Starting phenix.real_space_refine on Sun Feb 25 02:24:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zym_11569/02_2024/6zym_11569_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zym_11569/02_2024/6zym_11569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zym_11569/02_2024/6zym_11569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zym_11569/02_2024/6zym_11569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zym_11569/02_2024/6zym_11569_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zym_11569/02_2024/6zym_11569_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 7 6.06 5 P 243 5.49 5 Mg 5 5.21 5 S 220 5.16 5 C 29750 2.51 5 N 8522 2.21 5 O 9524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 35": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A GLU 64": "OE1" <-> "OE2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 240": "NH1" <-> "NH2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 417": "NH1" <-> "NH2" Residue "A ARG 419": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A PHE 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 642": "NH1" <-> "NH2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A GLU 759": "OE1" <-> "OE2" Residue "A GLU 805": "OE1" <-> "OE2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A GLU 897": "OE1" <-> "OE2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A GLU 967": "OE1" <-> "OE2" Residue "A ARG 1032": "NH1" <-> "NH2" Residue "A GLU 1206": "OE1" <-> "OE2" Residue "A GLU 1219": "OE1" <-> "OE2" Residue "A ARG 1275": "NH1" <-> "NH2" Residue "A GLU 1292": "OE1" <-> "OE2" Residue "A ARG 1341": "NH1" <-> "NH2" Residue "A ARG 1354": "NH1" <-> "NH2" Residue "A GLU 1360": "OE1" <-> "OE2" Residue "A GLU 1388": "OE1" <-> "OE2" Residue "A GLU 1395": "OE1" <-> "OE2" Residue "A GLU 1409": "OE1" <-> "OE2" Residue "A GLU 1499": "OE1" <-> "OE2" Residue "A GLU 1612": "OE1" <-> "OE2" Residue "A ARG 1617": "NH1" <-> "NH2" Residue "A ARG 1641": "NH1" <-> "NH2" Residue "A ARG 1681": "NH1" <-> "NH2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 512": "OE1" <-> "OE2" Residue "B GLU 540": "OE1" <-> "OE2" Residue "B GLU 573": "OE1" <-> "OE2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B GLU 623": "OE1" <-> "OE2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B GLU 782": "OE1" <-> "OE2" Residue "B GLU 932": "OE1" <-> "OE2" Residue "B GLU 945": "OE1" <-> "OE2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ARG 296": "NH1" <-> "NH2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D ARG 282": "NH1" <-> "NH2" Residue "D ARG 365": "NH1" <-> "NH2" Residue "D ARG 376": "NH1" <-> "NH2" Residue "D ARG 449": "NH1" <-> "NH2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "F GLU 339": "OE1" <-> "OE2" Residue "L GLU 15": "OE1" <-> "OE2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "L GLU 68": "OE1" <-> "OE2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "L GLU 133": "OE1" <-> "OE2" Residue "L GLU 154": "OE1" <-> "OE2" Residue "L ARG 158": "NH1" <-> "NH2" Residue "L ARG 169": "NH1" <-> "NH2" Residue "L GLU 178": "OE1" <-> "OE2" Residue "L GLU 190": "OE1" <-> "OE2" Residue "L GLU 213": "OE1" <-> "OE2" Residue "O GLU 200": "OE1" <-> "OE2" Residue "O ARG 201": "NH1" <-> "NH2" Residue "O ARG 228": "NH1" <-> "NH2" Residue "O GLU 232": "OE1" <-> "OE2" Residue "O ARG 236": "NH1" <-> "NH2" Residue "O ARG 239": "NH1" <-> "NH2" Residue "O GLU 252": "OE1" <-> "OE2" Residue "O ARG 262": "NH1" <-> "NH2" Residue "O GLU 266": "OE1" <-> "OE2" Residue "O ARG 267": "NH1" <-> "NH2" Residue "O ARG 274": "NH1" <-> "NH2" Residue "O ARG 290": "NH1" <-> "NH2" Residue "O ARG 308": "NH1" <-> "NH2" Residue "O TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 334": "OE1" <-> "OE2" Residue "O GLU 353": "OE1" <-> "OE2" Residue "O GLU 400": "OE1" <-> "OE2" Residue "P GLU 30": "OE1" <-> "OE2" Residue "P ARG 35": "NH1" <-> "NH2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 64": "NH1" <-> "NH2" Residue "P GLU 69": "OE1" <-> "OE2" Residue "P ASP 106": "OD1" <-> "OD2" Residue "P ARG 123": "NH1" <-> "NH2" Residue "P ARG 132": "NH1" <-> "NH2" Residue "P ARG 161": "NH1" <-> "NH2" Residue "P GLU 172": "OE1" <-> "OE2" Residue "P GLU 177": "OE1" <-> "OE2" Residue "P GLU 178": "OE1" <-> "OE2" Residue "P ARG 182": "NH1" <-> "NH2" Residue "P ARG 201": "NH1" <-> "NH2" Residue "Q ARG 8": "NH1" <-> "NH2" Residue "Q ARG 30": "NH1" <-> "NH2" Residue "Q GLU 31": "OE1" <-> "OE2" Residue "Q GLU 33": "OE1" <-> "OE2" Residue "Q ARG 58": "NH1" <-> "NH2" Residue "Q ARG 72": "NH1" <-> "NH2" Residue "Q GLU 76": "OE1" <-> "OE2" Residue "Q ARG 120": "NH1" <-> "NH2" Residue "Q ARG 140": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ARG 57": "NH1" <-> "NH2" Residue "R GLU 67": "OE1" <-> "OE2" Residue "R ARG 209": "NH1" <-> "NH2" Residue "R GLU 225": "OE1" <-> "OE2" Residue "S ARG 11": "NH1" <-> "NH2" Residue "S ARG 30": "NH1" <-> "NH2" Residue "T GLU 470": "OE1" <-> "OE2" Residue "T GLU 480": "OE1" <-> "OE2" Residue "T GLU 523": "OE1" <-> "OE2" Residue "T GLU 531": "OE1" <-> "OE2" Residue "T ARG 538": "NH1" <-> "NH2" Residue "T ARG 545": "NH1" <-> "NH2" Residue "T GLU 572": "OE1" <-> "OE2" Residue "T GLU 573": "OE1" <-> "OE2" Residue "T ARG 602": "NH1" <-> "NH2" Residue "T GLU 613": "OE1" <-> "OE2" Residue "T GLU 645": "OE1" <-> "OE2" Residue "V ARG 72": "NH1" <-> "NH2" Residue "V ARG 131": "NH1" <-> "NH2" Residue "V ARG 141": "NH1" <-> "NH2" Residue "V ARG 152": "NH1" <-> "NH2" Residue "p TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 298": "OE1" <-> "OE2" Residue "p ARG 326": "NH1" <-> "NH2" Residue "p ARG 396": "NH1" <-> "NH2" Residue "p ARG 446": "NH1" <-> "NH2" Residue "p ARG 458": "NH1" <-> "NH2" Residue "p GLU 466": "OE1" <-> "OE2" Residue "p ARG 476": "NH1" <-> "NH2" Residue "r ARG 381": "NH1" <-> "NH2" Residue "s ARG 3": "NH1" <-> "NH2" Residue "s ARG 16": "NH1" <-> "NH2" Residue "t ARG 18": "NH1" <-> "NH2" Residue "t GLU 27": "OE1" <-> "OE2" Residue "t GLU 33": "OE1" <-> "OE2" Residue "t GLU 39": "OE1" <-> "OE2" Residue "u PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 82": "NH1" <-> "NH2" Residue "u GLU 86": "OE1" <-> "OE2" Residue "u ARG 140": "NH1" <-> "NH2" Residue "x GLU 242": "OE1" <-> "OE2" Residue "x ARG 255": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 48271 Number of models: 1 Model: "" Number of chains: 32 Chain: "2" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 575 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna2p': 6, 'rna3p': 20} Chain: "5" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1548 Classifications: {'RNA': 74} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 28, 'rna3p_pyr': 38} Link IDs: {'rna2p': 8, 'rna3p': 65} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' A%rna3p_pur:plan2': 1, ' A%rna3p_pur:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "6" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1690 Classifications: {'RNA': 79} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 37, 'rna3p_pyr': 30} Link IDs: {'rna2p': 12, 'rna3p': 66} Chain: "9" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 112 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "A" Number of atoms: 14270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1722, 14270 Classifications: {'peptide': 1722} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 2, 'PTRANS': 91, 'TRANS': 1628} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 6953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 6953 Classifications: {'peptide': 895} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 54, 'TRANS': 840} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1703 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2481 Classifications: {'peptide': 315} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 303} Chain: "E" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 69} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2230 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 289} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 78 Chain: "L" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1611 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 192} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "O" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2108 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 4, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "P" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1577 Classifications: {'peptide': 195} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "Q" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1162 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 135} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 681 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "S" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 230 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "T" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1669 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 195} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1081 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 11, 'TRANS': 151} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 119 Chain: "Y" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 873 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 15, 'rna3p_pyr': 11} Link IDs: {'rna2p': 14, 'rna3p': 26} Chain breaks: 1 Chain: "Z" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 276 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 7} Chain: "p" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2372 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 13, 'TRANS': 311} Chain breaks: 1 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "r" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 259 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 34} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "s" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 158 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "t" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 418 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 54} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "u" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1286 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 147} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 23 Chain: "x" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 239 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "6" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 37054 SG CYS P 165 146.072 83.940 136.409 1.00 50.61 S ATOM 37120 SG CYS P 173 144.409 84.837 139.526 1.00 55.00 S ATOM 37168 SG CYS P 179 143.490 81.846 137.824 1.00 55.80 S ATOM 35991 SG CYS P 24 145.321 62.605 120.177 1.00 41.55 S ATOM 36013 SG CYS P 27 143.808 65.874 121.194 1.00 44.98 S ATOM 36456 SG CYS P 81 143.436 64.595 117.712 1.00 42.80 S ATOM 36478 SG CYS P 84 146.612 65.643 118.862 1.00 46.89 S ATOM 36162 SG CYS P 45 139.542 73.463 108.726 1.00 47.09 S ATOM 36185 SG CYS P 48 138.576 74.164 105.437 1.00 51.91 S ATOM 36381 SG CYS P 71 137.504 71.074 106.943 1.00 42.46 S ATOM 36403 SG CYS P 74 140.994 71.610 106.095 1.00 45.70 S ATOM 38327 SG CYS Q 101 122.649 79.054 144.359 1.00 36.44 S ATOM 38333 SG CYS Q 102 121.010 80.985 142.012 1.00 32.30 S ATOM 38358 SG CYS Q 105 123.653 78.542 140.723 1.00 35.44 S ATOM 38608 SG CYS Q 137 124.620 81.595 142.929 1.00 36.50 S ATOM 38327 SG CYS Q 101 122.649 79.054 144.359 1.00 36.44 S ATOM 38466 SG CYS Q 119 125.211 76.047 143.666 1.00 41.91 S ATOM 38618 SG CYS Q 139 126.675 78.893 144.948 1.00 43.50 S ATOM 38639 SG CYS Q 142 124.438 76.427 147.351 1.00 43.09 S ATOM 38358 SG CYS Q 105 123.653 78.542 140.723 1.00 35.44 S ATOM 38452 SG CYS Q 117 125.740 75.264 140.022 1.00 39.28 S ATOM 38466 SG CYS Q 119 125.211 76.047 143.666 1.00 41.91 S ATOM 38585 SG CYS Q 134 127.438 78.156 141.577 1.00 38.37 S ATOM 47008 SG CYS u 43 150.681 120.267 72.077 1.00 60.11 S ATOM 47030 SG CYS u 46 150.791 116.642 71.017 1.00 66.02 S ATOM 47321 SG CYS u 80 148.398 117.882 73.301 1.00 64.68 S ATOM 47345 SG CYS u 83 151.163 117.878 74.034 1.00 68.50 S Time building chain proxies: 24.73, per 1000 atoms: 0.51 Number of scatterers: 48271 At