (t) cc_final: 0.7628 (t) REVERT: x 102 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.7070 (ptp90) REVERT: x 126 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.5434 (mtm180) REVERT: x 261 ASN cc_start: 0.7346 (m110) cc_final: 0.6932 (m110) REVERT: x 298 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.7105 (ttp-110) outliers start: 234 outliers final: 124 residues processed: 1020 average time/residue: 1.9868 time to fit residues: 2709.9758 Evaluate side-chains 1008 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 855 time to evaluate : 5.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 178 LYS Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 188 LYS Chi-restraints excluded: chain N residue 204 ARG Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 201 ARG Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 115 VAL Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 18 LYS Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain S residue 5 HIS Chi-restraints excluded: chain S residue 7 ARG Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain T residue 111 GLU Chi-restraints excluded: chain T residue 114 LYS Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 140 GLU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 46 SER Chi-restraints excluded: chain V residue 57 LEU Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 83 GLN Chi-restraints excluded: chain W residue 130 LYS Chi-restraints excluded: chain X residue 88 HIS Chi-restraints excluded: chain X residue 106 SER Chi-restraints excluded: chain X residue 120 THR Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 161 LYS Chi-restraints excluded: chain X residue 163 ASN Chi-restraints excluded: chain X residue 185 LEU Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Z residue 22 HIS Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 ARG Chi-restraints excluded: chain Z residue 61 LYS Chi-restraints excluded: chain Z residue 94 VAL Chi-restraints excluded: chain Z residue 112 ARG Chi-restraints excluded: chain a residue 5 LYS Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 45 MET Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 107 SER Chi-restraints excluded: chain b residue 141 VAL Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 39 THR Chi-restraints excluded: chain c residue 49 LYS Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 112 ILE Chi-restraints excluded: chain e residue 134 CYS Chi-restraints excluded: chain e residue 148 LEU Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 195 CYS Chi-restraints excluded: chain e residue 207 VAL Chi-restraints excluded: chain e residue 243 THR Chi-restraints excluded: chain e residue 245 ARG Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 104 THR Chi-restraints excluded: chain f residue 246 LYS Chi-restraints excluded: chain f residue 269 VAL Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 325 ARG Chi-restraints excluded: chain f residue 331 LEU Chi-restraints excluded: chain f residue 335 VAL Chi-restraints excluded: chain f residue 362 THR Chi-restraints excluded: chain f residue 384 SER Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 168 THR Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain i residue 15 THR Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 32 SER Chi-restraints excluded: chain i residue 96 VAL Chi-restraints excluded: chain i residue 105 SER Chi-restraints excluded: chain i residue 121 ILE Chi-restraints excluded: chain j residue 33 MET Chi-restraints excluded: chain j residue 83 LEU Chi-restraints excluded: chain j residue 86 GLU Chi-restraints excluded: chain k residue 16 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain m residue 79 ASP Chi-restraints excluded: chain n residue 14 ARG Chi-restraints excluded: chain n residue 43 SER Chi-restraints excluded: chain n residue 77 HIS Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain p residue 23 VAL Chi-restraints excluded: chain r residue 8 SER Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 17 VAL Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 106 ILE Chi-restraints excluded: chain r residue 146 VAL Chi-restraints excluded: chain r residue 260 SER Chi-restraints excluded: chain r residue 285 THR Chi-restraints excluded: chain r residue 288 THR Chi-restraints excluded: chain t residue 35 LEU Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain u residue 109 MET Chi-restraints excluded: chain u residue 154 VAL Chi-restraints excluded: chain u residue 160 THR Chi-restraints excluded: chain u residue 161 THR Chi-restraints excluded: chain u residue 214 LEU Chi-restraints excluded: chain u residue 248 MET Chi-restraints excluded: chain u residue 256 ILE Chi-restraints excluded: chain v residue 27 LEU Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 78 ASP Chi-restraints excluded: chain v residue 87 THR Chi-restraints excluded: chain v residue 154 LYS Chi-restraints excluded: chain w residue 89 ILE Chi-restraints excluded: chain w residue 226 ASP Chi-restraints excluded: chain x residue 102 ARG Chi-restraints excluded: chain x residue 126 ARG Chi-restraints excluded: chain x residue 251 THR Chi-restraints excluded: chain x residue 275 VAL Chi-restraints excluded: chain x residue 298 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 752 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 444 optimal weight: 5.9990 chunk 570 optimal weight: 10.0000 chunk 441 optimal weight: 9.9990 chunk 657 optimal weight: 7.9990 chunk 436 optimal weight: 10.0000 chunk 777 optimal weight: 6.9990 chunk 486 optimal weight: 4.9990 chunk 474 optimal weight: 7.9990 chunk 359 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN I 50 GLN ** I 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN N 64 ASN O 74 GLN P 112 GLN Q 24 ASN Q 50 HIS Q 133 ASN R 9 GLN R 46 GLN ** S 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 GLN ** c 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 47 ASN d 16 ASN d 19 ASN e 17 GLN ** e 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 217 GLN f 173 ASN ** f 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 385 GLN h 150 HIS ** i 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 40 ASN ** n 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 HIS r 183 ASN ** t 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 197 ASN w 125 ASN x 310 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 113004 Z= 0.300 Angle : 0.892 25.926 166301 Z= 0.486 Chirality : 0.043 2.002 20526 Planarity : 0.010 0.133 10405 Dihedral : 24.327 179.594 50302 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.64 % Favored : 96.28 % Rotamer: Outliers : 5.46 % Allowed : 21.90 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.11), residues: 5247 helix: 0.23 (0.12), residues: 1886 sheet: -1.59 (0.18), residues: 712 loop : -0.40 (0.12), residues: 2649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP l 74 HIS 0.010 0.001 HIS e 19 PHE 0.037 0.002 PHE a 115 TYR 0.026 0.002 TYR w 227 ARG 0.012 0.001 ARG X 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 867 time to evaluate : 5.