Starting phenix.real_space_refine on Fri Dec 8 21:30:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gb2_4370/12_2023/6gb2_4370_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gb2_4370/12_2023/6gb2_4370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gb2_4370/12_2023/6gb2_4370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gb2_4370/12_2023/6gb2_4370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gb2_4370/12_2023/6gb2_4370_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gb2_4370/12_2023/6gb2_4370_neut_updated.pdb" } resolution = 3.2 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= 0.002 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1691 5.49 5 Mg 216 5.21 5 S 281 5.16 5 Na 1 4.78 5 C 63805 2.51 5 N 20243 2.21 5 O 24869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "CL GLU 42": "OE1" <-> "OE2" Residue "DL GLU 78": "OE1" <-> "OE2" Residue "FL GLU 78": "OE1" <-> "OE2" Residue "HL GLU 78": "OE1" <-> "OE2" Residue "B0 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B0 TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B0 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 ASP 142": "OD1" <-> "OD2" Residue "B1 PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B1 PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 ASP 153": "OD1" <-> "OD2" Residue "B2 TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B3 PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B5 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B6 ASP 47": "OD1" <-> "OD2" Residue "B8 TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B8 PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B8 PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B8 ASP 182": "OD1" <-> "OD2" Residue "B9 ASP 75": "OD1" <-> "OD2" Residue "B9 TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC GLU 429": "OE1" <-> "OE2" Residue "BC TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD GLU 125": "OE1" <-> "OE2" Residue "BD TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE ASP 265": "OD1" <-> "OD2" Residue "BE PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE ASP 334": "OD1" <-> "OD2" Residue "BE PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ ARG 227": "NH1" <-> "NH2" Residue "BK PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BL GLU 166": "OE1" <-> "OE2" Residue "BL GLU 182": "OE1" <-> "OE2" Residue "BN TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BN PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BO ASP 42": "OD1" <-> "OD2" Residue "BP TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BR ASP 50": "OD1" <-> "OD2" Residue "BS PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BU TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BU PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BV PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BV PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BW TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BW TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BW PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BW PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BX PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BY TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BY PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BY TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba ASP 363": "OD1" <-> "OD2" Residue "Ba TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb ASP 209": "OD1" <-> "OD2" Residue "Bb ASP 222": "OD1" <-> "OD2" Residue "Bb PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb ASP 324": "OD1" <-> "OD2" Residue "Bb PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bc PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bc TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bc TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Be PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Be TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Be PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bf TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bg GLU 96": "OE1" <-> "OE2" Residue "Bh PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh GLU 293": "OE1" <-> "OE2" Residue "Bh PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi ASP 175": "OD1" <-> "OD2" Residue "Bi TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bi TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bj ASP 145": "OD1" <-> "OD2" Residue "Bj PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bk TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bk TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bl TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bl TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bl ASP 154": "OD1" <-> "OD2" Residue "Bl GLU 163": "OE1" <-> "OE2" Residue "Bm TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bm TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bn TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bo PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bo TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bp PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bp PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bq TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bq PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bt ARG 11": "NH1" <-> "NH2" Residue "Bt GLU 40": "OE1" <-> "OE2" Residue "Bv TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bv GLU 101": "OE1" <-> "OE2" Residue "Bv ARG 104": "NH1" <-> "NH2" Residue "Bv ARG 136": "NH1" <-> "NH2" Residue "Bw TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw ASP 284": "OD1" <-> "OD2" Residue "Bw TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw GLU 315": "OE1" <-> "OE2" Residue "Bw TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw ASP 410": "OD1" <-> "OD2" Residue "Bx PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bx TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bx TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 111109 Number of models: 1 Model: "" Number of chains: 78 Chain: "CL" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 317 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 40} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "DL" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "EL" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 222 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "FL" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "GL" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "HL" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 205 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "B0" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "B1" Number of atoms: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2036 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 18, 'TRANS': 225} Chain: "B2" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1548 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "B3" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 968 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "B4" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 381 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 3, 'TRANS': 41} Chain: "B5" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "B6" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 425 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "B7" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 387 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "B8" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 833 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "B9" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 335 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "BA" Number of atoms: 32950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1549, 32950 Classifications: {'RNA': 1549} Modifications used: {'rna2p_pur': 172, 'rna2p_pyr': 109, 'rna3p_pur': 685, 'rna3p_pyr': 583} Link IDs: {'rna2p': 280, 'rna3p': 1268} Chain breaks: 1 Chain: "BB" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1427 Classifications: {'RNA': 67} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 35, 'rna3p_pyr': 27} Link IDs: {'rna2p': 5, 'rna3p': 61} Chain breaks: 2 Chain: "BC" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4364 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 549} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "BD" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1860 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 14, 'TRANS': 225} Chain: "BE" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 25, 'TRANS': 281} Chain: "BF" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2011 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 20, 'TRANS': 229} Chain: "BI" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "BJ" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1705 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 18, 'TRANS': 193} Chain: "BK" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1303 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 166} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "BL" Number of atoms: 537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 537 Classifications: {'peptide': 70} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 66} Chain: "BN" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1444 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "BO" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 896 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 9, 'TRANS': 105} Chain: "BP" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2312 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 27, 'TRANS': 260} Chain: "BQ" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1803 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 17, 'TRANS': 204} Chain: "BR" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1240 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "BS" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1168 Classifications: {'peptide': 143} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 136} Chain: "BT" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1845 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 207} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "BU" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1159 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "BV" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1231 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 144} Chain: "BW" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1374 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain: "BX" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1181 