special positions: 0 Unit cell: (180.2, 201.4, 187.62, 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 7 29.99 S 220 16.00 P 243 15.00 Mg 5 11.99 O 9524 8.00 N 8522 7.00 C 29750 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.92 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN P 301 " pdb="ZN ZN P 301 " - pdb=" NE2 HIS P 183 " pdb="ZN ZN P 301 " - pdb=" SG CYS P 179 " pdb="ZN ZN P 301 " - pdb=" SG CYS P 173 " pdb="ZN ZN P 301 " - pdb=" SG CYS P 165 " pdb=" ZN P 302 " pdb="ZN ZN P 302 " - pdb=" SG CYS P 84 " pdb="ZN ZN P 302 " - pdb=" SG CYS P 81 " pdb="ZN ZN P 302 " - pdb=" SG CYS P 24 " pdb="ZN ZN P 302 " - pdb=" SG CYS P 27 " pdb=" ZN P 303 " pdb="ZN ZN P 303 " - pdb=" SG CYS P 48 " pdb="ZN ZN P 303 " - pdb=" SG CYS P 45 " pdb="ZN ZN P 303 " - pdb=" SG CYS P 74 " pdb="ZN ZN P 303 " - pdb=" SG CYS P 71 " pdb=" ZN Q 201 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 101 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 102 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 137 " pdb="ZN ZN Q 201 " - pdb=" SG CYS Q 105 " pdb=" ZN Q 202 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 119 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 139 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 101 " pdb="ZN ZN Q 202 " - pdb=" SG CYS Q 142 " pdb=" ZN Q 203 " pdb="ZN ZN Q 203 " - pdb=" SG CYS Q 134 " pdb="ZN ZN Q 203 " - pdb=" SG CYS Q 117 " pdb="ZN ZN Q 203 " - pdb=" SG CYS Q 119 " pdb="ZN ZN Q 203 " - pdb=" SG CYS Q 105 " pdb=" ZN u1001 " pdb="ZN ZN u1001 " - pdb=" SG CYS u 83 " pdb="ZN ZN u1001 " - pdb=" SG CYS u 80 " pdb="ZN ZN u1001 " - pdb=" SG CYS u 43 " pdb="ZN ZN u1001 " - pdb=" SG CYS u 46 " Number of angles added : 39 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10322 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 152 helices and 45 sheets defined 31.9% alpha, 10.2% beta 43 base pairs and 112 stacking pairs defined. Time for finding SS restraints: 23.57 Creating SS restraints... Processing helix chain 'A' and resid 28 through 44 Processing helix chain 'A' and resid 63 through 73 removed outlier: 3.661A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 removed outlier: 4.592A pdb=" N LEU A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.526A pdb=" N LYS A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 155 removed outlier: 3.640A pdb=" N ILE A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 154 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 312 through 315 No H-bonds generated for 'chain 'A' and resid 312 through 315' Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 428 through 432 removed outlier: 3.618A pdb=" N ARG A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 428 through 432' Processing helix chain 'A' and resid 441 through 459 removed outlier: 3.848A pdb=" N GLN A 448 " --> pdb=" O ARG A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 489 through 510 removed outlier: 3.536A pdb=" N LEU A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 507 " --> pdb=" O MET A 503 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 538 removed outlier: 3.525A pdb=" N LYS A 537 " --> pdb=" O LYS A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 566 removed outlier: 3.639A pdb=" N CYS A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 Processing helix chain 'A' and resid 585 through 588 No H-bonds generated for 'chain 'A' and resid 585 through 588' Processing helix chain 'A' and resid 599 through 616 removed outlier: 3.825A pdb=" N HIS A 610 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 660 removed outlier: 3.502A pdb=" N ARG A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TRP A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 638 " --> pdb=" O TRP A 634 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET A 641 " --> pdb=" O TRP A 637 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG A 642 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR A 645 " --> pdb=" O MET A 641 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 679 through 696 removed outlier: 3.680A pdb=" N ALA A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET A 690 " --> pdb=" O ARG A 686 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS A 691 " --> pdb=" O ALA A 687 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 721 Processing helix chain 'A' and resid 733 through 763 removed outlier: 3.570A pdb=" N ASN A 757 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 796 removed outlier: 3.867A pdb=" N LEU A 776 " --> pdb=" O CYS A 772 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 781 " --> pdb=" O GLY A 777 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 789 " --> pdb=" O LYS A 785 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 819 removed outlier: 3.787A pdb=" N ALA A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 849 removed outlier: 4.520A pdb=" N THR A 836 " --> pdb=" O LYS A 833 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS A 837 " --> pdb=" O HIS A 834 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 840 " --> pdb=" O LYS A 837 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU A 843 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU A 848 " --> pdb=" O ARG A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 872 removed outlier: 4.249A pdb=" N GLU A 863 " --> pdb=" O SER A 859 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 871 " --> pdb=" O ILE A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 887 removed outlier: 3.749A pdb=" N SER A 879 " --> pdb=" O HIS A 875 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 931 removed outlier: 3.953A pdb=" N ILE A 917 " --> pdb=" O PRO A 913 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 922 " --> pdb=" O THR A 918 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 931 " --> pdb=" O TRP A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 960 Processing helix chain 'A' and resid 991 through 997 removed outlier: 4.070A pdb=" N ARG A 995 " --> pdb=" O THR A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1012 removed outlier: 3.729A pdb=" N TYR A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1053 removed outlier: 3.897A pdb=" N SER A1038 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE A1040 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL A1041 " --> pdb=" O SER A1038 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A1053 " --> pdb=" O LEU A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1062 Processing helix chain 'A' and resid 1103 through 1113 removed outlier: 3.664A pdb=" N ARG A1107 " --> pdb=" O ALA A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1138 No H-bonds generated for 'chain 'A' and resid 1136 through 1138' Processing helix chain 'A' and resid 1144 through 1160 removed outlier: 3.817A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1172 No H-bonds generated for 'chain 'A' and resid 1170 through 1172' Processing helix chain 'A' and resid 1234 through 1249 removed outlier: 3.850A pdb=" N ARG A1239 " --> pdb=" O GLU A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1271 Processing helix chain 'A' and resid 1282 through 1303 removed outlier: 3.556A pdb=" N LEU A1287 " --> pdb=" O GLU A1283 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A1303 " --> pdb=" O ILE A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1317 Processing helix chain 'A' and resid 1320 through 1322 No H-bonds generated for 'chain 'A' and resid 1320 through 1322' Processing helix chain 'A' and resid 1368 through 1371 Processing helix chain 'A' and resid 1376 through 1397 removed outlier: 4.017A pdb=" N ASP A1381 " --> pdb=" O SER A1377 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A1388 " --> pdb=" O ARG A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1407 No H-bonds generated for 'chain 'A' and resid 1405 through 1407' Processing helix chain 'A' and resid 1419 through 1421 No H-bonds generated for 'chain 'A' and resid 1419 through 1421' Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1436 through 1445 removed outlier: 4.897A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR A1445 " --> pdb=" O ASP A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1471 through 1478 removed outlier: 3.670A pdb=" N ILE A1475 " --> pdb=" O ARG A1471 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN A1476 " --> pdb=" O THR A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1491 through 1493 No H-bonds generated for 'chain 'A' and resid 1491 through 1493' Processing helix chain 'A' and resid 1531 through 1537 Processing helix chain 'A' and resid 1539 through 1542 No H-bonds generated for 'chain 'A' and resid 1539 through 1542' Processing helix chain 'A' and resid 1567 through 1576 removed outlier: 4.191A pdb=" N ILE A1571 " --> pdb=" O PRO A1567 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN A1575 " --> pdb=" O ILE A1571 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A1576 " --> pdb=" O SER A1572 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1599 Processing helix chain 'A' and resid 1676 through 1687 Processing helix chain 'A' and resid 1723 through 1735 removed outlier: 4.995A pdb=" N GLN A1728 " --> pdb=" O PRO A1724 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A1735 " --> pdb=" O ALA A1731 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1751 removed outlier: 3.584A pdb=" N LEU A1743 " --> pdb=" O ALA A1739 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A1744 " --> pdb=" O LEU A1740 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 72 No H-bonds generated for 'chain 'B' and resid 69 through 72' Processing helix chain 'B' and resid 116 through 125 removed outlier: 3.742A pdb=" N MET B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 152 removed outlier: 4.000A pdb=" N ASP B 147 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 152 " --> pdb=" O CYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 No H-bonds generated for 'chain 'B' and resid 174 through 177' Processing helix chain 'B' and resid 209 through 219 removed outlier: 3.660A pdb=" N SER B 212 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASP B 213 " --> pdb=" O ASN B 210 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU B 214 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 217 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 248 removed outlier: 3.836A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 292 removed outlier: 3.847A pdb=" N TYR B 276 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 336 through 342 removed outlier: 4.211A pdb=" N LYS B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 392 through 398 removed outlier: 3.957A pdb=" N GLU B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 423 removed outlier: 3.506A pdb=" N LYS B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 437 removed outlier: 3.869A pdb=" N HIS B 437 " --> pdb=" O MET B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 452 Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 597 through 613 removed outlier: 3.934A pdb=" N LEU B 600 " --> pdb=" O PRO B 597 " (cutoff:3.500A) Proline residue: B 601 - end of helix removed outlier: 3.605A pdb=" N LYS B 612 " --> pdb=" O LYS B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 646 Processing helix chain 'B' and resid 696 through 701 Processing helix chain 'B' and resid 711 through 722 Processing helix chain 'B' and resid 726 through 729 No H-bonds generated for 'chain 'B' and resid 726 through 729' Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 756 through 761 Processing helix chain 'B' and resid 768 through 771 No H-bonds generated for 'chain 'B' and resid 768 through 771' Processing helix chain 'B' and resid 805 through 823 Proline residue: B 810 - end of helix removed outlier: 4.230A pdb=" N ARG B 814 " --> pdb=" O PRO B 810 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 815 " --> pdb=" O THR B 811 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 816 " --> pdb=" O ALA B 812 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR B 817 " --> pdb=" O ARG B 813 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET B 822 " --> pdb=" O SER B 818 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 