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.6752 (mmt180) REVERT: I 180 ARG cc_start: 0.7774 (ttp-170) cc_final: 0.7377 (ttm-80) REVERT: N 46 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7770 (tt) REVERT: N 93 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7664 (mtt-85) REVERT: N 125 MET cc_start: 0.8692 (mmm) cc_final: 0.8428 (mmm) REVERT: N 204 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7497 (mtm110) REVERT: O 85 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.6923 (ttmm) REVERT: O 86 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7768 (pp) REVERT: O 103 ARG cc_start: 0.8291 (ttp80) cc_final: 0.7912 (ttp-170) REVERT: O 106 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8135 (pp) REVERT: O 198 LYS cc_start: 0.7403 (mmmt) cc_final: 0.7129 (ttpt) REVERT: Q 45 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: Q 55 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7747 (mt) REVERT: R 14 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.7966 (m) REVERT: R 18 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7868 (ptmt) REVERT: R 85 ARG cc_start: 0.7474 (ttt180) cc_final: 0.7098 (tmt170) REVERT: R 96 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7723 (mtpt) REVERT: S 2 VAL cc_start: 0.8058 (m) cc_final: 0.7818 (p) REVERT: S 7 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7414 (mmm160) REVERT: S 149 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6183 (OUTLIER) REVERT: T 20 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.7263 (t-170) REVERT: T 85 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7427 (ttt90) REVERT: T 86 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: T 117 ARG cc_start: 0.6787 (ttm110) cc_final: 0.6347 (ttm170) REVERT: U 38 ASP cc_start: 0.7932 (m-30) cc_final: 0.7708 (m-30) REVERT: V 92 TYR cc_start: 0.8539 (t80) cc_final: 0.8283 (t80) REVERT: V 100 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7501 (mmmt) REVERT: W 130 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7786 (mtpt) REVERT: Z 54 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7922 (ttm-80) REVERT: Z 112 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6456 (ttt90) REVERT: a 45 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7740 (mmm) REVERT: a 66 ARG cc_start: 0.6859 (tmt170) cc_final: 0.6427 (tmt170) REVERT: a 113 LYS cc_start: 0.7515 (mmmt) cc_final: 0.6721 (pttt) REVERT: c 78 LYS cc_start: 0.8027 (ptmm) cc_final: 0.6886 (tppt) REVERT: e 145 ARG cc_start: 0.7269 (mtp-110) cc_final: 0.7041 (mtp-110) REVERT: e 245 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7817 (ttt-90) REVERT: f 74 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: f 169 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7141 (mtt90) REVERT: f 246 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7577 (ttmp) REVERT: f 292 ARG cc_start: 0.8202 (mtm110) cc_final: 0.7981 (mtm110) REVERT: f 296 MET cc_start: 0.7923 (mtm) cc_final: 0.7463 (mtt) REVERT: f 325 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8471 (mtt90) REVERT: i 91 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7074 (mmp80) REVERT: j 86 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7528 (mm-30) REVERT: j 89 ARG cc_start: 0.8562 (ttp80) cc_final: 0.8259 (tmm160) REVERT: k 72 LYS cc_start: 0.8218 (mtmt) cc_final: 0.7949 (mttm) REVERT: l 82 TYR cc_start: 0.8865 (t80) cc_final: 0.8643 (t80) REVERT: n 14 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8266 (ptm160) REVERT: o 13 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7645 (ptt90) REVERT: r 14 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6278 (pm20) REVERT: r 33 HIS cc_start: 0.8029 (t-90) cc_final: 0.7468 (p-80) REVERT: r 203 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7692 (mpt-90) REVERT: r 281 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7671 (ttm) REVERT: t 11 TYR cc_start: 0.8095 (t80) cc_final: 0.7401 (t80) REVERT: u 52 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8256 (t) REVERT: u 68 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7665 (mttm) REVERT: u 202 ARG cc_start: 0.5738 (ttt-90) cc_final: 0.5131 (tpp-160) REVERT: v 35 THR cc_start: 0.7986 (t) cc_final: 0.7746 (t) REVERT: w 66 ARG cc_start: 0.7745 (ptp-170) cc_final: 0.7408 (ptp90) REVERT: x 102 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6936 (ptp90) REVERT: x 126 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.5314 (mtm180) REVERT: x 151 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8102 (tt) REVERT: x 161 ARG cc_start: 0.5617 (ttp80) cc_final: 0.5325 (ttp80) REVERT: x 298 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7101 (ttp-110) outliers start: 246 outliers final: 138 residues processed: 1004 average time/residue: 1.8668 time to fit residues: 2510.3192 Evaluate side-chains 1015 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 842 time to evaluate : 4.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 178 LYS Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 204 ARG Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 85 LYS Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain P residue 34 ASN Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 96 ILE Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 144 VAL Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 18 LYS Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 96 LYS Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain R residue 135 ARG Chi-restraints excluded: chain S residue 5 HIS Chi-restraints excluded: chain S residue 7 ARG Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain T residue 111 GLU Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 140 GLU Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 46 SER Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 83 GLN Chi-restraints excluded: chain W residue 130 LYS Chi-restraints excluded: chain X residue 88 HIS Chi-restraints excluded: chain X residue 106 SER Chi-restraints excluded: chain X residue 120 THR Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 161 LYS Chi-restraints excluded: chain X residue 163 ASN Chi-restraints excluded: chain X residue 171 LEU Chi-restraints excluded: chain X residue 185 LEU Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Z residue 22 HIS Chi-restraints excluded: chain Z residue 29 SER Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 ARG Chi-restraints excluded: chain Z residue 61 LYS Chi-restraints excluded: chain Z residue 94 VAL Chi-restraints excluded: chain Z residue 112 ARG Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 45 MET Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 107 SER Chi-restraints excluded: chain b residue 141 VAL Chi-restraints excluded: chain b residue 142 VAL Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 39 THR Chi-restraints excluded: chain c residue 49 LYS Chi-restraints excluded: chain d residue 13 SER Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 24 LEU Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 112 ILE Chi-restraints excluded: chain e residue 134 CYS Chi-restraints excluded: chain e residue 148 LEU Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 195 CYS Chi-restraints excluded: chain e residue 207 VAL Chi-restraints excluded: chain e residue 245 ARG Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 104 THR Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 169 ARG Chi-restraints excluded: chain f residue 246 LYS Chi-restraints excluded: chain f residue 269 VAL Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 325 ARG Chi-restraints excluded: chain f residue 331 LEU Chi-restraints excluded: chain f residue 335 VAL Chi-restraints excluded: chain f residue 362 THR Chi-restraints excluded: chain f residue 384 SER Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 168 THR Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain i residue 15 THR Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 32 SER Chi-restraints excluded: chain i residue 96 VAL Chi-restraints excluded: chain i residue 105 SER Chi-restraints excluded: chain i residue 121 ILE Chi-restraints excluded: chain j residue 33 MET Chi-restraints excluded: chain j residue 83 LEU Chi-restraints excluded: chain j residue 86 GLU Chi-restraints excluded: chain k residue 16 ASP Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain k residue 117 LYS Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain m residue 69 ARG Chi-restraints excluded: chain m residue 79 ASP Chi-restraints excluded: chain n residue 6 THR Chi-restraints excluded: chain n residue 14 ARG Chi-restraints excluded: chain n residue 43 SER Chi-restraints excluded: chain n residue 77 HIS Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain p residue 23 VAL Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 17 VAL Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 106 ILE Chi-restraints excluded: chain r residue 146 VAL Chi-restraints excluded: chain r residue 203 ARG Chi-restraints excluded: chain r residue 260 SER Chi-restraints excluded: chain r residue 281 MET Chi-restraints excluded: chain r residue 285 THR Chi-restraints excluded: chain r residue 288 THR Chi-restraints excluded: chain t residue 35 LEU Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain u residue 103 LEU Chi-restraints excluded: chain u residue 109 MET Chi-restraints excluded: chain u residue 154 VAL Chi-restraints excluded: chain u residue 160 THR Chi-restraints excluded: chain u residue 161 THR Chi-restraints excluded: chain u residue 214 LEU Chi-restraints excluded: chain u residue 248 MET Chi-restraints excluded: chain u residue 256 ILE Chi-restraints excluded: chain v residue 27 LEU Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 62 VAL Chi-restraints excluded: chain v residue 78 ASP Chi-restraints excluded: chain v residue 87 THR Chi-restraints excluded: chain v residue 154 LYS Chi-restraints excluded: chain w residue 89 ILE Chi-restraints excluded: chain w residue 118 ARG Chi-restraints excluded: chain w residue 127 LEU Chi-restraints excluded: chain w residue 226 ASP Chi-restraints excluded: chain x residue 102 ARG Chi-restraints excluded: chain x residue 126 ARG Chi-restraints excluded: chain x residue 151 LEU Chi-restraints excluded: chain x residue 251 THR Chi-restraints excluded: chain x residue 275 VAL Chi-restraints excluded: chain x residue 298 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 481 optimal weight: 8.9990 chunk 310 optimal weight: 5.9990 chunk 464 optimal weight: 9.9990 chunk 234 optimal weight: 20.0000 chunk 152 optimal weight: 30.0000 chunk 150 optimal weight: 9.9990 chunk 494 optimal weight: 20.0000 chunk 529 optimal weight: 2.9990 chunk 384 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 611 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN ** I 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN O 74 GLN Q 24 ASN Q 50 HIS Q 133 ASN R 46 GLN ** U 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 GLN X 156 GLN ** a 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 47 ASN d 16 ASN d 19 ASN e 17 GLN ** e 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 217 GLN f 173 ASN ** f 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 40 ASN ** n 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 HIS r 183 ASN r 237 HIS ** t 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 197 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 113004 Z= 0.336 Angle : 0.909 25.824 166301 Z= 0.493 Chirality : 0.044 2.006 20526 Planarity : 0.010 0.134 10405 Dihedral : 24.339 179.850 50302 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 5.20 % Allowed : 22.52 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.11), residues: 5247 helix: 0.19 (0.12), residues: 1889 sheet: -1.50 (0.18), residues: 708 loop : -0.49 (0.12), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP l 74 HIS 0.009 0.001 HIS Q 187 PHE 0.038 0.002 PHE a 115 TYR 0.027 0.002 TYR w 227 ARG 0.010 0.001 ARG X 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 861 time to evaluate : 5.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6753 (mmt180) REVERT: I 180 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.7417 (ttm-80) REVERT: I 188 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7618 (mtm110) REVERT: L 149 ARG cc_start: 0.8018 (ttp-110) cc_final: 0.7765 (ttp80) REVERT: N 46 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7690 (tt) REVERT: N 93 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7642 (mtt-85) REVERT: N 125 MET cc_start: 0.8700 (mmm) cc_final: 0.8450 (mmm) REVERT: N 204 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7403 (mtm110) REVERT: O 85 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.6952 (ttmm) REVERT: O 86 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7798 (pp) REVERT: O 103 ARG cc_start: 0.8333 (ttp80) cc_final: 0.7954 (ttp-170) REVERT: O 106 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8201 (pp) REVERT: O 198 LYS cc_start: 0.7301 (mmmt) cc_final: 0.7065 (ttpt) REVERT: Q 45 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7566 (tm-30) REVERT: Q 55 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7707 (mt) REVERT: R 14 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.8012 (m) REVERT: R 18 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7881 (ptmt) REVERT: S 2 VAL cc_start: 0.8144 (m) cc_final: 0.7885 (p) REVERT: S 7 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7428 (mmm160) REVERT: S 149 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6206 (OUTLIER) REVERT: T 20 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7300 (t-170) REVERT: T 85 ARG cc_start: 0.7857 (ttp-170) cc_final: 0.7502 (ttt90) REVERT: T 86 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7266 (tt0) REVERT: T 117 ARG cc_start: 0.6779 (ttm110) cc_final: 0.6447 (ttm-80) REVERT: U 38 ASP cc_start: 0.7970 (m-30) cc_final: 0.7760 (m-30) REVERT: U 145 VAL cc_start: 0.7868 (t) cc_final: 0.7661 (t) REVERT: V 83 MET cc_start: 0.6822 (mmm) cc_final: 0.5686 (tpt) REVERT: V 92 TYR cc_start: 0.8545 (t80) cc_final: 0.8297 (t80) REVERT: V 100 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7552 (mmmt) REVERT: V 106 TRP cc_start: 0.6298 (m100) cc_final: 0.5590 (m-10) REVERT: W 130 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7652 (mtpt) REVERT: Z 54 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7961 (ttm-80) REVERT: a 45 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7535 (mmm) REVERT: a 66 ARG cc_start: 0.6892 (tmt170) cc_final: 0.6465 (tmt170) REVERT: a 112 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6538 (ttt-90) REVERT: a 113 LYS cc_start: 0.7544 (mmmt) cc_final: 0.6754 (pttt) REVERT: a 116 GLN