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 12, 'TRANS': 136} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "BY" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1678 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 17, 'TRANS': 188} Chain: "Ba" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3173 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 35, 'TRANS': 357} Chain: "Bb" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2952 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 32, 'TRANS': 321} Chain: "Bc" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2408 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain: "Bd" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 832 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 11, 'TRANS': 87} Chain: "Be" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 11, 'TRANS': 110} Chain: "Bf" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 12, 'TRANS': 95} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "Bg" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1167 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 10, 'TRANS': 137} Chain: "Bh" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2319 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 18, 'TRANS': 270} Chain: "Bi" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2138 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 23, 'TRANS': 236} Chain: "Bj" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1775 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "Bk" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1087 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain breaks: 1 Chain: "Bl" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1097 Classifications: {'peptide': 133} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 116} Chain: "Bm" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 893 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "Bn" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 837 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "Bo" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 772 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "Bp" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 742 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "Bq" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 542 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 62} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "Bt" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 780 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "Bu" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "Bv" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1131 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 12, 'TRANS': 122} Chain: "Bw" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3126 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 360} Chain: "Bx" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1325 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 18, 'TRANS': 143} Chain: "Bz" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 410 Classifications: {'peptide': 82} Link IDs: {'TRANS': 81} Chain breaks: 5 Chain: "AV" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1498 Classifications: {'RNA': 71} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 29, 'rna3p_pyr': 35} Link IDs: {'rna2p': 6, 'rna3p': 64} Chain: "B3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 265 Unusual residues: {' MG': 203, 'SPM': 1} Classifications: {'RNA': 2, 'undetermined': 204} Modifications used: {'rna2p': 2} Link IDs: {'rna2p': 1, None: 204} Not linked: pdbres=" MGBA3001 " pdbres=" MGBA3002 " Not linked: pdbres=" MGBA3002 " pdbres=" MGBA3003 " Not linked: pdbres=" MGBA3003 " pdbres=" MGBA3004 " Not linked: pdbres=" MGBA3004 " pdbres=" MGBA3005 " Not linked: pdbres=" MGBA3005 " pdbres=" MGBA3006 " ... (remaining 199 not shown) Chain breaks: 1 Chain: "BB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BC" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 1, ' NA': 1, 'GSP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BD" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "BP" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BR" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'SPM': 1} Classifications: {'undetermined': 1} Chain: "Be" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Bl" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Bt" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AV" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "BC" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7436 SG CYSB5 110 197.141 63.135 131.463 1.00 46.92 S ATOM 7458 SG CYSB5 113 198.877 65.238 128.852 1.00 41.50 S ATOM 7539 SG CYSB5 123 195.240 64.342 128.430 1.00 41.42 S ATOM 7561 SG CYSB5 126 197.890 61.683 128.062 1.00 51.91 S ATOM 9810 SG CYSB9 73 92.999 87.401 172.305 1.00 44.49 S ATOM 9835 SG CYSB9 76 96.247 89.031 171.306 1.00 41.87 S ATOM 9959 SG CYSB9 89 96.165 85.352 172.126 1.00 46.87 S ATOM 56188 SG CYSBJ 64 112.633 117.394 190.958 1.00 66.61 S ATOM A0611 SG CYSBx 70 110.967 115.336 193.644 1.00 75.97 S ATOM A061M SG CYSBx 73 114.714 115.477 193.422 1.00 73.85 S ATOM A069V SG CYSBx 108 112.737 113.616 190.804 1.00 43.55 S Time building chain proxies: 41.60, per 1000 atoms: 0.37 Number of scatterers: 111109 At special positions: 0 Unit cell: (264.1, 230.74, 293.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 S 281 16.00 P 1691 15.00 Mg 216 11.99 Na 1 11.00 O 24869 8.00 N 20243 7.00 C 63805 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: 35.58 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNB5 500 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 126 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 110 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 113 " pdb="ZN ZNB5 500 " - pdb=" SG CYSB5 123 " pdb=" ZNB9 500 " pdb="ZN ZNB9 500 " - pdb=" ND1 HISB9 95 " pdb="ZN ZNB9 500 " - pdb=" SG CYSB9 73 " pdb="ZN ZNB9 500 " - pdb=" SG CYSB9 76 " pdb="ZN ZNB9 500 " - pdb=" SG CYSB9 89 " pdb=" ZNBJ 500 " pdb="ZN ZNBJ 500 " - pdb=" SG CYSBx 73 " pdb="ZN ZNBJ 500 " - pdb=" SG CYSBx 70 " pdb="ZN ZNBJ 500 " - pdb=" SG CYSBJ 64 " pdb="ZN ZNBJ 500 " - pdb=" SG CYSBx 108 " Number of angles added : 15 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17562 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 313 helices and 84 sheets defined 42.6% alpha, 13.7% beta 435 base pairs and 873 stacking pairs defined. Time for finding SS restraints: 60.62 Creating SS restraints... Processing helix chain 'CL' and resid 25 through 38 removed outlier: 3.865A pdb=" N GLNCL 29 " --> pdb=" O PROCL 25 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEUCL 38 " --> pdb=" O ASPCL 34 " (cutoff:3.500A) Processing helix chain 'CL' and resid 39 through 54 removed outlier: 3.641A pdb=" N THRCL 53 " --> pdb=" O LEUCL 49 " (cutoff:3.500A) Processing helix chain 'DL' and resid 64 through 74 removed outlier: 3.707A pdb=" N LEUDL 74 " --> pdb=" O ASPDL 70 " (cutoff:3.500A) Processing helix chain 'DL' and resid 75 through 90 removed outlier: 3.776A pdb=" N LEUDL 90 " --> pdb=" O LEUDL 86 " (cutoff:3.500A) Processing helix chain 'FL' and resid 64 through 74 removed outlier: 3.518A pdb=" N SERFL 73 " --> pdb=" O GLNFL 69 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEUFL 74 " --> pdb=" O ASPFL 70 " (cutoff:3.500A) Processing helix chain 'FL' and resid 75 through 90 Processing helix chain 'GL' and resid 64 through 74 removed outlier: 3.565A pdb=" N LEUGL 74 " --> pdb=" O ASPGL 70 " (cutoff:3.500A) Processing helix chain 'GL' and resid 75 through 90 removed outlier: 3.749A pdb=" N LEUGL 90 " --> pdb=" O LEUGL 86 " (cutoff:3.500A) Processing helix chain 'EL' and resid 64 through 75 removed outlier: 3.768A pdb=" N LEUEL 74 " --> pdb=" O ASPEL 70 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N THREL 75 " --> pdb=" O ILEEL 71 " (cutoff:3.500A) Processing helix chain 'EL' and resid 76 through 90 Processing helix chain 'HL' and resid 64 through 75 removed outlier: 3.888A pdb=" N LEUHL 74 " --> pdb=" O ASPHL 70 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THRHL 75 " --> pdb=" O ILEHL 71 " (cutoff:3.500A) Processing helix chain 'HL' and resid 76 through 89 removed outlier: 3.580A pdb=" N LYSHL 88 " --> pdb=" O GLUHL 84 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THRHL 89 " --> pdb=" O LEUHL 85 " (cutoff:3.500A) Processing helix chain 'B0' and resid 110 through 120 removed outlier: 4.095A pdb=" N LEUB0 120 " --> pdb=" O LEUB0 116 " (cutoff:3.500A) Processing helix chain 'B1' and resid 8 through 19 removed outlier: 4.339A pdb=" N LYSB1 12 " --> pdb=" O VALB1 8 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLNB1 13 " --> pdb=" O GLYB1 9 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEUB1 16 " --> pdb=" O LYSB1 12 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLUB1 18 " --> pdb=" O LEUB1 14 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLYB1 19 " --> pdb=" O ARGB1 15 " (cutoff:3.500A) Processing helix chain 'B1' and resid 20 through 25 removed outlier: 3.674A pdb=" N LEUB1 24 " --> pdb=" O ILEB1 20 " (cutoff:3.500A) Proline residue: B1 25 - end of helix No H-bonds generated for 'chain 'B1' and resid 20 through 25' Processing helix chain 'B1' and resid 26 through 35 removed outlier: 3.867A pdb=" N GLUB1 34 " --> pdb=" O ARGB1 30 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ALAB1 35 " --> pdb=" O SERB1 31 " (cutoff:3.500A) Processing helix chain 'B1' and resid 72 through 79 removed outlier: 4.031A pdb=" N GLNB1 76 " --> pdb=" O PROB1 72 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEUB1 77 " --> pdb=" O PROB1 73 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLYB1 78 " --> pdb=" O GLUB1 74 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEUB1 79 " --> pdb=" O SERB1 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'B1' and resid 72 through 79' Processing helix chain 'B1' and resid 128 through 139 Processing helix chain 'B1' and resid 140 through 148 removed outlier: 3.662A pdb=" N THRB1 148 " --> pdb=" O TYRB1 144 " (cutoff:3.500A) Processing helix chain 'B1' and resid 149 through 154 Processing helix chain 'B1' and resid 155 through 172 Processing helix chain 'B1' and resid 180 through 192 removed outlier: 3.828A pdb=" N ARGB1 190 " --> pdb=" O ALAB1 186 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYRB1 191 " --> pdb=" O ILEB1 187 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYSB1 192 " --> pdb=" O TYRB1 188 " (cutoff:3.500A) Processing helix chain 'B1' and resid 197 through 205 removed outlier: 3.501A pdb=" N GLUB1 202 " --> pdb=" O GLUB1 198 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TRPB1 203 " --> pdb=" O ALAB1 199 