853 removed outlier: 4.135A pdb=" N SER B 844 " --> pdb=" O ASP B 841 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA B 845 " --> pdb=" O CYS B 842 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 846 " --> pdb=" O VAL B 843 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG B 852 " --> pdb=" O VAL B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 880 No H-bonds generated for 'chain 'B' and resid 878 through 880' Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 926 through 941 removed outlier: 3.813A pdb=" N LEU B 929 " --> pdb=" O ALA B 926 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA B 930 " --> pdb=" O PRO B 927 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 936 " --> pdb=" O PHE B 933 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 939 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 137 through 162 removed outlier: 3.695A pdb=" N ILE C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 242 No H-bonds generated for 'chain 'C' and resid 239 through 242' Processing helix chain 'C' and resid 283 through 301 Processing helix chain 'E' and resid 85 through 88 No H-bonds generated for 'chain 'E' and resid 85 through 88' Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.720A pdb=" N GLU E 126 " --> pdb=" O ASP E 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 25 removed outlier: 3.860A pdb=" N LEU L 19 " --> pdb=" O GLU L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 34 No H-bonds generated for 'chain 'L' and resid 31 through 34' Processing helix chain 'L' and resid 43 through 53 Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.703A pdb=" N LYS L 70 " --> pdb=" O GLU L 66 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU L 72 " --> pdb=" O GLU L 68 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS L 73 " --> pdb=" O GLU L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 89 No H-bonds generated for 'chain 'L' and resid 86 through 89' Processing helix chain 'L' and resid 93 through 109 Processing helix chain 'L' and resid 148 through 159 Processing helix chain 'L' and resid 168 through 194 Processing helix chain 'O' and resid 191 through 199 Processing helix chain 'O' and resid 219 through 237 Processing helix chain 'O' and resid 243 through 255 removed outlier: 3.814A pdb=" N LEU O 255 " --> pdb=" O TRP O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 258 through 271 removed outlier: 3.534A pdb=" N SER O 263 " --> pdb=" O GLN O 259 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP O 270 " --> pdb=" O GLU O 266 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL O 271 " --> pdb=" O ARG O 267 " (cutoff:3.500A) Processing helix chain 'O' and resid 277 through 288 removed outlier: 3.658A pdb=" N LYS O 281 " --> pdb=" O THR O 277 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET O 285 " --> pdb=" O LYS O 281 " (cutoff:3.500A) Processing helix chain 'O' and resid 292 through 305 Processing helix chain 'O' and resid 310 through 322 removed outlier: 4.071A pdb=" N LYS O 315 " --> pdb=" O GLN O 311 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 339 removed outlier: 4.004A pdb=" N GLN O 331 " --> pdb=" O ALA O 327 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU O 338 " --> pdb=" O GLU O 334 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TRP O 339 " --> pdb=" O ARG O 335 " (cutoff:3.500A) Processing helix chain 'O' and resid 343 through 356 removed outlier: 4.164A pdb=" N ARG O 355 " --> pdb=" O ASN O 351 " (cutoff:3.500A) Processing helix chain 'O' and resid 360 through 372 removed outlier: 4.138A pdb=" N THR O 364 " --> pdb=" O ASP O 360 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU O 371 " --> pdb=" O GLU O 367 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 389 removed outlier: 4.065A pdb=" N ALA O 383 " --> pdb=" O TRP O 379 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS O 388 " --> pdb=" O ARG O 384 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS O 389 " --> pdb=" O PHE O 385 " (cutoff:3.500A) Processing helix chain 'O' and resid 392 through 405 removed outlier: 3.765A pdb=" N ARG O 401 " --> pdb=" O LYS O 397 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU O 404 " --> pdb=" O GLU O 400 " (cutoff:3.500A) Processing helix chain 'O' and resid 416 through 425 removed outlier: 3.769A pdb=" N ASN O 425 " --> pdb=" O LYS O 421 " (cutoff:3.500A) Processing helix chain 'O' and resid 432 through 438 removed outlier: 3.873A pdb=" N TYR O 436 " --> pdb=" O VAL O 432 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 78 removed outlier: 3.727A pdb=" N LYS P 78 " --> pdb=" O CYS P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 100 Processing helix chain 'P' and resid 113 through 127 removed outlier: 3.667A pdb=" N SER P 126 " --> pdb=" O GLU P 122 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN P 127 " --> pdb=" O ARG P 123 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 150 Processing helix chain 'P' and resid 166 through 170 removed outlier: 3.963A pdb=" N LYS P 170 " --> pdb=" O SER P 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 166 through 170' Processing helix chain 'P' and resid 199 through 202 No H-bonds generated for 'chain 'P' and resid 199 through 202' Processing helix chain 'P' and resid 208 through 215 removed outlier: 3.892A pdb=" N LYS P 212 " --> pdb=" O PRO P 208 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 34 removed outlier: 3.565A pdb=" N THR Q 34 " --> pdb=" O ARG Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 62 Proline residue: Q 48 - end of helix removed outlier: 3.665A pdb=" N ILE Q 52 " --> pdb=" O ILE Q 49 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS Q 53 " --> pdb=" O PHE Q 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR Q 59 " --> pdb=" O LYS Q 56 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE Q 60 " --> pdb=" O THR Q 57 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP Q 62 " --> pdb=" O TYR Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 72 through 81 Processing helix chain 'Q' and resid 86 through 92 removed outlier: 3.753A pdb=" N ALA Q 90 " --> pdb=" O LYS Q 86 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS Q 91 " --> pdb=" O ASN Q 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 72 removed outlier: 3.502A pdb=" N GLU R 64 " --> pdb=" O ARG R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 227 removed outlier: 3.743A pdb=" N GLU R 225 " --> pdb=" O LYS R 221 " (cutoff:3.500A) Processing helix chain 'T' and resid 450 through 464 removed outlier: 3.575A pdb=" N TYR T 460 " --> pdb=" O ARG T 456 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA T 462 " --> pdb=" O THR T 458 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE T 463 " --> pdb=" O ILE T 459 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 477 removed outlier: 3.547A pdb=" N ALA T 473 " --> pdb=" O PHE T 469 " (cutoff:3.500A) Processing helix chain 'T' and resid 483 through 498 removed outlier: 3.807A pdb=" N THR T 486 " --> pdb=" O GLU T 483 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS T 487 " --> pdb=" O SER T 484 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE T 493 " --> pdb=" O CYS T 490 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N CYS T 496 " --> pdb=" O ILE T 493 " (cutoff:3.500A) Processing helix chain 'T' and resid 505 through 515 Processing helix chain 'T' and resid 519 through 534 removed outlier: 3.844A pdb=" N ASP T 534 " --> pdb=" O LYS T 530 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 556 Processing helix chain 'T' and resid 565 through 567 No H-bonds generated for 'chain 'T' and resid 565 through 567' Processing helix chain 'T' and resid 580 through 606 removed outlier: 4.346A pdb=" N ILE T 585 " --> pdb=" O ILE T 581 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR T 593 " --> pdb=" O GLU T 589 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET T 594 " --> pdb=" O LEU T 590 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU T 596 " --> pdb=" O GLU T 592 " (cutoff:3.500A) Proline residue: T 597 - end of helix removed outlier: 3.749A pdb=" N ALA T 601 " --> pdb=" O PRO T 597 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG T 602 " --> pdb=" O LYS T 598 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU T 606 " --> pdb=" O ARG T 602 " (cutoff:3.500A) Processing helix chain 'T' and resid 621 through 633 removed outlier: 3.656A pdb=" N THR T 632 " --> pdb=" O ILE T 628 " (cutoff:3.500A) Processing helix chain 'T' and resid 641 through 648 removed outlier: 4.255A pdb=" N GLU T 645 " --> pdb=" O ASP T 641 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS T 646 " --> pdb=" O GLU T 642 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU T 647 " --> pdb=" O LEU T 643 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 44 removed outlier: 3.773A pdb=" N LYS V 37 " --> pdb=" O PRO V 33 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN V 38 " --> pdb=" O LYS V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 120 through 122 No H-bonds generated for 'chain 'V' and resid 120 through 122' Processing helix chain 'V' and resid 136 through 144 removed outlier: 4.028A pdb=" N MET V 144 " --> pdb=" O ASN V 140 " (cutoff:3.500A) Processing helix chain 'r' and resid 371 through 384 removed outlier: 3.921A pdb=" N GLU r 375 " --> pdb=" O ASN r 371 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG r 376 " --> pdb=" O GLU r 372 " (cutoff:3.500A) Processing helix chain 's' and resid 11 through 19 Processing helix chain 't' and resid 6 through 9 Processing helix chain 't' and resid 17 through 56 removed outlier: 3.963A pdb=" N VAL t 23 " --> pdb=" O ASN t 19 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS t 30 " --> pdb=" O ALA t 26 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU t 33 " --> pdb=" O LYS t 29 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG t 55 " --> pdb=" O GLU t 51 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR t 56 " --> pdb=" O GLU t 52 " (cutoff:3.500A) Processing helix chain 'u' and resid 134 through 161 removed outlier: 3.776A pdb=" N LYS u 142 " --> pdb=" O GLU u 138 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU u 160 " --> pdb=" O GLU u 156 " (cutoff:3.500A) Processing helix chain 'u' and resid 167 through 175 Processing helix chain 'x' and resid 232 through 237 Processing helix chain 'x' and resid 240 through 250 removed outlier: 3.645A pdb=" N LYS x 250 " --> pdb=" O ASP x 246 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 482 through 488 Processing sheet with id= B, first strand: chain 'A' and resid 516 through 518 Processing sheet with id= C, first strand: chain 'A' and resid 895 through 900 removed outlier: 3.576A pdb=" N GLY A 895 " --> pdb=" O ASP A 910 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1174 through 1178 removed outlier: 3.712A pdb=" N LEU A1087 " --> pdb=" O PHE A1098 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1016 through 1018 Processing sheet with id= F, first strand: chain 'A' and resid 1184 through 1189 removed outlier: 3.575A pdb=" N PHE A1187 " --> pdb=" O CYS A1194 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1661 through 1667 Processing sheet with id= H, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.699A pdb=" N GLY B 224 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N CYS B 135 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL B 226 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 252 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU B 227 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR B 254 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ILE B 229 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS B 256 " --> pdb=" O ILE B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 188 through 190 Processing sheet with id= J, first strand: chain 'B' and resid 309 through 311 removed outlier: 3.673A pdb=" N SER B 311 " --> pdb=" O ILE B 316 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 480 through 482 Processing sheet with id= L, first strand: chain 'B' and resid 523 through 526 removed outlier: 3.692A pdb=" N VAL B 509 " --> pdb=" O GLN B 523 