cc_start: 0.7989 (tp40) cc_final: 0.7503 (tp-100) REVERT: c 78 LYS cc_start: 0.7947 (ptmm) cc_final: 0.6863 (tppt) REVERT: e 245 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7471 (ttt-90) REVERT: f 74 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: f 155 LYS cc_start: 0.7670 (ttmp) cc_final: 0.7408 (ttmm) REVERT: f 169 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7153 (mtt90) REVERT: f 246 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7587 (ttmp) REVERT: f 292 ARG cc_start: 0.8160 (mtm110) cc_final: 0.7941 (mtm110) REVERT: f 296 MET cc_start: 0.7875 (mtm) cc_final: 0.7435 (mtt) REVERT: f 325 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8478 (mtt90) REVERT: i 91 ARG cc_start: 0.7995 (mtp85) cc_final: 0.7058 (mmp80) REVERT: j 86 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7527 (mm-30) REVERT: j 89 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8292 (tmm160) REVERT: k 37 GLN cc_start: 0.7499 (mm110) cc_final: 0.7209 (mp10) REVERT: k 70 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8065 (mt) REVERT: k 72 LYS cc_start: 0.8262 (mtmt) cc_final: 0.8018 (mttm) REVERT: l 82 TYR cc_start: 0.8885 (t80) cc_final: 0.8645 (t80) REVERT: l 89 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7603 (mpp) REVERT: n 14 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8265 (ptm160) REVERT: o 13 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7659 (ptt90) REVERT: r 14 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.6208 (pm20) REVERT: r 16 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7125 (pttm) REVERT: r 33 HIS cc_start: 0.8053 (t-90) cc_final: 0.7477 (p-80) REVERT: r 203 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7713 (mpt-90) REVERT: r 335 LYS cc_start: 0.5396 (tttp) cc_final: 0.5006 (tttp) REVERT: t 11 TYR cc_start: 0.8192 (t80) cc_final: 0.7495 (t80) REVERT: u 9 ASN cc_start: 0.8035 (p0) cc_final: 0.7829 (p0) REVERT: u 202 ARG cc_start: 0.5783 (ttt-90) cc_final: 0.5088 (tpp-160) REVERT: w 66 ARG cc_start: 0.7962 (ptp-170) cc_final: 0.7654 (ptp90) REVERT: x 102 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6862 (ptp90) REVERT: x 126 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.5316 (mtm180) REVERT: x 151 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8111 (tt) REVERT: x 161 ARG cc_start: 0.5700 (ttp80) cc_final: 0.5413 (ttp80) REVERT: x 206 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7787 (mtm110) outliers start: 234 outliers final: 139 residues processed: 997 average time/residue: 1.8722 time to fit residues: 2495.2669 Evaluate side-chains 1012 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 838 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain I residue 178 LYS Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 204 ARG Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 85 LYS Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain P residue 34 ASN Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 144 VAL Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 18 LYS Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 110 ASN Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain S residue 5 HIS Chi-restraints excluded: chain S residue 7 ARG Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain T residue 111 GLU Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 140 GLU Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 46 SER Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 130 LYS Chi-restraints excluded: chain X residue 88 HIS Chi-restraints excluded: chain X residue 106 SER Chi-restraints excluded: chain X residue 120 THR Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 163 ASN Chi-restraints excluded: chain X residue 171 LEU Chi-restraints excluded: chain X residue 185 LEU Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Z residue 22 HIS Chi-restraints excluded: chain Z residue 29 SER Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 ARG Chi-restraints excluded: chain Z residue 61 LYS Chi-restraints excluded: chain Z residue 83 ASN Chi-restraints excluded: chain Z residue 94 VAL Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 45 MET Chi-restraints excluded: chain a residue 112 ARG Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 107 SER Chi-restraints excluded: chain b residue 141 VAL Chi-restraints excluded: chain b residue 142 VAL Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 39 THR Chi-restraints excluded: chain d residue 13 SER Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 24 LEU Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 112 ILE Chi-restraints excluded: chain e residue 134 CYS Chi-restraints excluded: chain e residue 148 LEU Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 195 CYS Chi-restraints excluded: chain e residue 207 VAL Chi-restraints excluded: chain e residue 245 ARG Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 104 THR Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 169 ARG Chi-restraints excluded: chain f residue 246 LYS Chi-restraints excluded: chain f residue 269 VAL Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 325 ARG Chi-restraints excluded: chain f residue 335 VAL Chi-restraints excluded: chain f residue 362 THR Chi-restraints excluded: chain f residue 384 SER Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 168 THR Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain i residue 15 THR Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 32 SER Chi-restraints excluded: chain i residue 96 VAL Chi-restraints excluded: chain i residue 105 SER Chi-restraints excluded: chain i residue 121 ILE Chi-restraints excluded: chain j residue 83 LEU Chi-restraints excluded: chain j residue 86 GLU Chi-restraints excluded: chain k residue 16 ASP Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain k residue 70 LEU Chi-restraints excluded: chain k residue 117 LYS Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 89 MET Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain m residue 20 ILE Chi-restraints excluded: chain m residue 69 ARG Chi-restraints excluded: chain m residue 79 ASP Chi-restraints excluded: chain n residue 14 ARG Chi-restraints excluded: chain n residue 43 SER Chi-restraints excluded: chain n residue 77 HIS Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain p residue 23 VAL Chi-restraints excluded: chain r residue 8 SER Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 17 VAL Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 106 ILE Chi-restraints excluded: chain r residue 146 VAL Chi-restraints excluded: chain r residue 203 ARG Chi-restraints excluded: chain r residue 260 SER Chi-restraints excluded: chain r residue 285 THR Chi-restraints excluded: chain r residue 288 THR Chi-restraints excluded: chain t residue 35 LEU Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain u residue 103 LEU Chi-restraints excluded: chain u residue 109 MET Chi-restraints excluded: chain u residue 154 VAL Chi-restraints excluded: chain u residue 161 THR Chi-restraints excluded: chain u residue 214 LEU Chi-restraints excluded: chain u residue 248 MET Chi-restraints excluded: chain u residue 256 ILE Chi-restraints excluded: chain v residue 27 LEU Chi-restraints excluded: chain v residue 78 ASP Chi-restraints excluded: chain v residue 87 THR Chi-restraints excluded: chain v residue 154 LYS Chi-restraints excluded: chain w residue 89 ILE Chi-restraints excluded: chain w residue 118 ARG Chi-restraints excluded: chain w residue 127 LEU Chi-restraints excluded: chain w residue 226 ASP Chi-restraints excluded: chain x residue 102 ARG Chi-restraints excluded: chain x residue 126 ARG Chi-restraints excluded: chain x residue 151 LEU Chi-restraints excluded: chain x residue 206 ARG Chi-restraints excluded: chain x residue 251 THR Chi-restraints excluded: chain x residue 275 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 707 optimal weight: 5.9990 chunk 745 optimal weight: 10.0000 chunk 679 optimal weight: 7.9990 chunk 724 optimal weight: 3.9990 chunk 744 optimal weight: 7.9990 chunk 436 optimal weight: 7.9990 chunk 315 optimal weight: 20.0000 chunk 569 optimal weight: 4.9990 chunk 222 optimal weight: 10.0000 chunk 654 optimal weight: 7.9990 chunk 685 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN I 50 GLN ** I 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN O 74 GLN P 112 GLN Q 24 ASN Q 50 HIS Q 133 ASN R 46 GLN ** S 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 GLN ** a 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 34 ASN c 47 ASN d 16 ASN d 19 ASN e 17 GLN ** e 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 217 GLN ** f 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 40 ASN ** n 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 HIS r 183 ASN ** t 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 94 ASN ** u 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 197 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 113004 Z= 0.319 Angle : 0.901 25.856 166301 Z= 0.490 Chirality : 0.043 1.998 20526 Planarity : 0.010 0.133 10405 Dihedral : 24.326 179.939 50302 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 4.76 % Allowed : 23.41 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.62 (0.11), residues: 5247 helix: 0.23 (0.12), residues: 1887 sheet: -1.42 (0.18), residues: 702 loop : -0.48 (0.12), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP l 74 HIS 0.009 0.001 HIS Q 187 PHE 0.035 0.002 PHE a 115 TYR 0.025 0.002 TYR w 227 ARG 0.009 0.001 ARG x 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 861 time to evaluate : 4.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.6755 (mmt180) REVERT: I 180 ARG cc_start: 0.7776 (ttp-170) cc_final: 0.7420 (ttm-80) REVERT: I 188 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7656 (mtm110) REVERT: L 149 ARG cc_start: 0.8068 (ttp-110) cc_final: 0.7845 (ttp80) REVERT: N 46 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7693 (tt) REVERT: N 93 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7685 (mtt-85) REVERT: N 125 MET cc_start: 0.8699 (mmm) cc_final: 0.8458 (mmm) REVERT: N 204 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7374 (mtm110) REVERT: O 85 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.6959 (ttmm) REVERT: O 86 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7774 (pp) REVERT: O 103 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7923 (ttp-170) REVERT: O 106 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8153 (pp) REVERT: O 198 LYS cc_start: 0.7324 (mmmt) cc_final: 0.7095 (ttpt) REVERT: Q 45 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: Q 55 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7747 (mt) REVERT: R 14 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7995 (m) REVERT: R 18 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.7863 (ptmt) REVERT: R 141 CYS cc_start: 0.7495 (p) cc_final: 0.5933 (t) REVERT: S 2 VAL cc_start: 0.8088 (m) cc_final: 0.7871 (p) REVERT: S 7 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7458 (mmm160) REVERT: S 149 LEU cc_start: 0.6520 (OUTLIER) cc_final: 0.6247 (OUTLIER) REVERT: T 20 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7293 (t-170) REVERT: T 85 ARG cc_start: 0.7847 (ttp-170) cc_final: 0.7474 (ttt90) REVERT: T 117 ARG cc_start: 0.6741 (ttm110) cc_final: 0.6445 (ttm-80) REVERT: U 38 ASP cc_start: 0.7988 (m-30) cc_final: 0.7769 (m-30) REVERT: U 57 TYR cc_start: 0.8733 (m-80) cc_final: 0.8508 (m-80) REVERT: V 83 MET cc_start: 0.6865 (mmm) cc_final: 0.5738 (tpt) REVERT: V 92 TYR cc_start: 0.8543 (t80) cc_final: 0.8237 (t80) REVERT: V 100 LYS cc_start: 0.7966 (mmmm) cc_final: 0.7565 (mmmt) REVERT: V 106 TRP cc_start: 0.6417 (m100) cc_final: 0.5624 (m-10) REVERT: W 130 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7710 (mtpt) REVERT: Y 7 GLU cc_start: 0.8045 (tp30) cc_final: 0.7729 (tm-30) REVERT: Z 54 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7924 (ttm-80) REVERT: a 45 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7546 (mmm) REVERT: a 66 ARG cc_start: 0.6766 (tmt170) cc_final: 0.6372 (tmt170) REVERT: a 112 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6581 (ttt-90) REVERT: a 113 LYS cc_start: 0.7514 (mmmt) cc_final: 0.6415 (pttt) REVERT: a 116 GLN cc_start: 0.7984 (tp40) cc_final: 0.7505 (tp-100) REVERT: c 78 LYS cc_start: 0.7892 (ptmm) cc_final: 0.6826 (tppt) REVERT: e 245 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7480 (ttt-90) REVERT: f 74 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: f 155 LYS cc_start: 0.7775 (ttmp) cc_final: 0.7514 (ttmm) REVERT: f 169 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7134 (mtt90) REVERT: f 292 ARG cc_start: 0.8196 (mtm110) cc_final: 0.7978 (mtm110) REVERT: f 296 MET cc_start: 0.7781 (mtm) cc_final: 0.7401 (mtt) REVERT: f 325 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8465 (mtt90) REVERT: f 343 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7328 (pt) REVERT: i 91 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7075 (mmp80) REVERT: j 86 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7526 (mm-30) REVERT: j 89 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8303 (tmm160) REVERT: k 37 GLN cc_start: 0.7498 (mm110) cc_final: 0.7216 (mp10) REVERT: k 70 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8077 (mt) REVERT: k 72 LYS cc_start: 0.8256 (mtmt) cc_final: 0.8018 (mttm) REVERT: l 82 TYR cc_start: 0.8871 (t80) cc_final: 0.8642 (t80) REVERT: l 89 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7562 (mpp) REVERT: n 14 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8260 (ptm160) REVERT: o 13 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7657 (ptt90) REVERT: r 14 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6218 (pm20) REVERT: r 16 LYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7150 (pttm) REVERT: r 33 HIS cc_start: 0.8060 (t-90) cc_final: 0.7482 (p-80) REVERT: r 203 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7767 (mpt-90) REVERT: r 281 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7665 (ttm) REVERT: t 11 TYR cc_start: 0.8187 (t80) cc_final: 0.7595 (t80) REVERT: t 72 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7768 (mt) REVERT: u 9 ASN cc_start: 0.8039 (p0) cc_final: 0.7833 (p0) REVERT: x 102 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6891 (ptp90) REVERT: x 126 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.5360 (mtm180) REVERT: x 151 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8104 (tt) REVERT: x 161 ARG cc_start: 0.5657 (ttp80) cc_final: 0.5297 (tpp80) REVERT: x 206 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7709 (mtm110) outliers start: 214 outliers final: 144 residues processed: 984 average time/residue: 1.8605 time to fit residues: 2447.0729 Evaluate side-chains 1022 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 842 time to evaluate : 4.