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VALB1 204 " --> pdb=" O GLUB1 200 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLYB1 205 " --> pdb=" O ALAB1 201 " (cutoff:3.500A) Processing helix chain 'B1' and resid 207 through 220 Processing helix chain 'B1' and resid 225 through 245 removed outlier: 3.751A pdb=" N ILEB1 229 " --> pdb=" O PROB1 225 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SERB1 244 " --> pdb=" O GLNB1 240 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLUB1 245 " --> pdb=" O GLNB1 241 " (cutoff:3.500A) Processing helix chain 'B2' and resid 66 through 71 removed outlier: 4.942A pdb=" N PHEB2 70 " --> pdb=" O LEUB2 66 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASPB2 71 " --> pdb=" O GLUB2 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'B2' and resid 66 through 71' Processing helix chain 'B2' and resid 72 through 77 removed outlier: 4.069A pdb=" N TRPB2 76 " --> pdb=" O ASPB2 72 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLYB2 77 " --> pdb=" O PROB2 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B2' and resid 72 through 77' Processing helix chain 'B2' and resid 88 through 96 removed outlier: 3.631A pdb=" N LEUB2 92 " --> pdb=" O THRB2 88 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASNB2 94 " --> pdb=" O GLNB2 90 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYSB2 95 " --> pdb=" O GLNB2 91 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SERB2 96 " --> pdb=" O LEUB2 92 " (cutoff:3.500A) Processing helix chain 'B2' and resid 97 through 125 removed outlier: 3.816A pdb=" N TYRB2 105 " --> pdb=" O HISB2 101 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLUB2 110 " --> pdb=" O VALB2 106 " (cutoff:3.500A) Processing helix chain 'B2' and resid 131 through 160 removed outlier: 4.020A pdb=" N GLUB2 135 " --> pdb=" O PROB2 131 " (cutoff:3.500A) Processing helix chain 'B2' and resid 189 through 194 removed outlier: 3.795A pdb=" N ASNB2 193 " --> pdb=" O PROB2 189 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LYSB2 194 " --> pdb=" O TRPB2 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'B2' and resid 189 through 194' Processing helix chain 'B2' and resid 204 through 241 removed outlier: 4.163A pdb=" N GLUB2 208 " --> pdb=" O METB2 204 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARGB2 209 " --> pdb=" O PROB2 205 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHEB2 210 " --> pdb=" O TYRB2 206 " (cutoff:3.500A) Proline residue: B2 241 - end of helix Processing helix chain 'B3' and resid 42 through 48 removed outlier: 4.467A pdb=" N PHEB3 46 " --> pdb=" O PROB3 42 " (cutoff:3.500A) Proline residue: B3 48 - end of helix Processing helix chain 'B3' and resid 49 through 57 removed outlier: 3.928A pdb=" N HISB3 53 " --> pdb=" O SERB3 49 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLUB3 54 " --> pdb=" O PROB3 50 " (cutoff:3.500A) Processing helix chain 'B3' and resid 79 through 90 removed outlier: 3.612A pdb=" N GLYB3 90 " --> pdb=" O ILEB3 86 " (cutoff:3.500A) Processing helix chain 'B3' and resid 103 through 114 removed outlier: 4.147A pdb=" N LYSB3 109 " --> pdb=" O SERB3 105 " (cutoff:3.500A) Processing helix chain 'B3' and resid 130 through 135 removed outlier: 3.726A pdb=" N METB3 134 " --> pdb=" O THRB3 130 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ALAB3 135 " --> pdb=" O GLUB3 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 130 through 135' Processing helix chain 'B5' and resid 86 through 95 Processing helix chain 'B5' and resid 96 through 101 removed outlier: 5.642A pdb=" N ILEB5 101 " --> pdb=" O PROB5 97 " (cutoff:3.500A) Processing helix chain 'B5' and resid 123 through 146 removed outlier: 3.696A pdb=" N GLNB5 144 " --> pdb=" O GLNB5 140 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLUB5 145 " --> pdb=" O METB5 141 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLYB5 146 " --> pdb=" O GLYB5 142 " (cutoff:3.500A) Processing helix chain 'B7' and resid 59 through 67 Processing helix chain 'B7' and resid 68 through 75 removed outlier: 4.341A pdb=" N THRB7 75 " --> pdb=" O ARGB7 71 " (cutoff:3.500A) Processing helix chain 'B7' and resid 76 through 89 Processing helix chain 'B8' and resid 107 through 114 removed outlier: 3.918A pdb=" N ILEB8 111 " --> pdb=" O VALB8 107 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARGB8 113 " --> pdb=" O ALAB8 109 " (cutoff:3.500A) Processing helix chain 'B8' and resid 132 through 137 removed outlier: 4.128A pdb=" N LYSB8 136 " --> pdb=" O LYSB8 132 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N THRB8 137 " --> pdb=" O LEUB8 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'B8' and resid 132 through 137' Processing helix chain 'B8' and resid 138 through 146 Processing helix chain 'B8' and resid 151 through 163 removed outlier: 4.902A pdb=" N THRB8 163 " --> pdb=" O ASPB8 159 " (cutoff:3.500A) Processing helix chain 'B8' and resid 177 through 182 removed outlier: 3.703A pdb=" N GLNB8 181 " --> pdb=" O TYRB8 177 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASPB8 182 " --> pdb=" O GLNB8 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B8' and resid 177 through 182' Processing helix chain 'BC' and resid 192 through 202 Processing helix chain 'BC' and resid 204 through 209 removed outlier: 4.359A pdb=" N VALBC 208 " --> pdb=" O GLNBC 204 " (cutoff:3.500A) Processing helix chain 'BC' and resid 241 through 252 removed outlier: 3.616A pdb=" N ARGBC 247 " --> pdb=" O ALABC 243 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THRBC 252 " --> pdb=" O GLYBC 248 " (cutoff:3.500A) Processing helix chain 'BC' and resid 266 through 280 Processing helix chain 'BC' and resid 296 through 308 removed outlier: 3.657A pdb=" N VALBC 300 " --> pdb=" O ASPBC 296 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYRBC 307 " --> pdb=" O GLUBC 303 " (cutoff:3.500A) Processing helix chain 'BC' and resid 330 through 346 Processing helix chain 'BC' and resid 436 through 475 Processing helix chain 'BC' and resid 477 through 482 removed outlier: 4.215A pdb=" N TYRBC 481 " --> pdb=" O ALABC 477 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLYBC 482 " --> pdb=" O ARGBC 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 477 through 482' Processing helix chain 'BC' and resid 485 through 497 removed outlier: 4.649A pdb=" N PHEBC 494 " --> pdb=" O SERBC 490 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEUBC 495 " --> pdb=" O ILEBC 491 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLUBC 496 " --> pdb=" O LEUBC 492 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARGBC 497 " --> pdb=" O ARGBC 493 " (cutoff:3.500A) Processing helix chain 'BC' and resid 508 through 514 removed outlier: 4.706A pdb=" N ASPBC 512 " --> pdb=" O LYSBC 508 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SERBC 513 " --> pdb=" O ARGBC 509 " (cutoff:3.500A) Processing helix chain 'BC' and resid 524 through 538 removed outlier: 4.161A pdb=" N TYRBC 538 " --> pdb=" O ILEBC 534 " (cutoff:3.500A) Processing helix chain 'BC' and resid 557 through 568 Processing helix chain 'BC' and resid 579 through 590 Processing helix chain 'BC' and resid 598 through 614 Processing helix chain 'BD' and resid 184 through 189 removed outlier: 3.882A pdb=" N LEUBD 188 " --> pdb=" O PROBD 184 " (cutoff:3.500A) Proline residue: BD 189 - end of helix No H-bonds generated for 'chain 'BD' and resid 184 through 189' Processing helix chain 'BD' and resid 260 through 268 removed outlier: 3.620A pdb=" N ASNBD 264 " --> pdb=" O LYSBD 260 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLYBD 268 " --> pdb=" O ASNBD 264 " (cutoff:3.500A) Processing helix chain 'BD' and resid 250 through 255 removed outlier: 4.094A pdb=" N ASNBD 254 " --> pdb=" O VALBD 251 " (cutoff:3.500A) Processing helix chain 'BE' and resid 54 through 83 Proline residue: BE 59 - end of helix removed outlier: 4.861A pdb=" N CYSBE 78 " --> pdb=" O ALABE 74 " (cutoff:3.500A) Proline residue: BE 79 - end of helix removed outlier: 3.999A pdb=" N ASPBE 82 " --> pdb=" O CYSBE 78 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLUBE 83 " --> pdb=" O PROBE 79 " (cutoff:3.500A) Processing helix chain 'BE' and resid 134 through 139 removed outlier: 3.547A pdb=" N HISBE 138 " --> pdb=" O PROBE 134 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASNBE 139 " --> pdb=" O LYSBE 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 134 through 139' Processing helix chain 'BE' and resid 158 through 169 removed outlier: 3.616A pdb=" N LEUBE 168 " --> pdb=" O PHEBE 164 " (cutoff:3.500A) Processing helix chain 'BE' and resid 217 through 222 Processing helix chain 'BE' and resid 310 through 315 removed outlier: 4.802A pdb=" N LEUBE 314 " --> pdb=" O PHEBE 310 " (cutoff:3.500A) Proline residue: BE 315 - end of helix No H-bonds generated for 'chain 'BE' and resid 310 through 315' Processing helix chain 'BE' and resid 320 through 325 removed outlier: 4.079A pdb=" N ASPBE 324 " --> pdb=" O PHEBE 320 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLUBE 325 " --> pdb=" O PROBE 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 320 through 325' Processing helix chain 'BE' and resid 194 through 199 removed outlier: 4.294A pdb=" N ARGBE 199 " --> pdb=" O ALABE 196 " (cutoff:3.500A) Processing helix chain 'BF' and resid 92 through 109 removed outlier: 4.666A pdb=" N LYSBF 107 " --> pdb=" O GLNBF 103 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARGBF 108 " --> pdb=" O LYSBF 104 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILEBF 109 " --> pdb=" O ASNBF 105 " (cutoff:3.500A) Processing helix chain 'BF' and resid 166 through 185 removed outlier: 3.578A pdb=" N ASPBF 185 " --> pdb=" O LYSBF 181 " (cutoff:3.500A) Processing helix chain 'BF' and resid 199 through 211 removed outlier: 3.942A pdb=" N LEUBF 203 " --> pdb=" O ASPBF 199 " (cutoff:3.500A) Processing helix chain 'BF' and resid 227 through 238 removed outlier: 3.785A pdb=" N GLYBF 236 " --> pdb=" O ALABF 232 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEUBF 237 " --> pdb=" O ALABF 233 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYSBF 238 " --> pdb=" O THRBF 234 " (cutoff:3.500A) Processing helix chain 'BF' and resid 249 through 257 removed outlier: 5.330A pdb=" N GLNBF 257 " --> pdb=" O METBF 253 " (cutoff:3.500A) Processing helix chain 'BF' and resid 262 through 279 removed outlier: 3.728A pdb=" N GLUBF 271 " --> pdb=" O ALABF 267 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HISBF 276 " --> pdb=" O LYSBF 272 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASNBF 277 " --> pdb=" O LEUBF 273 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SERBF 278 " --> pdb=" O LEUBF 274 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARGBF 279 " --> pdb=" O TRPBF 275 " (cutoff:3.500A) Processing helix chain 