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 530 through 533 removed outlier: 3.938A pdb=" N LEU B 530 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 653 through 655 removed outlier: 4.172A pdb=" N HIS B 627 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR B 618 " --> pdb=" O LEU B 630 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 662 through 666 removed outlier: 3.956A pdb=" N HIS B 903 " --> pdb=" O TYR B 831 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N PHE B 833 " --> pdb=" O PHE B 901 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N PHE B 901 " --> pdb=" O PHE B 833 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLU B 835 " --> pdb=" O SER B 899 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N SER B 899 " --> pdb=" O GLU B 835 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLN B 837 " --> pdb=" O SER B 897 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER B 897 " --> pdb=" O GLN B 837 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 743 through 747 removed outlier: 6.950A pdb=" N VAL B 787 " --> pdb=" O ILE B 744 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL B 746 " --> pdb=" O VAL B 787 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE B 789 " --> pdb=" O VAL B 746 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR B 686 " --> pdb=" O LEU B 792 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 831 through 835 removed outlier: 6.399A pdb=" N PHE B 874 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL B 857 " --> pdb=" O PHE B 874 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.849A pdb=" N SER B 498 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N HIS B 477 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 496 " --> pdb=" O HIS B 477 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 176 through 180 Processing sheet with id= T, first strand: chain 'D' and resid 207 through 212 removed outlier: 6.718A pdb=" N GLY D 222 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE D 210 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL D 220 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL D 212 " --> pdb=" O TRP D 218 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TRP D 218 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ASP D 232 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU D 238 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 272 through 274 Processing sheet with id= V, first strand: chain 'D' and resid 291 through 296 removed outlier: 6.618A pdb=" N CYS D 306 " --> pdb=" O TYR D 292 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU D 294 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL D 304 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU D 296 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL D 302 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS D 324 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP D 316 " --> pdb=" O SER D 322 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER D 322 " --> pdb=" O ASP D 316 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 395 through 397 removed outlier: 3.562A pdb=" N GLN D 407 " --> pdb=" O GLN D 397 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 416 through 421 removed outlier: 6.867A pdb=" N GLY D 430 " --> pdb=" O ASN D 417 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU D 419 " --> pdb=" O VAL D 428 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL D 428 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL D 421 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 426 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR D 435 " --> pdb=" O ALA D 431 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN D 448 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASP D 440 " --> pdb=" O ASN D 446 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN D 446 " --> pdb=" O ASP D 440 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 194 through 200 removed outlier: 7.135A pdb=" N VAL D 488 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL D 199 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE D 486 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR D 485 " --> pdb=" O GLU D 481 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA D 467 " --> pdb=" O ALA D 480 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 333 through 338 removed outlier: 6.869A pdb=" N GLY D 348 " --> pdb=" O ALA D 334 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL D 336 " --> pdb=" O ILE D 346 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE D 346 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 354 through 357 removed outlier: 3.554A pdb=" N VAL D 366 " --> pdb=" O LEU D 356 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 375 through 380 removed outlier: 3.688A pdb=" N ARG D 376 " --> pdb=" O GLY D 390 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLY D 390 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL D 378 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA D 388 " --> pdb=" O VAL D 378 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'F' and resid 61 through 63 removed outlier: 4.342A pdb=" N ARG F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER F 346 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR F 352 " --> pdb=" O SER F 344 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER F 344 " --> pdb=" O TYR F 352 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 90 through 92 removed outlier: 4.413A pdb=" N ALA F 103 " --> pdb=" O LEU F 92 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 123 through 127 removed outlier: 3.546A pdb=" N SER F 126 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL F 133 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASP F 137 " --> pdb=" O ARG F 143 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG F 143 " --> pdb=" O ASP F 137 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 176 through 179 removed outlier: 3.653A pdb=" N THR F 169 " --> pdb=" O LYS F 177 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 198 through 200 removed outlier: 4.437A pdb=" N TYR F 229 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 275 through 278 removed outlier: 4.460A pdb=" N THR F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 291 through 293 Processing sheet with id= AJ, first strand: chain 'F' and resid 69 through 74 removed outlier: 6.657A pdb=" N ALA F 84 " --> pdb=" O TYR F 70 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS F 72 " --> pdb=" O ALA F 82 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA F 82 " --> pdb=" O CYS F 72 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 309 through 312 removed outlier: 3.609A pdb=" N TYR F 321 " --> pdb=" O VAL F 311 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'V' and resid 159 through 164 removed outlier: 6.572A pdb=" N GLU V 17 " --> pdb=" O ILE V 160 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA V 162 " --> pdb=" O TYR V 15 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR V 15 " --> pdb=" O ALA V 162 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL V 24 " --> pdb=" O GLN V 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN V 134 " --> pdb=" O VAL V 24 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU V 26 " --> pdb=" O VAL V 132 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N VAL V 132 " --> pdb=" O GLU V 26 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR V 127 " --> pdb=" O MET V 100 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU V 98 " --> pdb=" O PHE V 129 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE V 112 " --> pdb=" O GLY V 64 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET V 61 " --> pdb=" O ILE V 57 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'p' and resid 176 through 179 removed outlier: 3.909A pdb=" N ARG p 476 " --> pdb=" O GLY p 489 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'p' and resid 222 through 224 removed outlier: 3.931A pdb=" N ARG p 222 " --> pdb=" O PHE p 208 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU p 224 " --> pdb=" O VAL p 206 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'p' and resid 321 through 323 removed outlier: 3.586A pdb=" N SER p 321 " --> pdb=" O THR p 310 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR p 307 " --> pdb=" O SER p 303 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS p 302 " --> pdb=" O THR p 288 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR p 288 " --> pdb=" O CYS p 302 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'p' and resid 356 through 359 removed outlier: 3.611A pdb=" N TRP p 359 " --> pdb=" O ILE p 347 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR p 337 " --> pdb=" O ALA p 350 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'p' and resid 384 through 386 Processing sheet with id= AR, first strand: chain 'p' and resid 437 through 441 removed outlier: 4.278A pdb=" N TYR p 465 " --> pdb=" O PHE p 455 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'u' and resid 31 through 36 removed outlier: 7.262A pdb=" N ASN u 57 " --> pdb=" O LYS u 79 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LYS u 79 " --> pdb=" O ASN u 57 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG u 59 " --> pdb=" O TYR u 77 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE u 73 " --> pdb=" O VAL u 63 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N PHE u 74 " --> pdb=" O THR u 91 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE u 76 " --> pdb=" O PHE u 89 " (cutoff:3.500A) 1250 hydrogen bonds defined for protein. 3435 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 112 stacking parallelities Total time for adding SS restraints: 23.63 Time building geometry restraints manager: 22.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.31: 7531 1.31 - 1.48: 22338 1.48 - 1.65: 19662 1.65 - 1.82: 333 1.82 - 1.99: 11 Bond restraints: 49875 Sorted by residual: bond pdb=" CB THR T 535 " pdb=" OG1 THR T 535 " ideal model delta sigma weight residual 1.433 1.250 0.183 1.60e-02 3.91e+03 1.31e+02 bond pdb=" CB VAL u 136 " pdb=" CG1 VAL u 136 " ideal model delta sigma weight residual 1.521 1.198 0.323 3.30e-02 9.18e+02 9.55e+01 bond pdb=" CG1 ILE C 197 " pdb=" CD1 ILE C 197 " ideal model delta sigma weight residual 1.513 1.206 0.307 3.90e-02 6.57e+02 6.21e+01 bond pdb=" CB VAL u 136 " pdb=" CG2 VAL u 136 " ideal model delta sigma weight residual 1.521 1.315 0.206 3.30e-02 9.18e+02 3.88e+01 bond pdb=" CA CYS Q 102 " pdb=" C CYS Q 102 " ideal model delta sigma weight residual 1.526 1.600 -0.074 1.23e-02 6.61e+03 3.67e+01 ... (remaining 49870 not shown) Histogram of bond angle deviations from ideal: 68.54 - 81.84: 1 81.84 - 95.13: 9 95.13 - 108.43: 5672 108.43 - 121.72: 51609 121.72 - 135.02: 11421 Bond angle restraints: 68712 Sorted by residual: angle pdb=" NE ARG T 538 " pdb=" CZ ARG T 538 " pdb=" NH1 ARG T 538 " ideal model delta sigma weight residual 121.50 104.27 17.23 1.00e+00 1.00e+00 2.97e+02 angle pdb=" CB LEU A 506 " pdb=" CG LEU A 506 " pdb=" CD1 LEU A 506 " ideal model delta sigma weight residual 110.70 68.54 42.16 3.00e+00 1.11e-01 1.97e+02 angle pdb=" CA THR T 535 " pdb=" CB THR T 535 " pdb=" OG1 THR T 535 " ideal model delta sigma weight residual 109.60 90.07 19.53 1.50e+00 4.44e-01 1.70e+02 angle pdb=" NE ARG T 538 " pdb=" CZ ARG T 538 " pdb=" NH2 ARG T 538 " ideal model delta sigma weight residual 119.20 130.49 -11.29 9.00e-01 1.23e+00 1.57e+02 angle pdb=" CG1 VAL u 136 " pdb=" CB VAL u 136 " pdb=" CG2 VAL u 136 " ideal model delta sigma weight residual 110.80 83.29 27.51 2.20e+00 2.07e-01 1.56e+02 ... (remaining 68707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 29093 35.71 - 71.42: 1071 71.42 - 107.14: 128 107.14 - 142.85: 9 142.85 - 178.56: 6 Dihedral angle restraints: 30307 sinusoidal: 14363 harmonic: 15944 Sorted by residual: dihedral pdb=" O4' U 2 18 " pdb=" C1' U 2 18 " pdb=" N1 U 2 18 " pdb=" C2 U 2 18 " ideal model delta sinusoidal sigma weight residual 200.00 58.53 141.47 1 1.50e+01 4.44e-03 7.60e+01 dihedral pdb=" O4' C 5 68 " pdb=" C1' C 5 68 " pdb=" N1 C 5 68 " pdb=" C2 C 5 68 " ideal model delta