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain I residue 178 LYS Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 204 ARG Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 85 LYS Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain P residue 34 ASN Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 115 VAL Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain Q residue 144 VAL Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 18 LYS Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain S residue 5 HIS Chi-restraints excluded: chain S residue 7 ARG Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 111 GLU Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 140 GLU Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 46 SER Chi-restraints excluded: chain V residue 105 ASP Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 130 LYS Chi-restraints excluded: chain X residue 88 HIS Chi-restraints excluded: chain X residue 106 SER Chi-restraints excluded: chain X residue 120 THR Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 163 ASN Chi-restraints excluded: chain X residue 171 LEU Chi-restraints excluded: chain X residue 185 LEU Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Z residue 22 HIS Chi-restraints excluded: chain Z residue 29 SER Chi-restraints excluded: chain Z residue 40 TYR Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 ARG Chi-restraints excluded: chain Z residue 61 LYS Chi-restraints excluded: chain Z residue 94 VAL Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 45 MET Chi-restraints excluded: chain a residue 112 ARG Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 22 VAL Chi-restraints excluded: chain b residue 107 SER Chi-restraints excluded: chain b residue 141 VAL Chi-restraints excluded: chain b residue 142 VAL Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 39 THR Chi-restraints excluded: chain d residue 13 SER Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 24 LEU Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 112 ILE Chi-restraints excluded: chain e residue 134 CYS Chi-restraints excluded: chain e residue 148 LEU Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 195 CYS Chi-restraints excluded: chain e residue 207 VAL Chi-restraints excluded: chain e residue 245 ARG Chi-restraints excluded: chain f residue 66 LYS Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 104 THR Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 169 ARG Chi-restraints excluded: chain f residue 269 VAL Chi-restraints excluded: chain f residue 295 SER Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 325 ARG Chi-restraints excluded: chain f residue 335 VAL Chi-restraints excluded: chain f residue 343 ILE Chi-restraints excluded: chain f residue 362 THR Chi-restraints excluded: chain f residue 384 SER Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 154 LYS Chi-restraints excluded: chain h residue 168 THR Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain i residue 15 THR Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 32 SER Chi-restraints excluded: chain i residue 96 VAL Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 105 SER Chi-restraints excluded: chain i residue 121 ILE Chi-restraints excluded: chain j residue 83 LEU Chi-restraints excluded: chain j residue 86 GLU Chi-restraints excluded: chain k residue 16 ASP Chi-restraints excluded: chain k residue 70 LEU Chi-restraints excluded: chain k residue 117 LYS Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 89 MET Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain m residue 20 ILE Chi-restraints excluded: chain m residue 69 ARG Chi-restraints excluded: chain m residue 79 ASP Chi-restraints excluded: chain n residue 14 ARG Chi-restraints excluded: chain n residue 43 SER Chi-restraints excluded: chain n residue 77 HIS Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain o residue 70 THR Chi-restraints excluded: chain p residue 23 VAL Chi-restraints excluded: chain r residue 8 SER Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 17 VAL Chi-restraints excluded: chain r residue 28 THR Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 106 ILE Chi-restraints excluded: chain r residue 146 VAL Chi-restraints excluded: chain r residue 203 ARG Chi-restraints excluded: chain r residue 260 SER Chi-restraints excluded: chain r residue 281 MET Chi-restraints excluded: chain r residue 285 THR Chi-restraints excluded: chain r residue 288 THR Chi-restraints excluded: chain t residue 35 LEU Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 72 LEU Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain u residue 60 ILE Chi-restraints excluded: chain u residue 103 LEU Chi-restraints excluded: chain u residue 109 MET Chi-restraints excluded: chain u residue 154 VAL Chi-restraints excluded: chain u residue 161 THR Chi-restraints excluded: chain u residue 214 LEU Chi-restraints excluded: chain u residue 248 MET Chi-restraints excluded: chain u residue 256 ILE Chi-restraints excluded: chain v residue 27 LEU Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 78 ASP Chi-restraints excluded: chain v residue 87 THR Chi-restraints excluded: chain v residue 154 LYS Chi-restraints excluded: chain w residue 89 ILE Chi-restraints excluded: chain w residue 118 ARG Chi-restraints excluded: chain w residue 127 LEU Chi-restraints excluded: chain w residue 226 ASP Chi-restraints excluded: chain x residue 102 ARG Chi-restraints excluded: chain x residue 126 ARG Chi-restraints excluded: chain x residue 151 LEU Chi-restraints excluded: chain x residue 206 ARG Chi-restraints excluded: chain x residue 251 THR Chi-restraints excluded: chain x residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 722 optimal weight: 0.0970 chunk 475 optimal weight: 6.9990 chunk 766 optimal weight: 8.9990 chunk 467 optimal weight: 7.9990 chunk 363 optimal weight: 0.7980 chunk 532 optimal weight: 10.0000 chunk 803 optimal weight: 9.9990 chunk 739 optimal weight: 10.0000 chunk 640 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 494 optimal weight: 20.0000 overall best weight: 3.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN I 50 GLN ** I 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN O 74 GLN Q 24 ASN Q 50 HIS Q 133 ASN R 46 GLN ** S 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 GLN ** a 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 47 ASN d 16 ASN d 19 ASN e 17 GLN e 115 ASN e 161 ASN e 217 GLN ** f 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 40 ASN ** n 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 HIS r 145 ASN r 183 ASN ** t 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 94 ASN ** u 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 197 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 113004 Z= 0.236 Angle : 0.885 26.224 166301 Z= 0.484 Chirality : 0.041 1.968 20526 Planarity : 0.010 0.131 10405 Dihedral : 24.346 179.731 50302 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 4.16 % Allowed : 24.20 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.11), residues: 5247 helix: 0.31 (0.12), residues: 1887 sheet: -1.40 (0.18), residues: 702 loop : -0.46 (0.12), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP l 74 HIS 0.008 0.001 HIS S 5 PHE 0.041 0.002 PHE m 93 TYR 0.026 0.002 TYR u 99 ARG 0.017 0.001 ARG e 145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10494 Ramachandran restraints generated. 