'BF' and resid 84 through 89 Processing helix chain 'BI' and resid 74 through 79 removed outlier: 4.418A pdb=" N ARGBI 78 " --> pdb=" O HISBI 74 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VALBI 79 " --> pdb=" O ARGBI 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'BI' and resid 74 through 79' Processing helix chain 'BI' and resid 85 through 90 removed outlier: 3.632A pdb=" N ARGBI 89 " --> pdb=" O ASPBI 85 " (cutoff:3.500A) Proline residue: BI 90 - end of helix No H-bonds generated for 'chain 'BI' and resid 85 through 90' Processing helix chain 'BI' and resid 115 through 122 Processing helix chain 'BI' and resid 133 through 150 removed outlier: 4.164A pdb=" N LEUBI 139 " --> pdb=" O GLUBI 135 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHEBI 140 " --> pdb=" O ASNBI 136 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLNBI 148 " --> pdb=" O LYSBI 144 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLUBI 149 " --> pdb=" O LEUBI 145 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLYBI 150 " --> pdb=" O LEUBI 146 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 41 through 52 removed outlier: 3.528A pdb=" N GLUBJ 52 " --> pdb=" O METBJ 48 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 61 through 66 Proline residue: BJ 66 - end of helix Processing helix chain 'BJ' and resid 76 through 93 removed outlier: 3.507A pdb=" N ASNBJ 93 " --> pdb=" O VALBJ 89 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 105 through 120 removed outlier: 4.031A pdb=" N HISBJ 119 " --> pdb=" O GLNBJ 115 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 127 through 138 Proline residue: BJ 133 - end of helix Processing helix chain 'BJ' and resid 140 through 148 removed outlier: 4.713A pdb=" N LEUBJ 144 " --> pdb=" O TYRBJ 140 " (cutoff:3.500A) Proline residue: BJ 145 - end of helix removed outlier: 4.140A pdb=" N VALBJ 148 " --> pdb=" O LEUBJ 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'BJ' and resid 140 through 148' Processing helix chain 'BJ' and resid 160 through 172 removed outlier: 3.605A pdb=" N METBJ 164 " --> pdb=" O LYSBJ 160 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILEBJ 167 " --> pdb=" O GLUBJ 163 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLYBJ 170 " --> pdb=" O ARGBJ 166 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILEBJ 171 " --> pdb=" O ILEBJ 167 " (cutoff:3.500A) Proline residue: BJ 172 - end of helix Processing helix chain 'BJ' and resid 187 through 198 removed outlier: 3.622A pdb=" N LEUBJ 197 " --> pdb=" O ASNBJ 193 " (cutoff:3.500A) Proline residue: BJ 198 - end of helix Processing helix chain 'BJ' and resid 199 through 223 removed outlier: 4.105A pdb=" N VALBJ 208 " --> pdb=" O GLNBJ 204 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLYBJ 209 " --> pdb=" O GLYBJ 205 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEUBJ 214 " --> pdb=" O GLYBJ 210 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N THRBJ 215 " --> pdb=" O LEUBJ 211 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 224 through 239 removed outlier: 4.117A pdb=" N LEUBJ 229 " --> pdb=" O GLNBJ 225 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THRBJ 230 " --> pdb=" O PROBJ 226 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLNBJ 239 " --> pdb=" O GLNBJ 235 " (cutoff:3.500A) Processing helix chain 'BK' and resid 33 through 43 Proline residue: BK 37 - end of helix removed outlier: 3.671A pdb=" N ARGBK 42 " --> pdb=" O ILEBK 38 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLYBK 43 " --> pdb=" O LEUBK 39 " (cutoff:3.500A) Processing helix chain 'BK' and resid 45 through 58 removed outlier: 3.851A pdb=" N PHEBK 49 " --> pdb=" O SERBK 45 " (cutoff:3.500A) Processing helix chain 'BK' and resid 86 through 96 Processing helix chain 'BK' and resid 113 through 126 removed outlier: 3.645A pdb=" N VALBK 117 " --> pdb=" O THRBK 113 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLNBK 126 " --> pdb=" O ARGBK 122 " (cutoff:3.500A) Processing helix chain 'BK' and resid 127 through 134 removed outlier: 4.012A pdb=" N LEUBK 132 " --> pdb=" O ASPBK 128 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLNBK 133 " --> pdb=" O ALABK 129 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASPBK 134 " --> pdb=" O PHEBK 130 " (cutoff:3.500A) Processing helix chain 'BK' and resid 136 through 152 removed outlier: 3.617A pdb=" N VALBK 140 " --> pdb=" O PROBK 136 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SERBK 150 " --> pdb=" O GLYBK 146 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEUBK 151 " --> pdb=" O SERBK 147 " (cutoff:3.500A) Processing helix chain 'BK' and resid 164 through 192 removed outlier: 4.214A pdb=" N ALABK 172 " --> pdb=" O GLNBK 168 " (cutoff:3.500A) Processing helix chain 'BL' and resid 141 through 154 removed outlier: 3.879A pdb=" N GLNBL 154 " --> pdb=" O LYSBL 150 " (cutoff:3.500A) Processing helix chain 'BL' and resid 157 through 168 removed outlier: 3.788A pdb=" N LEUBL 168 " --> pdb=" O LEUBL 164 " (cutoff:3.500A) Processing helix chain 'BL' and resid 177 through 192 removed outlier: 3.566A pdb=" N GLYBL 192 " --> pdb=" O LEUBL 188 " (cutoff:3.500A) Processing helix chain 'BN' and resid 5 through 15 Processing helix chain 'BN' and resid 27 through 41 removed outlier: 3.665A pdb=" N METBN 34 " --> pdb=" O LYSBN 30 " (cutoff:3.500A) Processing helix chain 'BN' and resid 70 through 75 Processing helix chain 'BN' and resid 91 through 99 Processing helix chain 'BN' and resid 101 through 113 Proline residue: BN 113 - end of helix Processing helix chain 'BN' and resid 115 through 126 removed outlier: 4.610A pdb=" N ARGBN 119 " --> pdb=" O ASNBN 115 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THRBN 120 " --> pdb=" O LEUBN 116 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLNBN 123 " --> pdb=" O ARGBN 119 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARGBN 124 " --> pdb=" O THRBN 120 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEUBN 125 " --> pdb=" O METBN 121 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N HISBN 126 " --> pdb=" O METBN 122 " (cutoff:3.500A) Processing helix chain 'BN' and resid 134 through 141 removed outlier: 3.902A pdb=" N ASNBN 140 " --> pdb=" O ASPBN 136 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEUBN 141 " --> pdb=" O ILEBN 137 " (cutoff:3.500A) Processing helix chain 'BN' and resid 159 through 167 Proline residue: BN 167 - end of helix Processing helix chain 'BO' and resid 44 through 49 removed outlier: 3.506A pdb=" N THRBO 49 " --> pdb=" O ALABO 45 " (cutoff:3.500A) Processing helix chain 'BO' and resid 124 through 131 removed outlier: 4.731A pdb=" N ARGBO 128 " --> pdb=" O PROBO 124 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLNBO 129 " --> pdb=" O SERBO 125 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARGBO 130 " --> pdb=" O SERBO 126 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLUBO 131 " --> pdb=" O LEUBO 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'BO' and resid 124 through 131' Processing helix chain 'BO' and resid 134 through 142 removed outlier: 3.948A pdb=" N ILEBO 140 " --> pdb=" O LYSBO 136 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALABO 141 " --> pdb=" O VALBO 137 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLNBO 142 " --> pdb=" O LEUBO 138 " (cutoff:3.500A) Processing helix chain 'BP' and resid 10 through 20 removed outlier: 4.296A pdb=" N ASPBP 14 " --> pdb=" O PROBP 10 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEUBP 15 " --> pdb=" O ARGBP 11 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARGBP 17 " --> pdb=" O LEUBP 13 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALABP 18 " --> pdb=" O ASPBP 14 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEUBP 19 " --> pdb=" O LEUBP 15 " (cutoff:3.500A) Proline residue: BP 20 - end of helix Processing helix chain 'BP' and resid 55 through 60 removed outlier: 4.190A pdb=" N ARGBP 59 " --> pdb=" O GLYBP 55 " (cutoff:3.500A) Processing helix chain 'BP' and resid 73 through 78 removed outlier: 3.577A pdb=" N ILEBP 78 " --> pdb=" O PHEBP 74 " (cutoff:3.500A) Processing helix chain 'BP' and resid 86 through 91 removed outlier: 3.617A pdb=" N ARGBP 90 " --> pdb=" O GLYBP 86 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N HISBP 91 " --> pdb=" O HISBP 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP' and resid 86 through 91' Processing helix chain 'BP' and resid 97 through 108 Processing helix chain 'BP' and resid 117 through 125 Processing helix chain 'BP' and resid 160 through 171 removed outlier: 4.214A pdb=" N ASNBP 170 " --> pdb=" O ALABP 166 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLYBP 171 " --> pdb=" O ILEBP 167 " (cutoff:3.500A) Processing helix chain 'BP' and resid 180 through 190 Proline residue: BP 190 - end of helix Processing helix chain 'BP' and resid 191 through 197 removed outlier: 3.805A pdb=" N ARGBP 196 " --> pdb=" O PROBP 192 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLYBP 197 " --> pdb=" O PHEBP 193 " (cutoff:3.500A) Processing helix chain 'BP' and resid 207 through 216 Proline residue: BP 212 - end of helix removed outlier: 4.152A pdb=" N ASPBP 216 " --> pdb=" O PROBP 212 " (cutoff:3.500A) Processing helix chain 'BP' and resid 225 through 241 removed outlier: 3.818A pdb=" N PHEBP 229 " --> pdb=" O ASPBP 225 " (cutoff:3.500A) Proline residue: BP 230 - end of helix removed outlier: 3.551A pdb=" N ALABP 237 " --> pdb=" O ARGBP 233 " (cutoff:3.500A) Processing helix chain 'BP' and resid 252 through 258 removed outlier: 4.054A pdb=" N THRBP 258 " --> pdb=" O LYSBP 254 " (cutoff:3.500A) Processing helix chain 'BP' and resid 287 through 296 Processing helix chain 'BQ' and resid 68 through 74 removed outlier: 5.059A pdb=" N ILEBQ 72 " --> pdb=" O ASNBQ 68 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLYBQ 74 " --> pdb=" O SERBQ 70 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 98 through 113 Processing helix chain 'BQ' and resid 170 through 184 removed outlier: 4.153A pdb=" N LEUBQ 178 " --> pdb=" O GLYBQ 174 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VALBQ 179 " --> pdb=" O PHEBQ 175 " (cutoff:3.500A) Proline residue: BQ 184 - end of helix Processing helix chain 'BQ' and resid 191 through 209 removed outlier: 3.539A pdb=" N GLUBQ 206 " --> pdb=" O GLNBQ 202 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASNBQ 209 " --> pdb=" O ARGBQ 205 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 214 through 222 removed outlier: 3.571A pdb=" N ALABQ 221 " --> pdb=" O ARGBQ 217 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 225 through 231 removed outlier: 4.709A pdb=" N VALBQ 229 " --> pdb=" O GLYBQ 225 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SERBQ 231 " --> pdb=" O ARGBQ 227 