sinusoidal sigma weight residual 200.00 66.80 133.20 1 1.50e+01 4.44e-03 7.19e+01 dihedral pdb=" O4' C 6 25 " pdb=" C1' C 6 25 " pdb=" N1 C 6 25 " pdb=" C2 C 6 25 " ideal model delta sinusoidal sigma weight residual 232.00 53.44 178.56 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 30304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.941: 7703 0.941 - 1.883: 0 1.883 - 2.824: 0 2.824 - 3.766: 0 3.766 - 4.707: 4 Chirality restraints: 7707 Sorted by residual: chirality pdb=" C2 IHP A3001 " pdb=" C1 IHP A3001 " pdb=" C3 IHP A3001 " pdb=" O12 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.52 2.19 -4.71 2.00e-01 2.50e+01 5.54e+02 chirality pdb=" C3 IHP A3001 " pdb=" C2 IHP A3001 " pdb=" C4 IHP A3001 " pdb=" O13 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.34 2.31 -4.65 2.00e-01 2.50e+01 5.40e+02 chirality pdb=" C5 IHP A3001 " pdb=" C4 IHP A3001 " pdb=" C6 IHP A3001 " pdb=" O15 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.42 2.21 -4.63 2.00e-01 2.50e+01 5.35e+02 ... (remaining 7704 not shown) Planarity restraints: 7966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU t 38 " 0.028 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" CD GLU t 38 " -0.099 2.00e-02 2.50e+03 pdb=" OE1 GLU t 38 " 0.034 2.00e-02 2.50e+03 pdb=" OE2 GLU t 38 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 434 " 0.045 2.00e-02 2.50e+03 3.48e-02 1.82e+01 pdb=" CG HIS A 434 " -0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS A 434 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 HIS A 434 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS A 434 " 0.033 2.00e-02 2.50e+03 pdb=" NE2 HIS A 434 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO V 5 " 0.063 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO V 6 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO V 6 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO V 6 " 0.052 5.00e-02 4.00e+02 ... (remaining 7963 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.26: 20 2.26 - 2.92: 19495 2.92 - 3.58: 67986 3.58 - 4.24: 115564 4.24 - 4.90: 190707 Nonbonded interactions: 393772 Sorted by model distance: nonbonded pdb=" P G Y 59 " pdb=" O2' A Y 155 " model vdw 1.605 3.400 nonbonded pdb=" OP1 G 6 72 " pdb="MG MG 6 101 " model vdw 1.958 2.170 nonbonded pdb=" OP2 G 6 75 " pdb="MG MG 6 103 " model vdw 2.047 2.170 nonbonded pdb=" OP2 G Y 59 " pdb="MG MG 6 101 " model vdw 2.054 2.170 nonbonded pdb=" OH TYR C 113 " pdb=" O ASP D 402 " model vdw 2.106 2.440 ... (remaining 393767 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 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: 0.030 Extract box with map and model: 21.040 Check model and map are aligned: 0.700 Set scattering table: 0.450 Process input model: 153.060 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.011 0.323 49875 Z= 0.727 Angle : 1.211 42.160 68712 Z= 0.629 Chirality : 0.122 4.707 7707 Planarity : 0.008 0.097 7966 Dihedral : 18.067 178.561 19985 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.99 % Favored : 89.99 % Rotamer: Outliers : 0.09 % Allowed : 0.38 % Favored : 99.54 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.10), residues: 5386 helix: -2.12 (0.10), residues: 1878 sheet: -1.94 (0.18), residues: 695 loop : -2.82 (0.10), residues: 2813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP O 346 HIS 0.014 0.002 HIS A 434 PHE 0.043 0.003 PHE p 431 TYR 0.064 0.003 TYR A 178 ARG 0.051 0.001 ARG u 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 797 time to evaluate : 5.492 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8430 (mt) cc_final: 0.8090 (tt) REVERT: A 160 HIS cc_start: 0.6792 (t-90) cc_final: 0.6568 (t-90) REVERT: A 304 ILE cc_start: 0.8535 (mm) cc_final: 0.8269 (tt) REVERT: A 559 ASP cc_start: 0.7800 (p0) cc_final: 0.7523 (p0) REVERT: A 925 TYR cc_start: 0.8690 (t80) cc_final: 0.8452 (t80) REVERT: B 638 ASP cc_start: 0.8890 (t70) cc_final: 0.8387 (t0) REVERT: D 213 GLU cc_start: 0.8484 (pp20) cc_final: 0.8281 (pp20) REVERT: T 499 GLN cc_start: 0.7334 (mt0) cc_final: 0.7109 (pt0) outliers start: 4 outliers final: 0 residues processed: 801 average time/residue: 0.6089 time to fit residues: 805.6041 Evaluate side-chains 669 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 669 time to evaluate : 5.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 470 optimal weight: 0.7980 chunk 422 optimal weight: 0.9980 chunk 234 optimal weight: 7.9990 chunk 144 optimal weight: 0.5980 chunk 284 optimal weight: 7.9990 chunk 225 optimal weight: 3.9990 chunk 436 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 265 optimal weight: 8.9990 chunk 324 optimal weight: 4.9990 chunk 505 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 617 ASN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1169 GLN A1246 GLN A1367 ASN B 87 GLN B 436 GLN ** B 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 HIS ** C 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN D 446 ASN E 128 GLN ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 GLN O 325 ASN ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 480 HIS r 380 ASN s 4 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 49875 Z= 0.188 Angle : 0.643 11.654 68712 Z= 0.329 Chirality : 0.043 0.558 7707 Planarity : 0.005 0.069 7966 Dihedral : 16.892 177.456 9593 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.74 % Favored : 91.24 % Rotamer: Outliers : 1.41 % Allowed : 9.26 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -2.75 (0.11), residues: 5386 helix: -0.98 (0.11), residues: 1873 sheet: -1.58 (0.19), residues: 691 loop : -2.54 (0.11), residues: 2822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 750 HIS 0.005 0.001 HIS C 231 PHE 0.021 0.001 PHE A1719 TYR 0.025 0.001 TYR O 399 ARG 0.005 0.000 ARG F 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 757 time to evaluate : 5.314 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8426 (mt) cc_final: 0.8043 (tt) REVERT: A 75 ASP cc_start: 0.7464 (p0) cc_final: 0.6863 (p0) REVERT: A 866 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8444 (mm) REVERT: A 923 ASP cc_start: 0.8337 (t0) cc_final: 0.8048 (t0) REVERT: A 925 TYR cc_start: 0.8761 (t80) cc_final: 0.8198 (t80) REVERT: B 123 MET cc_start: 0.8343 (mtm) cc_final: 0.8104 (mtp) REVERT: B 638 ASP cc_start: 0.8925 (t70) cc_final: 0.8428 (t0) REVERT: C 138 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7384 (tm-30) REVERT: C 142 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6408 (mt-10) REVERT: C 199 MET cc_start: 0.8148 (ptp) cc_final: 0.7865 (mtp) REVERT: D 284 TYR cc_start: 0.8848 (m-80) cc_final: 0.8589 (m-80) REVERT: E 137 TYR cc_start: 0.8012 (p90) cc_final: 0.7698 (p90) REVERT: F 255 MET cc_start: 0.7356 (mtm) cc_final: 0.7043 (mtp) REVERT: O 387 GLU cc_start: 0.7032 (pp20) cc_final: 0.6732 (pp20) REVERT: P 90 TYR cc_start: 0.8353 (m-80) cc_final: 0.8047 (m-80) REVERT: T 499 GLN cc_start: 0.7289 (mt0) cc_final: 0.7077 (pt0) REVERT: T 568 ILE cc_start: 0.8018 (pt) cc_final: 0.7786 (pt) REVERT: T 645 GLU cc_start: 0.7381 (pp20) cc_final: 0.6971 (pp20) REVERT: p 264 MET cc_start: 0.7756 (tpt) cc_final: 0.7530 (tpp) REVERT: u 61 GLU cc_start: 0.7294 (pt0) cc_final: 0.7054 (pt0) REVERT: u 77 TYR cc_start: 0.7800 (m-80) cc_final: 0.7564 (m-80) outliers start: 64 outliers final: 46 residues processed: 789 average time/residue: 0.6268 time to fit residues: 815.3683 Evaluate side-chains 746 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 699 time to evaluate : 5.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 899 SER Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain O residue 254 SER Chi-restraints excluded: chain O residue 414 HIS Chi-restraints excluded: chain P residue 195 ASP Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain S residue 9 THR Chi-restraints excluded: chain T residue 558 ASP Chi-restraints excluded: chain V residue 133 CYS Chi-restraints excluded: chain p residue 185 VAL Chi-restraints excluded: chain p residue 279 THR Chi-restraints excluded: chain p residue 440 THR Chi-restraints excluded: chain p residue 475 VAL Chi-restraints excluded: chain t residue 20 VAL Chi-restraints excluded: chain u residue 20 ILE Chi-restraints excluded: chain u residue 95 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 281 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 420 optimal weight: 0.0870 chunk 344 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 506 optimal weight: 8.9990 chunk 547 optimal weight: 4.9990 chunk 451 optimal weight: 10.0000 chunk 502 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 406 optimal weight: 10.0000 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 ASN A 775 ASN A1169 GLN ** A1367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1428 HIS C 189 ASN C 243 GLN D 287 HIS E 121 ASN F 253 ASN F 278 GLN L 30 GLN ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 236 GLN p 353 ASN ** p 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 371 ASN r 380 ASN s 4 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 49875 Z= 0.288 Angle : 0.636 10.423 68712 Z= 0.325 Chirality : 0.044 0.362 7707 Planarity : 0.005 0.062 7966 Dihedral : 16.808 179.324 9593 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.01 % Favored : 89.97 % Rotamer: Outliers : 2.41 % Allowed : 12.67 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -2.45 (0.11), residues: 5386 helix: -0.59 (0.12), residues: 1890 sheet: -1.52 (0.18), residues: 726 loop : -2.46 (0.11), residues: 2770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 750 HIS 0.010 0.001 HIS B 437 PHE 0.016 0.001 PHE p 221 TYR 0.025 0.002 TYR D 260 ARG 0.004 0.000 ARG D 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 730 time to evaluate : 5.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8431 (mt) cc_final: 0.8037 (tt) REVERT: A 75 ASP cc_start: 0.7536 (p0) cc_final: 0.6958 (p0) REVERT: A 559 ASP cc_start: 0.7877 (p0) cc_final: 0.7618 (p0) REVERT: A 923 ASP cc_start: 0.8395 (t0) cc_final: 0.7897 (t0) REVERT: A 925 TYR cc_start: 0.8817 (t80) cc_final: 0.8612 (t80) REVERT: B 123 MET cc_start: 0.8367 (mtm) cc_final: 0.8081 (mtp) REVERT: B 176 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6827 (mm-30) REVERT: B 230 ASP cc_start: 0.8905 (m-30) cc_final: 0.8556 (m-30) REVERT: B 638 ASP cc_start: 0.8959 (t70) cc_final: 0.8450 (t0) REVERT: C 138 GLU cc_start: 0.7777 (tm-30) cc_final: 0.6818 (tm-30) REVERT: C 142 GLU cc_start: 0.6527 (mt-10) cc_final: 0.5893 (mt-10) REVERT: D 264 CYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7660 (t) REVERT: D 284 TYR cc_start: 0.8931 (m-80) cc_final: 0.8594 (m-80) REVERT: D 303 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8657 (pt) REVERT: L 40 ARG cc_start: 0.6391 (tmt170) cc_final: 0.6179 (tmt170) REVERT: O 387 GLU cc_start: 0.7122 (pp20) cc_final: 0.6804 (pp20) REVERT: P 106 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7072 (p0) REVERT: P 200 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7375 (m-30) REVERT: T 499 GLN cc_start: 0.7394 (mt0) cc_final: 0.7047 (pt0) REVERT: T 568 ILE cc_start: 0.7996 (pt) cc_final: 0.7775 (pt) REVERT: V 128 ILE cc_start: 0.7867 (mp) cc_final: 0.7651 (mt) REVERT: t 36 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8085 (ttpt) REVERT: t 38 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6830 (tm-30) REVERT: t 43 GLU cc_start: 0.6840 (tm-30) cc_final: 0.6209 (tm-30) REVERT: u 77 TYR cc_start: 0.7769 (m-80) cc_final: 0.7492 (m-80) outliers start: 109 outliers final: 74 residues processed: 791 average time/residue: 0.6111 time to fit residues: 795.7368 Evaluate side-chains 757 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 678 time to evaluate : 5.