5247 Oldfield, 0 Emsley, 5247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 856 time to evaluate : 4.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6702 (mmt-90) REVERT: I 180 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.7398 (ttm-80) REVERT: N 46 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7679 (tt) REVERT: N 93 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7661 (mtt-85) REVERT: N 125 MET cc_start: 0.8683 (mmm) cc_final: 0.8413 (mmm) REVERT: N 204 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7360 (mtm110) REVERT: O 85 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6915 (ttmm) REVERT: O 86 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7739 (pp) REVERT: O 103 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7891 (ttp-170) REVERT: O 106 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8173 (pp) REVERT: O 198 LYS cc_start: 0.7301 (mmmt) cc_final: 0.7077 (ttpt) REVERT: Q 45 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: Q 55 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7725 (mt) REVERT: R 14 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.8012 (m) REVERT: R 18 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7840 (ptmt) REVERT: R 85 ARG cc_start: 0.7598 (tpt170) cc_final: 0.7209 (tmt170) REVERT: R 141 CYS cc_start: 0.7482 (p) cc_final: 0.5982 (t) REVERT: S 2 VAL cc_start: 0.8063 (m) cc_final: 0.7854 (p) REVERT: S 7 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7488 (mmm160) REVERT: S 149 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6241 (OUTLIER) REVERT: T 20 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.7262 (t-170) REVERT: T 85 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7413 (ttt90) REVERT: T 117 ARG cc_start: 0.6726 (ttm110) cc_final: 0.6437 (ttm-80) REVERT: U 38 ASP cc_start: 0.7971 (m-30) cc_final: 0.7753 (m-30) REVERT: U 57 TYR cc_start: 0.8708 (m-80) cc_final: 0.8466 (m-80) REVERT: V 83 MET cc_start: 0.6860 (mmm) cc_final: 0.5715 (tpt) REVERT: V 92 TYR cc_start: 0.8539 (t80) cc_final: 0.8278 (t80) REVERT: V 100 LYS cc_start: 0.7960 (mmmm) cc_final: 0.7558 (mmmt) REVERT: V 106 TRP cc_start: 0.6414 (m100) cc_final: 0.5622 (m-10) REVERT: W 130 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7696 (mtpt) REVERT: Z 54 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7924 (ttm-80) REVERT: Z 66 LYS cc_start: 0.7811 (ttpp) cc_final: 0.7535 (tttm) REVERT: a 45 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7524 (mmm) REVERT: a 66 ARG cc_start: 0.6758 (tmt170) cc_final: 0.6364 (tmt170) REVERT: a 112 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6552 (ttt-90) REVERT: a 113 LYS cc_start: 0.7549 (mmmt) cc_final: 0.6451 (pttt) REVERT: a 116 GLN cc_start: 0.7940 (tp40) cc_final: 0.7461 (tp-100) REVERT: c 78 LYS cc_start: 0.7882 (ptmm) cc_final: 0.6819 (tppt) REVERT: e 245 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7795 (ttt-90) REVERT: f 74 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7995 (mt-10) REVERT: f 155 LYS cc_start: 0.7760 (ttmp) cc_final: 0.7496 (ttmm) REVERT: f 169 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7127 (mtt90) REVERT: f 209 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7173 (mtm180) REVERT: f 296 MET cc_start: 0.7757 (mtm) cc_final: 0.7359 (mtt) REVERT: f 325 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8459 (mtt90) REVERT: i 91 ARG cc_start: 0.7998 (mtp85) cc_final: 0.7055 (mmp80) REVERT: j 89 ARG cc_start: 0.8563 (ttp80) cc_final: 0.8302 (tmm160) REVERT: k 37 GLN cc_start: 0.7476 (mm110) cc_final: 0.7200 (mp10) REVERT: k 70 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7969 (mt) REVERT: k 72 LYS cc_start: 0.8249 (mtmt) cc_final: 0.8012 (mttm) REVERT: l 82 TYR cc_start: 0.8819 (t80) cc_final: 0.8578 (t80) REVERT: l 89 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7553 (mpp) REVERT: n 14 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8233 (ptm160) REVERT: o 13 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7641 (ptt90) REVERT: o 71 LEU cc_start: 0.8984 (tp) cc_final: 0.8773 (tt) REVERT: r 33 HIS cc_start: 0.8050 (t-90) cc_final: 0.7476 (p-80) REVERT: r 203 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7765 (mpt-90) REVERT: r 281 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7706 (ttm) REVERT: t 11 TYR cc_start: 0.8190 (t80) cc_final: 0.7611 (t80) REVERT: t 72 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7749 (mt) REVERT: u 9 ASN cc_start: 0.8035 (p0) cc_final: 0.7829 (p0) REVERT: u 108 ARG cc_start: 0.5545 (OUTLIER) cc_final: 0.3775 (mtt-85) REVERT: u 202 ARG cc_start: 0.4975 (ttm170) cc_final: 0.3037 (tpp-160) REVERT: x 102 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6847 (ptp90) REVERT: x 126 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.5137 (mtm180) REVERT: x 151 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8111 (tt) REVERT: x 161 ARG cc_start: 0.5650 (ttp80) cc_final: 0.5290 (tpp80) REVERT: x 206 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7699 (mtm110) outliers start: 187 outliers final: 133 residues processed: 962 average time/residue: 1.7906 time to fit residues: 2302.4578 Evaluate side-chains 1010 residues out of total 4578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 843 time to evaluate : 4.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 13 ARG Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain I residue 178 LYS Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 204 ARG Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 85 LYS Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain O residue 126 ILE Chi-restraints excluded: chain P residue 34 ASN Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 138 SER Chi-restraints excluded: chain Q residue 45 GLU Chi-restraints excluded: chain Q residue 55 LEU Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 125 LYS Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 18 LYS Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 93 SER Chi-restraints excluded: chain R residue 121 GLN Chi-restraints excluded: chain S residue 5 HIS Chi-restraints excluded: chain S residue 7 ARG Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 149 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 111 GLU Chi-restraints excluded: chain T residue 131 VAL Chi-restraints excluded: chain T residue 138 LEU Chi-restraints excluded: chain T residue 140 GLU Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 46 SER Chi-restraints excluded: chain V residue 105 ASP Chi-restraints excluded: chain W residue 30 ASN Chi-restraints excluded: chain W residue 130 LYS Chi-restraints excluded: chain X residue 88 HIS Chi-restraints excluded: chain X residue 120 THR Chi-restraints excluded: chain X residue 122 ASP Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain X residue 138 VAL Chi-restraints excluded: chain X residue 163 ASN Chi-restraints excluded: chain X residue 185 LEU Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Z residue 22 HIS Chi-restraints excluded: chain Z residue 40 TYR Chi-restraints excluded: chain Z residue 53 VAL Chi-restraints excluded: chain Z residue 54 ARG Chi-restraints excluded: chain Z residue 61 LYS Chi-restraints excluded: chain Z residue 91 THR Chi-restraints excluded: chain Z residue 94 VAL Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain a residue 45 MET Chi-restraints excluded: chain a residue 112 ARG Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 107 SER Chi-restraints excluded: chain b residue 141 VAL Chi-restraints excluded: chain b residue 142 VAL Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain c residue 10 LEU Chi-restraints excluded: chain c residue 29 SER Chi-restraints excluded: chain c residue 39 THR Chi-restraints excluded: chain d residue 13 SER Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 24 LEU Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 89 LEU Chi-restraints excluded: chain e residue 102 LEU Chi-restraints excluded: chain e residue 112 ILE Chi-restraints excluded: chain e residue 134 CYS Chi-restraints excluded: chain e residue 148 LEU Chi-restraints excluded: chain e residue 168 ILE Chi-restraints excluded: chain e residue 195 CYS Chi-restraints excluded: chain e residue 207 VAL Chi-restraints excluded: chain e residue 245 ARG Chi-restraints excluded: chain f residue 66 LYS Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 104 THR Chi-restraints excluded: chain f residue 133 ARG Chi-restraints excluded: chain f residue 169 ARG Chi-restraints excluded: chain f residue 209 ARG Chi-restraints excluded: chain f residue 269 VAL Chi-restraints excluded: chain f residue 323 THR Chi-restraints excluded: chain f residue 325 ARG Chi-restraints excluded: chain f residue 335 VAL Chi-restraints excluded: chain f residue 362 THR Chi-restraints excluded: chain f residue 384 SER Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 154 LYS Chi-restraints excluded: chain h residue 168 THR Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain i residue 15 THR Chi-restraints excluded: chain i residue 16 LYS Chi-restraints excluded: chain i residue 32 SER Chi-restraints excluded: chain i residue 96 VAL Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 105 SER Chi-restraints excluded: chain i residue 121 ILE Chi-restraints excluded: chain j residue 83 LEU Chi-restraints excluded: chain k residue 16 ASP Chi-restraints excluded: chain k residue 70 LEU Chi-restraints excluded: chain k residue 117 LYS Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 88 LYS Chi-restraints excluded: chain l residue 89 MET Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 149 ILE Chi-restraints excluded: chain m residue 69 ARG Chi-restraints excluded: chain m residue 79 ASP Chi-restraints excluded: chain n residue 14 ARG Chi-restraints excluded: chain n residue 43 SER Chi-restraints excluded: chain n residue 77 HIS Chi-restraints excluded: chain o residue 13 ARG Chi-restraints excluded: chain p residue 23 VAL Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 56 LEU Chi-restraints excluded: chain r residue 106 ILE Chi-restraints excluded: chain r residue 146 VAL Chi-restraints excluded: chain r residue 165 GLU Chi-restraints excluded: chain r residue 203 ARG Chi-restraints excluded: chain r residue 260 SER Chi-restraints excluded: chain r residue 281 MET Chi-restraints excluded: chain r residue 285 THR Chi-restraints excluded: chain r residue 288 THR Chi-restraints excluded: chain t residue 35 LEU Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 72 LEU Chi-restraints excluded: chain t residue 93 LEU Chi-restraints excluded: chain u residue 60 ILE Chi-restraints excluded: chain u residue 103 LEU Chi-restraints excluded: chain u residue 108 ARG Chi-restraints excluded: chain u residue 109 MET Chi-restraints excluded: chain u residue 154 VAL Chi-restraints excluded: chain u residue 160 THR Chi-restraints excluded: chain u residue 161 THR Chi-restraints excluded: chain u residue 214 LEU Chi-restraints excluded: chain u residue 248 MET Chi-restraints excluded: chain u residue 256 ILE Chi-restraints excluded: chain v residue 27 LEU Chi-restraints excluded: chain v residue 50 VAL Chi-restraints excluded: chain v residue 78 ASP Chi-restraints excluded: chain v residue 87 THR Chi-restraints excluded: chain v residue 154 LYS Chi-restraints excluded: chain w residue 89 ILE Chi-restraints excluded: chain w residue 110 GLN Chi-restraints excluded: chain w residue 118 ARG Chi-restraints excluded: chain w residue 127 LEU Chi-restraints excluded: chain w residue 226 ASP Chi-restraints excluded: chain x residue 102 ARG Chi-restraints excluded: chain x residue 126 ARG Chi-restraints excluded: chain x residue 151 LEU Chi-restraints excluded: chain x residue 206 ARG Chi-restraints excluded: chain x residue 251 THR Chi-restraints excluded: chain x residue 275 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 392 optimal weight: 6.9990 chunk 508 optimal weight: 10.0000 chunk 681 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 590 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 177 optimal weight: 30.0000 chunk 641 optimal weight: 8.9990 chunk 268 optimal weight: 10.0000 chunk 658 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** I 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN ** I 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 ASN O 74 GLN Q 24 ASN Q 50 HIS ** Q 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 133 ASN R 46 GLN ** S 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 83 GLN ** a 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 GLN ** c 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 47 ASN d 16 ASN d 19 ASN e 17 GLN ** e 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 161 ASN e 217 GLN ** f 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 40 ASN ** n 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 HIS r 145 ASN r 183 ASN ** t 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 94 ASN ** u 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 197 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.154004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127757 restraints weight = 127914.867| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.15 r_work: 0.3163 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 113004 Z= 0.347 Angle : 0.917 25.696 166301 Z= 0.496 Chirality : 0.045 2.000 20526 Planarity : 0.010 0.135 10405 Dihedral : 24.316 179.477 50302 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.08 % Favored : 95.84 % Rotamer: Outliers : 4.40 % Allowed : 24.23 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.11), residues: 5247 helix: 0.21 (0.12), residues: 1897 sheet: -1.40 (0.18), residues: 713 loop : -0.53 (0.12), residues: 2637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP l 74 HIS 0.010 0.001 HIS e 19 PHE 0.036 0.002 PHE a 115 TYR 0.028 0.002 TYR w 227 ARG 0.011 0.001 ARG e 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38035.61 seconds wall clock time: 662 minutes 14.82 seconds (39734.82 seconds total)