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 232 through 238 removed outlier: 4.494A pdb=" N THRBQ 236 " --> pdb=" O PROBQ 232 " (cutoff:3.500A) Processing helix chain 'BR' and resid 21 through 40 Processing helix chain 'BR' and resid 46 through 66 removed outlier: 4.333A pdb=" N GLYBR 54 " --> pdb=" O ASPBR 50 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYRBR 55 " --> pdb=" O GLUBR 51 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILEBR 60 " --> pdb=" O ALABR 56 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASPBR 61 " --> pdb=" O GLUBR 57 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEUBR 65 " --> pdb=" O ASPBR 61 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLYBR 66 " --> pdb=" O TYRBR 62 " (cutoff:3.500A) Processing helix chain 'BR' and resid 69 through 80 Processing helix chain 'BR' and resid 82 through 98 removed outlier: 4.344A pdb=" N ILEBR 86 " --> pdb=" O GLUBR 82 " (cutoff:3.500A) Proline residue: BR 87 - end of helix removed outlier: 3.660A pdb=" N LEUBR 93 " --> pdb=" O LEUBR 89 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALABR 94 " --> pdb=" O PHEBR 90 " (cutoff:3.500A) Proline residue: BR 95 - end of helix removed outlier: 4.647A pdb=" N GLNBR 98 " --> pdb=" O ALABR 94 " (cutoff:3.500A) Processing helix chain 'BR' and resid 144 through 161 removed outlier: 3.709A pdb=" N LEUBR 153 " --> pdb=" O LEUBR 149 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SERBR 161 " --> pdb=" O GLNBR 157 " (cutoff:3.500A) Processing helix chain 'BS' and resid 54 through 60 Processing helix chain 'BS' and resid 109 through 116 removed outlier: 4.247A pdb=" N HISBS 115 " --> pdb=" O ALABS 111 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEUBS 116 " --> pdb=" O ILEBS 112 " (cutoff:3.500A) Processing helix chain 'BS' and resid 121 through 140 Processing helix chain 'BS' and resid 149 through 156 removed outlier: 3.634A pdb=" N ALABS 154 " --> pdb=" O PROBS 150 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SERBS 155 " --> pdb=" O TRPBS 151 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASPBS 156 " --> pdb=" O GLUBS 152 " (cutoff:3.500A) Processing helix chain 'BS' and resid 157 through 169 Processing helix chain 'BT' and resid 88 through 106 removed outlier: 4.181A pdb=" N PHEBT 92 " --> pdb=" O ASNBT 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYSBT 104 " --> pdb=" O LEUBT 100 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILEBT 105 " --> pdb=" O GLUBT 101 " (cutoff:3.500A) Processing helix chain 'BT' and resid 188 through 194 removed outlier: 4.868A pdb=" N ASPBT 192 " --> pdb=" O LEUBT 188 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEUBT 194 " --> pdb=" O LEUBT 190 " (cutoff:3.500A) Processing helix chain 'BT' and resid 195 through 200 removed outlier: 5.311A pdb=" N PHEBT 200 " --> pdb=" O GLUBT 196 " (cutoff:3.500A) Processing helix chain 'BT' and resid 244 through 249 removed outlier: 4.043A pdb=" N CYSBT 248 " --> pdb=" O ARGBT 244 " (cutoff:3.500A) Processing helix chain 'BT' and resid 250 through 268 removed outlier: 3.614A pdb=" N GLNBT 258 " --> pdb=" O METBT 254 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYSBT 259 " --> pdb=" O ARGBT 255 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TRPBT 260 " --> pdb=" O GLUBT 256 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SERBT 261 " --> pdb=" O ALABT 257 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLNBT 262 " --> pdb=" O GLNBT 258 " (cutoff:3.500A) Proline residue: BT 263 - end of helix removed outlier: 4.686A pdb=" N GLUBT 266 " --> pdb=" O GLNBT 262 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHEBT 267 " --> pdb=" O PROBT 263 " (cutoff:3.500A) Processing helix chain 'BT' and resid 275 through 292 removed outlier: 3.909A pdb=" N SERBT 292 " --> pdb=" O ALABT 288 " (cutoff:3.500A) Processing helix chain 'BT' and resid 77 through 82 Proline residue: BT 82 - end of helix Processing helix chain 'BU' and resid 16 through 29 removed outlier: 3.974A pdb=" N VALBU 24 " --> pdb=" O ARGBU 20 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N HISBU 27 " --> pdb=" O GLUBU 23 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALABU 28 " --> pdb=" O VALBU 24 " (cutoff:3.500A) Processing helix chain 'BU' and resid 39 through 44 Processing helix chain 'BU' and resid 46 through 79 removed outlier: 4.345A pdb=" N LYSBU 61 " --> pdb=" O ARGBU 57 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARGBU 62 " --> pdb=" O ARGBU 58 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HISBU 79 " --> pdb=" O ALABU 75 " (cutoff:3.500A) Processing helix chain 'BU' and resid 82 through 94 removed outlier: 3.722A pdb=" N CYSBU 93 " --> pdb=" O ASNBU 89 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLNBU 94 " --> pdb=" O LEUBU 90 " (cutoff:3.500A) Processing helix chain 'BU' and resid 98 through 108 Processing helix chain 'BU' and resid 109 through 134 removed outlier: 3.531A pdb=" N ASPBU 134 " --> pdb=" O ALABU 130 " (cutoff:3.500A) Processing helix chain 'BV' and resid 72 through 94 Processing helix chain 'BV' and resid 154 through 159 removed outlier: 3.604A pdb=" N VALBV 158 " --> pdb=" O GLYBV 154 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ARGBV 159 " --> pdb=" O LYSBV 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'BV' and resid 154 through 159' Processing helix chain 'BW' and resid 47 through 55 removed outlier: 5.220A pdb=" N LYSBW 51 " --> pdb=" O ARGBW 47 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASNBW 53 " --> pdb=" O TRPBW 49 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYSBW 54 " --> pdb=" O GLUBW 50 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILEBW 55 " --> pdb=" O LYSBW 51 " (cutoff:3.500A) Processing helix chain 'BW' and resid 81 through 93 removed outlier: 3.841A pdb=" N LEUBW 88 " --> pdb=" O LYSBW 84 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILEBW 92 " --> pdb=" O LEUBW 88 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARGBW 93 " --> pdb=" O ALABW 89 " (cutoff:3.500A) Processing helix chain 'BW' and resid 96 through 108 removed outlier: 3.718A pdb=" N PHEBW 106 " --> pdb=" O ALABW 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SERBW 107 " --> pdb=" O GLNBW 103 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ASPBW 108 " --> pdb=" O LEUBW 104 " (cutoff:3.500A) Processing helix chain 'BW' and resid 109 through 129 removed outlier: 4.301A pdb=" N GLNBW 113 " --> pdb=" O LYSBW 109 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILEBW 114 " --> pdb=" O LYSBW 110 " (cutoff:3.500A) Processing helix chain 'BW' and resid 189 through 204 removed outlier: 3.641A pdb=" N ARGBW 204 " --> pdb=" O GLUBW 200 " (cutoff:3.500A) Processing helix chain 'BX' and resid 49 through 60 Processing helix chain 'BX' and resid 114 through 136 Processing helix chain 'BY' and resid 28 through 36 Proline residue: BY 36 - end of helix Processing helix chain 'BY' and resid 116 through 121 removed outlier: 3.974A pdb=" N VALBY 120 " --> pdb=" O LEUBY 116 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYSBY 121 " --> pdb=" O HISBY 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'BY' and resid 116 through 121' Processing helix chain 'BY' and resid 178 through 184 Processing helix chain 'BY' and resid 193 through 203 Processing helix chain 'Ba' and resid 35 through 40 removed outlier: 5.724A pdb=" N LYSBa 40 " --> pdb=" O ARGBa 36 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 47 through 52 removed outlier: 4.286A pdb=" N GLUBa 51 " --> pdb=" O ASPBa 47 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILEBa 52 " --> pdb=" O ARGBa 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ba' and resid 47 through 52' Processing helix chain 'Ba' and resid 116 through 125 Processing helix chain 'Ba' and resid 133 through 142 Processing helix chain 'Ba' and resid 149 through 163 Processing helix chain 'Ba' and resid 172 through 196 Proline residue: Ba 178 - end of helix removed outlier: 4.538A pdb=" N GLNBa 191 " --> pdb=" O LEUBa 187 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILEBa 192 " --> pdb=" O CYSBa 188 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEUBa 193 " --> pdb=" O LYSBa 189 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LYSBa 194 " --> pdb=" O SERBa 190 " (cutoff:3.500A) Proline residue: Ba 196 - end of helix Processing helix chain 'Ba' and resid 241 through 252 removed outlier: 3.513A pdb=" N VALBa 245 " --> pdb=" O SERBa 241 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASNBa 250 " --> pdb=" O GLUBa 246 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HISBa 251 " --> pdb=" O ALABa 247 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VALBa 252 " --> pdb=" O THRBa 248 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 299 through 304 removed outlier: 3.645A pdb=" N ARGBa 303 " --> pdb=" O LEUBa 299 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHEBa 304 " --> pdb=" O ARGBa 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ba' and resid 299 through 304' Processing helix chain 'Ba' and resid 305 through 329 removed outlier: 3.705A pdb=" N GLNBa 324 " --> pdb=" O SERBa 320 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYRBa 329 " --> pdb=" O ALABa 325 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 407 through 420 removed outlier: 3.927A pdb=" N PHEBa 411 " --> pdb=" O GLNBa 407 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 44 through 49 removed outlier: 4.189A pdb=" N LEUBb 48 " --> pdb=" O ASPBb 44 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LYSBb 49 " --> pdb=" O LEUBb 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bb' and resid 44 through 49' Processing helix chain 'Bb' and resid 53 through 67 removed outlier: 3.617A pdb=" N ARGBb 66 " --> pdb=" O GLUBb 62 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYSBb 67 " --> pdb=" O GLNBb 63 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 73 through 79 removed outlier: 3.579A pdb=" N HISBb 77 " --> pdb=" O THRBb 73 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 98 through 116 removed outlier: 3.709A pdb=" N ASNBb 116 " --> pdb=" O GLUBb 112 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 117 through 126 removed outlier: 3.765A pdb=" N GLNBb 126 " --> pdb=" O ALABb 122 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 131 through 142 Processing helix chain 'Bb' and resid 143 through 156 Processing helix chain 'Bb' and resid 157 through 162 Processing helix chain 'Bb' and resid 194 through 199 Processing helix chain 'Bb' and resid 281 through 286 removed outlier: 3.607A pdb=" N THRBb 285 " --> pdb=" O PHEBb 281 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ARGBb 286 " --> pdb=" O SERBb 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bb' and resid 281 through 286' Processing helix chain 