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1602 ASP Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 899 SER Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain O residue 254 SER Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 414 HIS Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 106 ASP Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 195 ASP Chi-restraints excluded: chain P residue 200 ASP Chi-restraints excluded: chain P residue 209 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain T residue 493 ILE Chi-restraints excluded: chain T residue 522 MET Chi-restraints excluded: chain T residue 581 ILE Chi-restraints excluded: chain T residue 629 ASN Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 133 CYS Chi-restraints excluded: chain p residue 185 VAL Chi-restraints excluded: chain p residue 279 THR Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 440 THR Chi-restraints excluded: chain p residue 475 VAL Chi-restraints excluded: chain t residue 20 VAL Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain u residue 20 ILE Chi-restraints excluded: chain u residue 45 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 500 optimal weight: 0.7980 chunk 380 optimal weight: 7.9990 chunk 262 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 241 optimal weight: 0.3980 chunk 340 optimal weight: 8.9990 chunk 508 optimal weight: 3.9990 chunk 538 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 481 optimal weight: 9.9990 chunk 145 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1169 GLN A1428 HIS B 436 GLN C 243 GLN D 283 HIS E 121 ASN F 278 GLN L 30 GLN ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 588 GLN T 623 ASN ** p 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 49875 Z= 0.244 Angle : 0.601 10.143 68712 Z= 0.308 Chirality : 0.043 0.347 7707 Planarity : 0.005 0.060 7966 Dihedral : 16.733 178.042 9593 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.60 % Favored : 90.38 % Rotamer: Outliers : 2.59 % Allowed : 14.77 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -2.23 (0.11), residues: 5386 helix: -0.33 (0.12), residues: 1885 sheet: -1.40 (0.19), residues: 706 loop : -2.39 (0.11), residues: 2795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 750 HIS 0.007 0.001 HIS D 203 PHE 0.017 0.001 PHE F 86 TYR 0.019 0.001 TYR B 275 ARG 0.006 0.000 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 710 time to evaluate : 5.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8391 (mt) cc_final: 0.8020 (tt) REVERT: A 75 ASP cc_start: 0.7559 (p0) cc_final: 0.6950 (p0) REVERT: A 491 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: A 559 ASP cc_start: 0.7881 (p0) cc_final: 0.7624 (p0) REVERT: A 614 TYR cc_start: 0.8554 (m-80) cc_final: 0.8087 (m-80) REVERT: A 861 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7855 (mtt-85) REVERT: B 123 MET cc_start: 0.8249 (mtm) cc_final: 0.7931 (mtp) REVERT: B 433 MET cc_start: 0.8426 (tmm) cc_final: 0.8175 (ttt) REVERT: B 617 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8527 (tp) REVERT: B 638 ASP cc_start: 0.8958 (t70) cc_final: 0.8445 (t0) REVERT: C 138 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7358 (tm-30) REVERT: C 189 ASN cc_start: 0.8333 (t160) cc_final: 0.8073 (t0) REVERT: D 264 CYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7383 (t) REVERT: D 284 TYR cc_start: 0.8894 (m-80) cc_final: 0.8615 (m-80) REVERT: D 365 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.7893 (ttm-80) REVERT: O 387 GLU cc_start: 0.7219 (pp20) cc_final: 0.6857 (pp20) REVERT: P 90 TYR cc_start: 0.8344 (m-80) cc_final: 0.8082 (m-80) REVERT: P 106 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7200 (p0) REVERT: P 200 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7373 (m-30) REVERT: T 568 ILE cc_start: 0.7982 (pt) cc_final: 0.7746 (pt) REVERT: t 43 GLU cc_start: 0.6760 (tm-30) cc_final: 0.6342 (tm-30) outliers start: 117 outliers final: 81 residues processed: 787 average time/residue: 0.6152 time to fit residues: 803.3878 Evaluate side-chains 761 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 675 time to evaluate : 5.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 899 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 264 CYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 414 HIS Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 106 ASP Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 195 ASP Chi-restraints excluded: chain P residue 200 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain R residue 214 THR Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain T residue 493 ILE Chi-restraints excluded: chain T residue 522 MET Chi-restraints excluded: chain T residue 537 HIS Chi-restraints excluded: chain T residue 581 ILE Chi-restraints excluded: chain T residue 629 ASN Chi-restraints excluded: chain T residue 640 THR Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain p residue 185 VAL Chi-restraints excluded: chain p residue 279 THR Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 440 THR Chi-restraints excluded: chain p residue 475 VAL Chi-restraints excluded: chain t residue 20 VAL Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain u residue 20 ILE Chi-restraints excluded: chain u residue 45 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 448 optimal weight: 0.0470 chunk 305 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 400 optimal weight: 0.7980 chunk 222 optimal weight: 0.8980 chunk 459 optimal weight: 2.9990 chunk 372 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 483 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1169 GLN A1428 HIS A1595 GLN B 313 GLN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN F 188 GLN F 278 GLN ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 353 ASN ** p 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 49875 Z= 0.239 Angle : 0.595 9.787 68712 Z= 0.304 Chirality : 0.043 0.348 7707 Planarity : 0.004 0.060 7966 Dihedral : 16.688 178.019 9593 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.69 % Favored : 90.29 % Rotamer: Outliers : 3.27 % Allowed : 15.61 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -2.09 (0.11), residues: 5386 helix: -0.15 (0.12), residues: 1874 sheet: -1.32 (0.19), residues: 706 loop : -2.34 (0.11), residues: 2806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP p 209 HIS 0.006 0.001 HIS D 203 PHE 0.015 0.001 PHE F 86 TYR 0.018 0.001 TYR B 275 ARG 0.007 0.000 ARG F 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 717 time to evaluate : 5.280 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8388 (mt) cc_final: 0.8011 (tt) REVERT: A 491 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: A 559 ASP cc_start: 0.7872 (p0) cc_final: 0.7592 (p0) REVERT: A 614 TYR cc_start: 0.8575 (m-80) cc_final: 0.8106 (m-80) REVERT: A 861 ARG cc_start: 0.8033 (mtp180) cc_final: 0.7814 (mtt-85) REVERT: B 123 MET cc_start: 0.8230 (mtm) cc_final: 0.7897 (mtp) REVERT: B 583 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.7985 (p0) REVERT: B 638 ASP cc_start: 0.8960 (t70) cc_final: 0.8454 (t0) REVERT: B 665 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8393 (m) REVERT: B 668 GLU cc_start: 0.5805 (mp0) cc_final: 0.5432 (mp0) REVERT: C 116 TYR cc_start: 0.8398 (t80) cc_final: 0.8174 (t80) REVERT: C 138 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7047 (tm-30) REVERT: C 142 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6180 (mt-10) REVERT: C 189 ASN cc_start: 0.8267 (t160) cc_final: 0.8050 (t0) REVERT: D 284 TYR cc_start: 0.8885 (m-80) cc_final: 0.8573 (m-80) REVERT: D 303 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8642 (pt) REVERT: D 365 ARG cc_start: 0.8407 (ttm-80) cc_final: 0.8060 (ttm-80) REVERT: D 474 GLU cc_start: 0.7793 (mp0) cc_final: 0.7561 (mp0) REVERT: O 387 GLU cc_start: 0.7171 (pp20) cc_final: 0.6875 (pp20) REVERT: P 106 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7204 (p0) REVERT: P 200 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: R 29 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7479 (mp10) REVERT: p 231 GLN cc_start: 0.8490 (pp30) cc_final: 0.7868 (pp30) REVERT: p 315 ASN cc_start: 0.8467 (p0) cc_final: 0.8249 (p0) REVERT: p 480 HIS cc_start: 0.6816 (t70) cc_final: 0.6429 (t70) REVERT: t 43 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6361 (tm-30) outliers start: 148 outliers final: 102 residues processed: 815 average time/residue: 0.6181 time to fit residues: 832.6437 Evaluate side-chains 790 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 681 time to evaluate : 6.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1602 ASP Chi-restraints excluded: chain A residue 1699 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 387 ASP Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 816 VAL Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 899 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 414 HIS Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 106 ASP Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 195 ASP Chi-restraints excluded: chain P residue 200 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 214 THR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain T residue 493 ILE Chi-restraints excluded: chain T residue 537 HIS Chi-restraints excluded: chain T residue 581 ILE Chi-restraints excluded: chain T residue 629 ASN Chi-restraints excluded: chain T residue 640 THR Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain p residue 185 VAL Chi-restraints excluded: chain p residue 188 LEU Chi-restraints excluded: chain p residue 279 THR Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 440 THR Chi-restraints excluded: chain p residue 475 VAL Chi-restraints excluded: chain r residue 387 VAL Chi-restraints excluded: chain t residue 20 VAL Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain u residue 20 ILE Chi-restraints excluded: chain u residue 45 THR Chi-restraints excluded: chain x residue 230 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 181 optimal weight: 0.9990 chunk 484 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 316 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 538 optimal weight: 8.9990 chunk 447 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 282 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1169 GLN A1428 HIS A1595 GLN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 GLN L 30 GLN ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 HIS p 353 ASN ** p 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 485 GLN r 371 ASN s 4 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 49875 Z= 0.207 Angle : 0.584 10.122 68712 Z= 0.297 Chirality : 0.042 0.334 7707 Planarity : 0.004 0.055 7966 Dihedral : 16.639 178.162 9593 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 3.12 % Allowed : 16.67 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -1.99 (0.11), residues: 5386 helix: -0.02 (0.12), residues: 1867 sheet: -1.26 (0.19), residues: 693 loop : -2.31 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 262 HIS 0.004 0.001 HIS L 99 PHE 0.013 0.001 PHE u 39 TYR 0.017 0.001 TYR B 275 ARG 0.008 0.000 ARG F 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 718 time to evaluate : 5.752 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8384 (mt) cc_final: 0.8006 (tt) REVERT: A 75 ASP cc_start: 0.7557 (p0) cc_final: 0.6954 (p0) REVERT: A 491 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: A 559 ASP cc_start: 0.7860 (p0) cc_final: 0.7569 (p0) REVERT: A 614 TYR cc_start: 0.8570 (m-80) cc_final: 0.8097 (m-80) REVERT: A 847 LYS cc_start: 0.7345 (ttpt) cc_final: 0.6963 (mtpt) REVERT: A 871 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: B 123 MET cc_start: 0.8176 (mtm) cc_final: 0.7833 (mtp) REVERT: B 638 ASP cc_start: 0.8957 (t70) cc_final: 0.8452 (t0) REVERT: B 668 GLU cc_start: 0.5765 (mp0) cc_final: 0.5343 (mp0) REVERT: C 189 ASN cc_start: 0.8274 (t160) cc_final: 0.8031 (t0) REVERT: D 284 TYR cc_start: 0.8846 (m-80) cc_final: 0.8591 (m-80) REVERT: D 365 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.8064 (ttm-80) REVERT: D 474 GLU cc_start: 0.7757 (mp0) cc_final: 0.7505 (mp0) REVERT: F 262 TRP cc_start: 0.6253 (m-10) cc_final: 0.5968 (m-10) REVERT: O 387 GLU cc_start: 0.7170 (pp20) cc_final: 0.6870 (pp20) REVERT: P 106 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7211 (p0) REVERT: P 146 MET cc_start: 0.7028 (ppp) cc_final: 0.6480 (ppp) REVERT: R 29 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7440 (mp10) REVERT: T 568 ILE cc_start: 0.8026 (pt) cc_final: 0.7807 (pt) REVERT: p 231 GLN cc_start: 0.8502 (pp30) cc_final: 0.7828 (pp30) REVERT: t 36 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8041 (ttpt) REVERT: t 43 GLU cc_start: 0.6728 (tm-30) cc_final: 0.6309 (tm-30) REVERT: u 106 ARG cc_start: 0.8474 (mmm-85) cc_final: 0.8252 (tpt90) outliers start: 141 outliers final: 105 residues processed: 807 average time/residue: 0.6072 time to fit residues: 814.3613 Evaluate side-chains 792 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 682 time to evaluate : 5.