'Bb' and resid 292 through 297 removed outlier: 3.955A pdb=" N THRBb 297 " --> pdb=" O LEUBb 293 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 299 through 308 removed outlier: 3.704A pdb=" N HISBb 307 " --> pdb=" O PHEBb 303 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 324 through 333 removed outlier: 4.351A pdb=" N THRBb 328 " --> pdb=" O ASPBb 324 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARGBb 329 " --> pdb=" O ASPBb 325 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VALBb 330 " --> pdb=" O SERBb 326 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHEBb 331 " --> pdb=" O VALBb 327 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HISBb 332 " --> pdb=" O THRBb 328 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 362 through 370 removed outlier: 4.858A pdb=" N LEUBb 366 " --> pdb=" O PROBb 362 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASPBb 367 " --> pdb=" O LEUBb 363 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARGBb 368 " --> pdb=" O ARGBb 364 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYRBb 369 " --> pdb=" O TYRBb 365 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARGBb 370 " --> pdb=" O LEUBb 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bb' and resid 362 through 370' Processing helix chain 'Bc' and resid 33 through 57 removed outlier: 3.626A pdb=" N LEUBc 37 " --> pdb=" O SERBc 33 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILEBc 38 " --> pdb=" O PROBc 34 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THRBc 56 " --> pdb=" O GLNBc 52 " (cutoff:3.500A) Proline residue: Bc 57 - end of helix Processing helix chain 'Bc' and resid 84 through 93 removed outlier: 4.268A pdb=" N HISBc 91 " --> pdb=" O SERBc 87 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEUBc 92 " --> pdb=" O CYSBc 88 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 94 through 100 Processing helix chain 'Bc' and resid 132 through 155 removed outlier: 3.958A pdb=" N PHEBc 155 " --> pdb=" O ILEBc 151 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 183 through 188 removed outlier: 3.716A pdb=" N ASPBc 187 " --> pdb=" O ASPBc 183 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLUBc 188 " --> pdb=" O LYSBc 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bc' and resid 183 through 188' Processing helix chain 'Bc' and resid 192 through 210 removed outlier: 3.759A pdb=" N LYSBc 209 " --> pdb=" O ALABc 205 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASPBc 210 " --> pdb=" O LEUBc 206 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 219 through 228 removed outlier: 4.043A pdb=" N GLUBc 225 " --> pdb=" O LYSBc 221 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILEBc 226 " --> pdb=" O VALBc 222 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHEBc 227 " --> pdb=" O ALABc 223 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 230 through 245 removed outlier: 3.914A pdb=" N ASNBc 244 " --> pdb=" O LYSBc 240 " (cutoff:3.500A) Proline residue: Bc 245 - end of helix Processing helix chain 'Bc' and resid 305 through 318 removed outlier: 3.651A pdb=" N ARGBc 317 " --> pdb=" O LEUBc 313 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYSBc 318 " --> pdb=" O GLUBc 314 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 268 through 273 removed outlier: 3.968A pdb=" N ILEBc 271 " --> pdb=" O ARGBc 268 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N PHEBc 273 " --> pdb=" O SERBc 270 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 107 through 154 Processing helix chain 'Bd' and resid 155 through 162 removed outlier: 3.875A pdb=" N THRBd 162 " --> pdb=" O HISBd 158 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 95 through 101 removed outlier: 4.009A pdb=" N GLUBd 98 " --> pdb=" O LEUBd 95 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARGBd 99 " --> pdb=" O ASNBd 96 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLNBd 100 " --> pdb=" O LYSBd 97 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARGBd 101 " --> pdb=" O GLUBd 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bd' and resid 95 through 101' Processing helix chain 'Be' and resid 51 through 56 removed outlier: 3.652A pdb=" N ILEBe 55 " --> pdb=" O ILEBe 51 " (cutoff:3.500A) Proline residue: Be 56 - end of helix No H-bonds generated for 'chain 'Be' and resid 51 through 56' Processing helix chain 'Be' and resid 85 through 94 removed outlier: 3.502A pdb=" N THRBe 93 " --> pdb=" O LEUBe 89 " (cutoff:3.500A) Processing helix chain 'Be' and resid 95 through 105 Processing helix chain 'Bf' and resid 68 through 73 removed outlier: 3.983A pdb=" N THRBf 72 " --> pdb=" O PROBf 68 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYSBf 73 " --> pdb=" O TYRBf 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bf' and resid 68 through 73' Processing helix chain 'Bf' and resid 88 through 99 removed outlier: 3.729A pdb=" N LEUBf 96 " --> pdb=" O LEUBf 92 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLUBf 97 " --> pdb=" O LYSBf 93 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLUBf 98 " --> pdb=" O THRBf 94 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYSBf 99 " --> pdb=" O ARGBf 95 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 104 through 117 Processing helix chain 'Bf' and resid 127 through 134 removed outlier: 3.671A pdb=" N ARGBf 133 " --> pdb=" O TYRBf 129 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARGBf 134 " --> pdb=" O HISBf 130 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 16 through 21 removed outlier: 4.520A pdb=" N GLYBg 20 " --> pdb=" O HISBg 16 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARGBg 21 " --> pdb=" O ASNBg 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bg' and resid 16 through 21' Processing helix chain 'Bg' and resid 37 through 50 removed outlier: 3.968A pdb=" N ARGBg 41 " --> pdb=" O ALABg 37 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLYBg 42 " --> pdb=" O PROBg 38 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALABg 43 " --> pdb=" O SERBg 39 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 51 through 59 Proline residue: Bg 59 - end of helix Processing helix chain 'Bg' and resid 93 through 107 removed outlier: 3.662A pdb=" N ILEBg 97 " --> pdb=" O SERBg 93 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 131 through 137 removed outlier: 4.569A pdb=" N ASNBg 135 " --> pdb=" O HISBg 131 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYSBg 136 " --> pdb=" O PROBg 132 " (cutoff:3.500A) Proline residue: Bg 137 - end of helix No H-bonds generated for 'chain 'Bg' and resid 131 through 137' Processing helix chain 'Bh' and resid 34 through 54 removed outlier: 4.767A pdb=" N ALABh 38 " --> pdb=" O GLYBh 34 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLUBh 44 " --> pdb=" O ARGBh 40 " (cutoff:3.500A) Proline residue: Bh 54 - end of helix Processing helix chain 'Bh' and resid 59 through 64 removed outlier: 3.647A pdb=" N LYSBh 63 " --> pdb=" O ARGBh 59 " (cutoff:3.500A) Proline residue: Bh 64 - end of helix No H-bonds generated for 'chain 'Bh' and resid 59 through 64' Processing helix chain 'Bh' and resid 67 through 80 Processing helix chain 'Bh' and resid 84 through 94 removed outlier: 3.902A pdb=" N VALBh 93 " --> pdb=" O LYSBh 89 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASNBh 94 " --> pdb=" O THRBh 90 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 95 through 109 removed outlier: 3.607A pdb=" N LEUBh 108 " --> pdb=" O LYSBh 104 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLYBh 109 " --> pdb=" O ARGBh 105 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 113 through 120 removed outlier: 4.142A pdb=" N LEUBh 119 " --> pdb=" O ALABh 115 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LYSBh 120 " --> pdb=" O LEUBh 116 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 122 through 146 Proline residue: Bh 146 - end of helix Processing helix chain 'Bh' and resid 149 through 162 Processing helix chain 'Bh' and resid 163 through 174 Processing helix chain 'Bh' and resid 187 through 206 Processing helix chain 'Bh' and resid 207 through 224 removed outlier: 3.965A pdb=" N ILEBh 220 " --> pdb=" O ARGBh 216 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THRBh 221 " --> pdb=" O ASPBh 217 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLNBh 222 " --> pdb=" O PHEBh 218 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N METBh 223 " --> pdb=" O LEUBh 219 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THRBh 224 " --> pdb=" O ILEBh 220 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 227 through 233 removed outlier: 4.497A pdb=" N METBh 231 " --> pdb=" O GLUBh 227 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THRBh 233 " --> pdb=" O PHEBh 229 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 236 through 249 Processing helix chain 'Bh' and resid 288 through 306 Processing helix chain 'Bi' and resid 48 through 54 removed outlier: 4.212A pdb=" N SERBi 52 " --> pdb=" O PROBi 48 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYSBi 54 " --> pdb=" O TYRBi 50 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 65 through 72 removed outlier: 3.663A pdb=" N HISBi 69 " --> pdb=" O LEUBi 65 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEUBi 72 " --> pdb=" O PROBi 68 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 93 through 101 removed outlier: 3.769A pdb=" N SERBi 98 " --> pdb=" O ASPBi 94 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SERBi 99 " --> pdb=" O ALABi 95 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEUBi 100 " --> pdb=" O ARGBi 96 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SERBi 101 " --> pdb=" O ILEBi 97 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 102 through 115 removed outlier: 3.805A pdb=" N ALABi 106 " --> pdb=" O LYSBi 102 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASNBi 115 " --> pdb=" O ARGBi 111 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 116 through 129 Processing helix chain 'Bi' and resid 133 through 155 removed outlier: 3.629A pdb=" N PHEBi 137 " --> pdb=" O LYSBi 133 " (cutoff:3.500A) Proline residue: Bi 138 - end of helix removed outlier: 3.660A pdb=" N ASNBi 154 " --> pdb=" O LEUBi 150 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 156 through 164 removed outlier: 3.611A pdb=" N LEUBi 160 " --> pdb=" O ASPBi 156 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THRBi 162 " --> pdb=" O ASPBi 158 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 165 through 173 Proline residue: Bi 170 - end of helix Processing helix chain 'Bj' and resid 64 through 82 Processing helix chain 'Bj' and resid 85 through 104 removed outlier: 3.820A pdb=" N GLUBj 94 " --> pdb=" O ARGBj 90 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALABj 99 " --> pdb=" O ALABj 95 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SERBj 103 " --> pdb=" O ALABj 99 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASPBj 104 " --> pdb=" O LYSBj 100 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 116 through 132 removed outlier: 3.868A pdb=" N LEUBj 120 " --> pdb=" O LEUBj 116 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHEBj 131 " --> pdb=" O LYSBj 127 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LYSBj 132 " --> pdb=" O PHEBj 128 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 137 through 143 removed outlier: 4.540A pdb=" N ASPBj 141 " --> pdb=" O LEUBj 137 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYSBj 142 " --> pdb=" O THRBj 138 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 183 through 197 removed outlier: 3.603A pdb=" N SERBj 196 " --> pdb=" O LEUBj 192 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLUBj 197 " --> pdb=" O ALABj 193 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 256 through 264 removed outlier: 3.835A pdb=" N LEUBj 264 " --> pdb=" O LEUBj 260 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 266 through 277 removed outlier: 3.801A pdb=" N GLNBj 271 " --> pdb=" O LYSBj 267 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VALBj 272 " --> pdb=" O TYRBj 268 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARGBj 273 " --> pdb=" O LEUBj 269 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ARGBj 274 " --> pdb=" O ALABj 270 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHEBj 275 " --> pdb=" O GLNBj 271 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEUBj 277 " --> pdb=" O ARGBj 273 " (cutoff:3.500A) Processing helix chain 'Bk' and resid 59 through 64 removed outlier: 4.023A pdb=" N VALBk 63 " --> pdb=" O TYRBk 59 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYSBk 64 " --> pdb=" O LYSBk 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bk' and resid 59 through 64' Processing helix chain 'Bk' and resid 99 through 118 Processing helix chain 'Bk' and resid 163 through 178 removed outlier: 3.614A pdb=" N GLUBk 172 " --> pdb=" O GLUBk 168 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 44 through 52 removed outlier: 3.872A pdb=" N VALBl 48 " --> pdb=" O GLUBl 44 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARGBl 50 " --> pdb=" O HISBl 46 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEUBl 51 " --> pdb=" O PHEBl 47 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEUBl 52 " --> pdb=" O VALBl 48 " (cutoff:3.500A) Processing helix chain 'Bl' and resid 116 through 132 removed outlier: 3.672A pdb=" N LEUBl 120 " --> pdb=" O ASPBl 116 " (cutoff:3.500A) Proline residue: Bl 130 - end of helix Processing helix chain 'Bl' and resid 153 through 165 removed outlier: 3.509A pdb=" N LYSBl 164 " --> pdb=" O TRPBl 160 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLYBl 165 " --> pdb=" O LEUBl 161 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 66 through 80 Processing helix chain 'Bm' and resid 94 through 110 Processing helix chain 'Bm' and resid 114 through 122 removed outlier: 4.773A pdb=" N HISBm 119 " --> pdb=" O ASNBm 115 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLNBm 120 " --> pdb=" O SERBm 116 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N CYSBm 122 " --> pdb=" O LEUBm 118 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 123 through 133 removed outlier: 4.280A pdb=" N VALBm 127 " --> pdb=" O ARGBm 123 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VALBm 133 " --> pdb=" O ASPBm 129 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 139 through 148 removed outlier: 3.675A pdb=" N ALABm 146 " --> pdb=" O ASPBm 142 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SERBm 147 " --> pdb=" O GLUBm 143 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ASNBm 148 " --> pdb=" O LEUBm 144 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 48 through 54 removed outlier: 3.507A pdb=" N PHEBn 54 " --> pdb=" O LYSBn 50 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 59 through 64 Processing helix chain 'Bn' and resid 69 through 74 removed outlier: 4.581A pdb=" N LEUBn 73 " --> pdb=" O HISBn 69 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILEBn 74 " --> pdb=" O PROBn 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bn' and resid 69 through 74' Processing helix chain 'Bn' and resid 86 through 98 Processing helix chain 'Bn' and resid 103 through 123 Processing helix chain 'Bo' and resid 24 through 32 removed outlier: 3.604A pdb=" N ARGBo 28 " --> pdb=" O GLYBo 24 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 41 through 46 removed outlier: 3.635A pdb=" N LEUBo 46 " --> pdb=" O PROBo 42 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 60 through 108 removed outlier: 3.676A pdb=" N GLUBo 103 " --> pdb=" O LEUBo 99 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLNBo 106 " --> pdb=" O GLUBo 102 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASNBo 108 " --> pdb=" O GLYBo 104 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 114 through 119 removed outlier: 4.695A pdb=" N GLNBo 118 " --> pdb=" O GLYBo 114 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASNBo 119 " --> pdb=" O ALABo 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bo' and resid 114 through 119' Processing helix chain 'Bp' and resid 2 through 9 removed outlier: 3.715A pdb=" N LEUBp 8 " --> pdb=" O ALABp 4 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLYBp 9 " --> pdb=" O LEUBp 5 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 27 through 39 removed outlier: 3.769A pdb=" N SERBp 39 " --> pdb=" O GLNBp 35 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 40 through 47 removed outlier: 4.346A pdb=" N ASNBp 46 " --> pdb=" O VALBp 42 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEUBp 47 " --> pdb=" O ARGBp 43 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 82 through 98 removed outlier: 3.689A pdb=" N ALABp 96 " --> pdb=" O SERBp 92 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARGBp 97 " --> pdb=" O HISBp 93 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLYBp 98 " --> pdb=" O ILEBp 94 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 76 through 84 removed outlier: 3.972A pdb=" N GLYBq 81 " --> pdb=" O ILEBq 77 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VALBq 84 " --> pdb=" O GLUBq 80 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 93 through 99 removed outlier: 4.401A pdb=" N PHEBq 97 " --> pdb=" O PROBq 93 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLUBq 98 " --> pdb=" O GLUBq 94 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 106 through 111 removed outlier: 3.694A pdb=" N LEUBq 110 " --> pdb=" O LYSBq 106 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASPBq 111 " --> pdb=" O LEUBq 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bq' and resid 106 through 111' Processing helix chain 'Bq' and resid 114 through 135 removed outlier: 3.965A pdb=" N TRPBq 118 " --> pdb=" O THRBq 114 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYSBq 134 " --> pdb=" O ASNBq 130 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASNBq 135 " --> pdb=" O ARGBq 131 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 28 through 51 removed outlier: 3.968A pdb=" N SERBt 50 " --> pdb=" O GLNBt 46 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARGBt 51 " --> pdb=" O TYRBt 47 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 55 through 60 removed outlier: 3.509A pdb=" N GLUBt 59 " --> pdb=" O THRBt 55 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARGBt 60 " --> pdb=" O ALABt 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bt' and resid 55 through 60' Processing helix chain 'Bt' and resid 63 through 81 removed outlier: 4.472A pdb=" N ARGBt 67 " --> pdb=" O ALABt 63 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARGBt 81 " --> pdb=" O ALABt 77 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 87 through 97 removed outlier: 3.885A pdb=" N GLNBt 91 " --> pdb=" O ARGBt 87 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEUBt 95 " --> pdb=" O GLNBt 91 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEUBt 96 " --> pdb=" O LEUBt 92 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VALBt 97 " --> pdb=" O GLYBt 93 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 44 through 50 Proline residue: Bu 50 - end of helix Processing helix chain 'Bu' and resid 62 through 67 removed outlier: 3.792A pdb=" N LYSBu 66 " --> pdb=" O PROBu 62 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLNBu 67 " --> pdb=" O ASPBu 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bu' and resid 62 through 67' Processing helix chain 'Bu' and resid 72 through 77 removed outlier: 4.137A pdb=" N LEUBu 76 " --> pdb=" O PROBu 72 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N THRBu 77 " --> pdb=" O VALBu 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bu' and resid 72 through 77' Processing helix chain 'Bu' and resid 111 through 123 removed outlier: 3.739A pdb=" N ALABu 119 " --> pdb=" O ARGBu 115 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VALBu 120 " --> pdb=" O LEUBu 116 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYSBu 123 " --> pdb=" O ALABu 119 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 141 through 163 Proline residue: Bu 163 - end of helix Processing helix chain 'Bu' and resid 170 through 189 removed outlier: 4.001A pdb=" N LEUBu 174 " --> pdb=" O GLUBu 170 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ARGBu 176 " --> pdb=" O ALABu 172 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SERBu 177 " --> pdb=" O GLUBu 173 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEUBu 187 " --> pdb=" O ASNBu 183 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 48 through 53 removed outlier: 3.787A pdb=" N LEUBv 52 " --> pdb=" O PROBv 48 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SERBv 53 " --> pdb=" O ARGBv 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bv' and resid 48 through 53' Processing helix chain 'Bv' and resid 54 through 64 Processing helix chain 'Bv' and resid 71 through 76 removed outlier: 4.289A pdb=" N LEUBv 75 " --> pdb=" O ALABv 71 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TRPBv 76 " --> pdb=" O ALABv 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bv' and resid 71 through 76' Processing helix chain 'Bv' and resid 78 through 93 Processing helix chain 'Bv' and resid 95 through 159 removed outlier: 3.650A pdb=" N GLNBv 106 " --> pdb=" O SERBv 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYSBv 127 " --> pdb=" O GLUBv 123 " (cutoff:3.500A) Proline residue: Bv 129 - end of helix removed outlier: 3.530A pdb=" N LEUBv 156 " --> pdb=" O ARGBv 152 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 55 