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1251 SER Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 816 VAL Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 899 SER Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain F residue 136 TRP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 414 HIS Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 106 ASP Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 195 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 214 THR Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain T residue 493 ILE Chi-restraints excluded: chain T residue 522 MET Chi-restraints excluded: chain T residue 629 ASN Chi-restraints excluded: chain T residue 640 THR Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 132 VAL Chi-restraints excluded: chain p residue 185 VAL Chi-restraints excluded: chain p residue 188 LEU Chi-restraints excluded: chain p residue 279 THR Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 440 THR Chi-restraints excluded: chain p residue 475 VAL Chi-restraints excluded: chain t residue 20 VAL Chi-restraints excluded: chain t residue 36 LYS Chi-restraints excluded: chain u residue 20 ILE Chi-restraints excluded: chain u residue 45 THR Chi-restraints excluded: chain u residue 57 ASN Chi-restraints excluded: chain x residue 230 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 519 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 307 optimal weight: 0.6980 chunk 393 optimal weight: 7.9990 chunk 304 optimal weight: 0.9990 chunk 453 optimal weight: 0.0970 chunk 300 optimal weight: 2.9990 chunk 536 optimal weight: 8.9990 chunk 335 optimal weight: 5.9990 chunk 327 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 HIS A1169 GLN A1595 GLN B 436 GLN ** B 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 GLN ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 464 GLN V 87 HIS p 236 GLN p 353 ASN ** p 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 49875 Z= 0.185 Angle : 0.573 11.093 68712 Z= 0.290 Chirality : 0.042 0.323 7707 Planarity : 0.004 0.059 7966 Dihedral : 16.577 178.676 9593 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 3.09 % Allowed : 17.53 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -1.85 (0.11), residues: 5386 helix: 0.13 (0.13), residues: 1863 sheet: -1.27 (0.19), residues: 714 loop : -2.23 (0.11), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP p 209 HIS 0.006 0.001 HIS u 102 PHE 0.015 0.001 PHE F 86 TYR 0.017 0.001 TYR u 68 ARG 0.008 0.000 ARG F 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 724 time to evaluate : 5.331 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8383 (mt) cc_final: 0.8019 (tt) REVERT: A 491 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: A 505 ASN cc_start: 0.8610 (t0) cc_final: 0.8221 (t0) REVERT: A 614 TYR cc_start: 0.8600 (m-80) cc_final: 0.8153 (m-80) REVERT: A 707 ARG cc_start: 0.7544 (mtp180) cc_final: 0.7041 (ttt180) REVERT: A 801 ILE cc_start: 0.8738 (tp) cc_final: 0.8510 (tp) REVERT: A 861 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7677 (mtp180) REVERT: A 871 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: B 123 MET cc_start: 0.8148 (mtm) cc_final: 0.7804 (mtp) REVERT: B 583 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7959 (p0) REVERT: B 638 ASP cc_start: 0.8916 (t70) cc_final: 0.8440 (t0) REVERT: B 668 GLU cc_start: 0.5769 (mp0) cc_final: 0.5428 (mp0) REVERT: C 189 ASN cc_start: 0.8229 (t160) cc_final: 0.7980 (t0) REVERT: D 284 TYR cc_start: 0.8831 (m-80) cc_final: 0.8609 (m-80) REVERT: D 365 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.8099 (ttm-80) REVERT: D 474 GLU cc_start: 0.7819 (mp0) cc_final: 0.7511 (mp0) REVERT: E 114 TYR cc_start: 0.8305 (t80) cc_final: 0.8045 (t80) REVERT: L 173 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6828 (mp0) REVERT: O 387 GLU cc_start: 0.7133 (pp20) cc_final: 0.6864 (pp20) REVERT: P 106 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7264 (p0) REVERT: P 146 MET cc_start: 0.6968 (ppp) cc_final: 0.6378 (ppp) REVERT: R 29 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: T 470 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: T 568 ILE cc_start: 0.8000 (pt) cc_final: 0.7781 (pt) REVERT: r 376 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7752 (ttp-170) REVERT: t 36 LYS cc_start: 0.8271 (ttmm) cc_final: 0.8055 (ttpt) REVERT: t 43 GLU cc_start: 0.6867 (tm-30) cc_final: 0.6466 (tm-30) REVERT: u 106 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.8236 (tpt90) outliers start: 140 outliers final: 108 residues processed: 813 average time/residue: 0.6146 time to fit residues: 830.9243 Evaluate side-chains 801 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 686 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 984 MET Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1602 ASP Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 816 VAL Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 899 SER Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain F residue 136 TRP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 173 GLU Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 414 HIS Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 106 ASP Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 195 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 214 THR Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain T residue 470 GLU Chi-restraints excluded: chain T residue 493 ILE Chi-restraints excluded: chain T residue 537 HIS Chi-restraints excluded: chain T residue 629 ASN Chi-restraints excluded: chain T residue 640 THR Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 132 VAL Chi-restraints excluded: chain p residue 185 VAL Chi-restraints excluded: chain p residue 279 THR Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 440 THR Chi-restraints excluded: chain p residue 475 VAL Chi-restraints excluded: chain r residue 387 VAL Chi-restraints excluded: chain t residue 20 VAL Chi-restraints excluded: chain u residue 20 ILE Chi-restraints excluded: chain u residue 45 THR Chi-restraints excluded: chain u residue 57 ASN Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain x residue 230 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 332 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 320 optimal weight: 5.9990 chunk 161 optimal weight: 0.2980 chunk 105 optimal weight: 0.0010 chunk 104 optimal weight: 1.9990 chunk 341 optimal weight: 1.9990 chunk 365 optimal weight: 0.0980 chunk 265 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 421 optimal weight: 8.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1169 GLN ** B 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 GLN O 426 GLN ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 499 GLN V 87 HIS ** p 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 ASN t 7 ASN u 162 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 49875 Z= 0.179 Angle : 0.571 9.703 68712 Z= 0.290 Chirality : 0.041 0.317 7707 Planarity : 0.004 0.055 7966 Dihedral : 16.529 179.037 9593 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 3.21 % Allowed : 18.15 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -1.77 (0.11), residues: 5386 helix: 0.20 (0.13), residues: 1872 sheet: -1.20 (0.19), residues: 720 loop : -2.21 (0.11), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 750 HIS 0.011 0.001 HIS B 437 PHE 0.014 0.001 PHE F 86 TYR 0.025 0.001 TYR F 117 ARG 0.008 0.000 ARG F 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 701 time to evaluate : 5.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8379 (mt) cc_final: 0.8011 (tt) REVERT: A 396 ASP cc_start: 0.7138 (t70) cc_final: 0.6937 (m-30) REVERT: A 491 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: A 505 ASN cc_start: 0.8590 (t0) cc_final: 0.8206 (t0) REVERT: A 559 ASP cc_start: 0.7834 (p0) cc_final: 0.7539 (p0) REVERT: A 614 TYR cc_start: 0.8594 (m-80) cc_final: 0.8117 (m-80) REVERT: A 801 ILE cc_start: 0.8740 (tp) cc_final: 0.8524 (tp) REVERT: A 861 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7645 (mtp180) REVERT: A 871 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: B 123 MET cc_start: 0.8097 (mtm) cc_final: 0.7749 (mtp) REVERT: B 583 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7984 (p0) REVERT: B 638 ASP cc_start: 0.8919 (t70) cc_final: 0.8443 (t0) REVERT: B 668 GLU cc_start: 0.5833 (mp0) cc_final: 0.5434 (mp0) REVERT: C 189 ASN cc_start: 0.8202 (t160) cc_final: 0.7950 (t0) REVERT: D 248 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8731 (p) REVERT: D 284 TYR cc_start: 0.8812 (m-80) cc_final: 0.8599 (m-80) REVERT: D 365 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8115 (ttm-80) REVERT: D 474 GLU cc_start: 0.7816 (mp0) cc_final: 0.7513 (mp0) REVERT: O 387 GLU cc_start: 0.7111 (pp20) cc_final: 0.6846 (pp20) REVERT: P 106 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7260 (p0) REVERT: R 29 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7515 (mp10) REVERT: T 470 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: T 568 ILE cc_start: 0.7988 (pt) cc_final: 0.7771 (pt) REVERT: T 594 MET cc_start: 0.7264 (mtm) cc_final: 0.7053 (mtm) REVERT: r 376 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7726 (ttp-170) REVERT: t 36 LYS cc_start: 0.8276 (ttmm) cc_final: 0.8056 (ttpt) REVERT: t 43 GLU cc_start: 0.6855 (tm-30) cc_final: 0.6463 (tm-30) outliers start: 145 outliers final: 113 residues processed: 794 average time/residue: 0.6284 time to fit residues: 830.6527 Evaluate side-chains 801 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 681 time to evaluate : 5.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1602 ASP Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 816 VAL Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 899 SER Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain F residue 136 TRP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 151 MET Chi-restraints excluded: chain L residue 173 GLU Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 414 HIS Chi-restraints excluded: chain O residue 417 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 106 ASP Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 195 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 214 THR Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain T residue 470 GLU Chi-restraints excluded: chain T residue 493 ILE Chi-restraints excluded: chain T residue 581 ILE Chi-restraints excluded: chain T residue 629 ASN Chi-restraints excluded: chain T residue 640 THR Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 132 VAL Chi-restraints excluded: chain V residue 150 GLN Chi-restraints excluded: chain p residue 180 HIS Chi-restraints excluded: chain p residue 185 VAL Chi-restraints excluded: chain p residue 188 LEU Chi-restraints excluded: chain p residue 279 THR Chi-restraints excluded: chain p residue 300 MET Chi-restraints excluded: chain p residue 327 THR Chi-restraints excluded: chain p residue 440 THR Chi-restraints excluded: chain p residue 475 VAL Chi-restraints excluded: chain r residue 387 VAL Chi-restraints excluded: chain t residue 20 VAL Chi-restraints excluded: chain u residue 20 ILE Chi-restraints excluded: chain u residue 45 THR Chi-restraints excluded: chain u residue 57 ASN Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain x residue 230 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 488 optimal weight: 0.0060 chunk 514 optimal weight: 4.9990 chunk 469 optimal weight: 0.9990 chunk 500 optimal weight: 0.7980 chunk 301 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 392 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 452 optimal weight: 5.9990 chunk 473 optimal weight: 1.9990 chunk 498 optimal weight: 9.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1169 GLN A1428 HIS ** B 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 371 HIS ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 GLN ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 499 GLN V 87 HIS ** p 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 ASN u 162 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 49875 Z= 0.261 Angle : 0.605 9.713 68712 Z= 0.306 Chirality : 0.043 0.355 7707 Planarity : 0.004 0.055 7966 Dihedral : 16.526 179.356 9593 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.01 % Allowed : 18.48 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -1.78 (0.11), residues: 5386 helix: 0.19 (0.13), residues: 1873 sheet: -1.10 (0.20), residues: 710 loop : -2.24 (0.11), residues: 2803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 955 HIS 0.005 0.001 HIS L 99 PHE 0.012 0.001 PHE D 447 TYR 0.029 0.001 TYR F 117 ARG 0.008 0.000 ARG F 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 684 time to evaluate : 5.338 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8396 (mt) cc_final: 0.8026 (tt) REVERT: A 88 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8387 (t80) REVERT: A 396 ASP cc_start: 0.7272 (t70) cc_final: 0.7066 (m-30) REVERT: A 491 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: A 559 ASP cc_start: 0.7869 (p0) cc_final: 0.7569 (p0) REVERT: A 614 TYR cc_start: 0.8588 (m-80) cc_final: 0.8074 (m-80) REVERT: A 861 ARG cc_start: 0.7968 (mtt-85) cc_final: 0.7704 (mtp180) REVERT: A 1600 GLU cc_start: 0.7143 (mp0) cc_final: 0.6932 (mp0) REVERT: B 123 MET cc_start: 0.8128 (mtm) cc_final: 0.7798 (mtp) REVERT: B 583 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8004 (p0) REVERT: B 638 ASP cc_start: 0.8967 (t70) cc_final: 0.8473 (t0) REVERT: B 668 GLU cc_start: 0.5861 (mp0) cc_final: 0.5452 (mp0) REVERT: C 189 ASN cc_start: 0.8292 (t160) cc_final: 0.8041 (t0) REVERT: D 284 TYR cc_start: 0.8888 (m-80) cc_final: 0.8619 (m-80) REVERT: D 365 ARG cc_start: 0.8534 (ttm-80) cc_final: 0.8171 (ttm-80) REVERT: D 474 GLU cc_start: 0.7902 (mp0) cc_final: 0.7536 (mp0) REVERT: O 387 GLU cc_start: 0.7161 (pp20) cc_final: 0.6859 (pp20) REVERT: Q 27 GLN cc_start: 0.8238 (tt0) cc_final: 0.8006 (mt0) REVERT: R 29 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7478 (mp10) REVERT: T 470 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: T 536 ILE cc_start: 0.8576 (pt) cc_final: 0.8157 (mt) REVERT: T 568 ILE cc_start: 0.7972 (pt) cc_final: 0.7738 (pt) REVERT: T 594 MET cc_start: 0.7298 (mtm) cc_final: 0.7056 (mtm) REVERT: p 480 HIS cc_start: 0.7027 (t70) cc_final: 0.6788 (t70) REVERT: t 43 GLU cc_start: 0.6849 (tm-30) cc_final: 0.6432 (tm-30) outliers start: 136 outliers final: 115 residues processed: 773 average time/residue: 0.6314 time to fit residues: 814.9501 Evaluate side-chains 792 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 672 time to evaluate : 5.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1602 ASP Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 816 VAL Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 899 SER Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain F residue 136 TRP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 151 MET Chi-restraints excluded: chain L residue 173 GLU Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 414 HIS Chi-restraints excluded: chain O residue 417 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 195 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 214 THR Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain T residue 470 GLU Chi-restraints excluded: chain T residue 493 ILE Chi-restraints excluded: chain T residue 537 HIS Chi-restraints excluded: chain T residue 581 ILE Chi-restraints excluded: chain T residue 629 ASN Chi-restraints excluded: chain T residue 640 THR Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 132 VAL Chi-restraints excluded: chain p residue 180 HIS Chi-restraints excluded: chain p residue 185 VAL Chi-restraints excluded: chain p residue 188 LEU Chi-restraints excluded: chain p residue 279 THR Chi-restraints excluded: chain p residue 327 THR Chi-restraints excluded: chain p residue 440 THR Chi-restraints excluded: chain p residue 475 VAL Chi-restraints excluded: chain r residue 387 VAL Chi-restraints excluded: chain t residue 20 VAL Chi-restraints excluded: chain u residue 20 ILE Chi-restraints excluded: chain u residue 45 THR Chi-restraints excluded: chain u residue 57 ASN Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain x residue 230 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 328 optimal weight: 2.9990 chunk 529 optimal weight: 0.0010 chunk 322 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 367 optimal weight: 3.9990 chunk 554 optimal weight: 0.0070 chunk 510 optimal weight: 2.9990 chunk 441 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 341 optimal weight: 9.9990 chunk 270 optimal weight: 3.9990 overall best weight: 1.3208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1169 GLN B 436 GLN ** B 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN F 278 GLN ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 499 GLN V 87 HIS ** p 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 ASN u 162 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 49875 Z= 0.218 Angle : 0.590 9.775 68712 Z= 0.299 Chirality : 0.042 0.336 7707 Planarity : 0.004 0.056 7966 Dihedral : 16.499 179.234 9593 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 2.83 % Allowed : 18.74 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -1.73 (0.11), residues: 5386 helix: 0.24 (0.12), residues: 1878 sheet: -1.08 (0.20), residues: 702 loop : -2.22 (0.11), residues: 2806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP p 209 HIS 0.004 0.001 HIS L 99 PHE 0.013 0.001 PHE u 39 TYR 0.023 0.001 TYR F 117 ARG 0.008 0.000 ARG F 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10772 Ramachandran restraints generated. 5386 Oldfield, 0 Emsley, 5386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 683 time to evaluate : 6.093 Fit side-chains REVERT: A 40 LEU cc_start: 0.8375 (mt) cc_final: 0.7989 (tt) REVERT: A 88 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.8387 (t80) REVERT: A 491 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: A 559 ASP cc_start: 0.7858 (p0) cc_final: 0.7558 (p0) REVERT: A 614 TYR cc_start: 0.8607 (m-80) cc_final: 0.8101 (m-80) REVERT: A 861 ARG cc_start: 0.8006 (mtt-85) cc_final: 0.7742 (mtp180) REVERT: A 1600 GLU cc_start: 0.7122 (mp0) cc_final: 0.6908 (mp0) REVERT: B 123 MET cc_start: 0.8056 (mtm) cc_final: 0.7712 (mtp) REVERT: B 583 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8000 (p0) REVERT: B 638 ASP cc_start: 0.8963 (t70) cc_final: 0.8471 (t0) REVERT: B 668 GLU cc_start: 0.5896 (mp0) cc_final: 0.5483 (mp0) REVERT: C 189 ASN cc_start: 0.8298 (t160) cc_final: 0.8054 (t0) REVERT: D 284 TYR cc_start: 0.8862 (m-80) cc_final: 0.8619 (m-80) REVERT: D 365 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.8175 (ttm-80) REVERT: D 474 GLU cc_start: 0.7876 (mp0) cc_final: 0.7495 (mp0) REVERT: F 143 ARG cc_start: 0.7665 (tmm-80) cc_final: 0.7440 (tmm-80) REVERT: O 363 ARG cc_start: 0.8507 (ttp-110) cc_final: 0.8287 (mtm-85) REVERT: O 387 GLU cc_start: 0.7217 (pp20) cc_final: 0.6920 (pp20) REVERT: Q 27 GLN cc_start: 0.8211 (tt0) cc_final: 0.8003 (mt0) REVERT: R 29 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7526 (mp10) REVERT: T 470 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: T 536 ILE cc_start: 0.8591 (pt) cc_final: 0.8154 (mt) REVERT: T 568 ILE cc_start: 0.7979 (pt) cc_final: 0.7759 (pt) REVERT: r 376 ARG cc_start: 0.8041 (ttp-170) cc_final: 0.7776 (ttp-170) REVERT: t 36 LYS cc_start: 0.8252 (ttmm) cc_final: 0.8030 (ttpt) REVERT: t 43 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6472 (tm-30) REVERT: u 163 ARG cc_start: 0.5213 (tpm170) cc_final: 0.4901 (tpm170) outliers start: 128 outliers final: 117 residues processed: 768 average time/residue: 0.6432 time to fit residues: 820.8732 Evaluate side-chains 791 residues out of total 4830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 669 time to evaluate : 5.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 88 TYR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 857 ASN Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1018 ASN Chi-restraints excluded: chain A residue 1130 ASN Chi-restraints excluded: chain A residue 1161 LEU Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1484 ILE Chi-restraints excluded: chain A residue 1602 ASP Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 436 GLN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 816 VAL Chi-restraints excluded: chain B residue 828 MET Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 875 ILE Chi-restraints excluded: chain B residue 899 SER Chi-restraints excluded: chain B residue 918 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain E residue 116 GLU Chi-restraints excluded: chain F residue 136 TRP Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 291 CYS Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 173 GLU Chi-restraints excluded: chain L residue 231 ASN Chi-restraints excluded: chain O residue 230 THR Chi-restraints excluded: chain O residue 277 THR Chi-restraints excluded: chain O residue 417 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 195 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 214 THR Chi-restraints excluded: chain S residue 5 ILE Chi-restraints excluded: chain T residue 470 GLU Chi-restraints excluded: chain T residue 493 ILE Chi-restraints excluded: chain T residue 537 HIS Chi-restraints excluded: chain T residue 581 ILE Chi-restraints excluded: chain T residue 629 ASN Chi-restraints excluded: chain T residue 640 THR Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 132 VAL Chi-restraints excluded: chain p residue 180 HIS Chi-restraints excluded: chain p residue 185 VAL Chi-restraints excluded: chain p residue 188 LEU Chi-restraints excluded: chain p residue 279 THR Chi-restraints excluded: chain p residue 327 THR Chi-restraints excluded: chain p residue 440 THR Chi-restraints excluded: chain p residue 475 VAL Chi-restraints excluded: chain r residue 387 VAL Chi-restraints excluded: chain t residue 20 VAL Chi-restraints excluded: chain u residue 20 ILE Chi-restraints excluded: chain u residue 45 THR Chi-restraints excluded: chain u residue 57 ASN Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain x residue 230 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 557 random chunks: chunk 350 optimal weight: 8.9990 chunk 470 optimal weight: 5.9990 chunk 135 optimal weight: 0.0370 chunk 407 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 442 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 454 optimal weight: 0.7980 chunk 56 optimal weight: 0.0770 chunk 81 optimal weight: 6.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1169 GLN A1172 ASN ** B 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN F 278 GLN ** L 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 414 HIS ** P 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 499 GLN V 87 HIS ** p 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 4 ASN u 162 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.146397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.110919 restraints weight = 75886.916| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.95 r_work: 0.3095 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 49875 Z= 0.158 Angle : 0.570 9.631 68712 Z= 0.289 Chirality : 0.041 0.321 7707 Planarity : 0.004 0.057 7966 Dihedral : 16.453 179.352 9593 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 2.48 % Allowed : 19.16 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: -1.64 (0.11), residues: 5386 helix: 0.35 (0.13), residues: 1879 sheet: -1.10 (0.20), residues: 713 loop : -2.17 (0.11), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 750 HIS 0.030 0.001 HIS O 414 PHE 0.016 0.001 PHE u 39 TYR 0.020 0.001 TYR F 117 ARG 0.008 0.000 ARG F 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13651.97 seconds wall clock time: 247 minutes 33.49 seconds (14853.49 seconds total)