through 73 Processing helix chain 'Bw' and resid 75 through 85 Processing helix chain 'Bw' and resid 101 through 111 removed outlier: 3.887A pdb=" N TRPBw 105 " --> pdb=" O ASNBw 101 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 132 through 149 removed outlier: 3.599A pdb=" N LEUBw 136 " --> pdb=" O ASPBw 132 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYSBw 143 " --> pdb=" O ALABw 139 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 164 through 184 Proline residue: Bw 169 - end of helix removed outlier: 3.715A pdb=" N GLYBw 180 " --> pdb=" O ALABw 176 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 186 through 193 removed outlier: 4.453A pdb=" N ALABw 190 " --> pdb=" O ASNBw 186 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALABw 191 " --> pdb=" O PROBw 187 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ALABw 193 " --> pdb=" O LEUBw 189 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 261 through 266 removed outlier: 4.704A pdb=" N LEUBw 265 " --> pdb=" O LYSBw 261 " (cutoff:3.500A) Proline residue: Bw 266 - end of helix No H-bonds generated for 'chain 'Bw' and resid 261 through 266' Processing helix chain 'Bw' and resid 301 through 309 removed outlier: 3.596A pdb=" N ASNBw 309 " --> pdb=" O LEUBw 305 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 312 through 338 removed outlier: 3.584A pdb=" N VALBw 316 " --> pdb=" O ASPBw 312 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHEBw 318 " --> pdb=" O ILEBw 314 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHEBw 327 " --> pdb=" O ILEBw 323 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLYBw 338 " --> pdb=" O ALABw 334 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 374 through 379 removed outlier: 3.985A pdb=" N GLNBw 379 " --> pdb=" O ALABw 375 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 408 through 421 removed outlier: 3.872A pdb=" N LEUBw 412 " --> pdb=" O ASNBw 408 " (cutoff:3.500A) Processing helix chain 'Bx' and resid 70 through 76 removed outlier: 3.807A pdb=" N TRPBx 75 " --> pdb=" O PROBx 71 " (cutoff:3.500A) Processing helix chain 'Bx' and resid 85 through 94 removed outlier: 4.444A pdb=" N GLNBx 91 " --> pdb=" O LEUBx 87 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHEBx 92 " --> pdb=" O LEUBx 88 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILEBx 93 " --> pdb=" O LEUBx 89 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ARGBx 94 " --> pdb=" O SERBx 90 " (cutoff:3.500A) Processing helix chain 'Bx' and resid 101 through 106 Processing helix chain 'Bx' and resid 108 through 126 Processing helix chain 'Bx' and resid 135 through 142 removed outlier: 3.781A pdb=" N PHEBx 139 " --> pdb=" O LEUBx 135 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N VALBx 140 " --> pdb=" O PROBx 136 " (cutoff:3.500A) Proline residue: Bx 141 - end of helix No H-bonds generated for 'chain 'Bx' and resid 135 through 142' Processing helix chain 'Bx' and resid 178 through 183 removed outlier: 4.031A pdb=" N LYSBx 182 " --> pdb=" O SERBx 178 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASPBx 183 " --> pdb=" O PROBx 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bx' and resid 178 through 183' Processing helix chain 'Bz' and resid 301 through 315 removed outlier: 3.637A pdb=" N ALABz 315 " --> pdb=" O ALABz 311 " (cutoff:3.500A) Processing helix chain 'Bz' and resid 399 through 415 removed outlier: 3.633A pdb=" N ALABz 403 " --> pdb=" O ALABz 399 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALABz 415 " --> pdb=" O ALABz 411 " (cutoff:3.500A) Processing helix chain 'Bz' and resid 601 through 615 removed outlier: 3.696A pdb=" N ALABz 615 " --> pdb=" O ALABz 611 " (cutoff:3.500A) Processing helix chain 'Bz' and resid 700 through 710 Processing helix chain 'Bz' and resid 1001 through 1016 Processing sheet with id= 1, first strand: chain 'B0' and resid 75 through 78 Processing sheet with id= 2, first strand: chain 'B0' and resid 81 through 84 removed outlier: 4.229A pdb=" N CYSB0 88 " --> pdb=" O GLYB0 84 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B1' and resid 49 through 53 removed outlier: 5.130A pdb=" N LYSB1 49 " --> pdb=" O VALB1 62 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLNB1 58 " --> pdb=" O ASNB1 53 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B1' and resid 85 through 91 Processing sheet with id= 5, first strand: chain 'B2' and resid 167 through 172 Processing sheet with id= 6, first strand: chain 'B3' and resid 97 through 101 removed outlier: 5.314A pdb=" N LEUB3 66 " --> pdb=" O LEUB3 122 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEUB3 116 " --> pdb=" O ILEB3 72 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B3' and resid 137 through 140 Processing sheet with id= 8, first strand: chain 'B4' and resid 64 through 68 Processing sheet with id= 9, first strand: chain 'B5' and resid 155 through 161 Processing sheet with id= 10, first strand: chain 'B6' and resid 28 through 33 removed outlier: 6.079A pdb=" N PHEB6 28 " --> pdb=" O SERB6 22 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEUB6 17 " --> pdb=" O ILEB6 62 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B6' and resid 41 through 45 removed outlier: 6.290A pdb=" N LEUB6 41 " --> pdb=" O GLUB6 58 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B8' and resid 122 through 125 removed outlier: 5.246A pdb=" N TRPB8 122 " --> pdb=" O CYSB8 150 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B9' and resid 63 through 67 removed outlier: 3.624A pdb=" N LYSB9 64 " --> pdb=" O LYSB9 96 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N HISB9 95 " --> pdb=" O CYSB9 89 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N CYSB9 89 " --> pdb=" O HISB9 95 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRPB9 85 " --> pdb=" O GLNB9 99 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'BC' and resid 217 through 224 removed outlier: 3.668A pdb=" N GLYBC 218 " --> pdb=" O ASPBC 234 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLUBC 228 " --> pdb=" O LEUBC 224 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HISBC 188 " --> pdb=" O VALBC 258 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALABC 260 " --> pdb=" O HISBC 188 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLNBC 319 " --> pdb=" O ILEBC 283 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'BC' and resid 355 through 360 removed outlier: 5.639A pdb=" N VALBC 355 " --> pdb=" O GLUBC 433 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLUBC 429 " --> pdb=" O VALBC 359 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VALBC 386 " --> pdb=" O VALBC 434 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SERBC 385 " --> pdb=" O VALBC 396 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'BC' and resid 361 through 365 removed outlier: 3.566A pdb=" N GLUBC 361 " --> pdb=" O THRBC 373 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'BC' and resid 545 through 549 removed outlier: 7.679A pdb=" N ILEBC 520 " --> pdb=" O VALBC 549 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N HISBC 550 " --> pdb=" O VALBC 518 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'BC' and resid 592 through 596 Processing sheet with id= 19, first strand: chain 'BC' and resid 616 through 623 removed outlier: 6.678A pdb=" N CYSBC 711 " --> pdb=" O VALBC 623 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASPBC 707 " --> pdb=" O ILEBC 628 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLUBC 625 " --> pdb=" O GLNBC 649 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLYBC 645 " --> pdb=" O LEUBC 629 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'BC' and resid 668 through 672 removed outlier: 3.746A pdb=" N TRPBC 669 " --> pdb=" O LEUBC 661 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'BC' and resid 674 through 678 Processing sheet with id= 22, first strand: chain 'BC' and resid 517 through 522 Processing sheet with id= 23, first strand: chain 'BC' and resid 643 through 649 removed outlier: 4.428A pdb=" N METBC 690 " --> pdb=" O VALBC 648 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'BC' and resid 657 through 663 Processing sheet with id= 25, first strand: chain 'BD' and resid 129 through 132 removed outlier: 3.719A pdb=" N ALABD 129 " --> pdb=" O LEUBD 142 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEUBD 142 " --> pdb=" O ILEBD 128 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLYBD 180 " --> pdb=" O THRBD 163 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEUBD 165 " --> pdb=" O GLYBD 180 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'BD' and resid 192 through 195 removed outlier: 4.353A pdb=" N THRBD 192 " --> pdb=" O LEUBD 217 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILEBD 226 " --> pdb=" O LEUBD 218 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARGBD 233 " --> pdb=" O LEUBD 229 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEUBD 238 " --> pdb=" O TYRBD 296 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'BD' and resid 139 through 145 removed outlier: 5.312A pdb=" N ASPBD 139 " --> pdb=" O ALABD 154 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'BE' and resid 98 through 101 Processing sheet with id= 29, first strand: chain 'BE' and resid 105 through 111 removed outlier: 4.049A pdb=" N GLYBE 105 " --> pdb=" O LEUBE 121 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLNBE 115 " --> pdb=" O THRBE 111 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ASNBE 281 " --> pdb=" O VALBE 124 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARGBE 275 " --> pdb=" O TYRBE 284 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLUBE 330 " --> pdb=" O THRBE 278 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'BE' and resid 174 through 181 removed outlier: 5.430A pdb=" N LYSBE 175 " --> pdb=" O GLYBE 149 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYSBE 127 " --> pdb=" O LEUBE 193 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THRBE 191 " --> pdb=" O VALBE 129 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'BE' and resid 201 through 204 removed outlier: 4.291A pdb=" N GLNBE 202 " --> pdb=" O VALBE 273 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'BF' and resid 47 through 50 removed outlier: 3.794A pdb=" N VALBF 47 " --> pdb=" O VALBF 77 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'BF' and resid 186 through 189 Processing sheet with id= 34, first strand: chain 'BI' and resid 55 through 58 removed outlier: 6.770A pdb=" N ILEBI 55 " --> pdb=" O VALBI 83 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'BI' and resid 94 through 98 removed outlier: 3.957A pdb=" N ASPBI 110 " --> pdb=" O LEUBI 98 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'BJ' and resid 95 through 101 removed outlier: 3.990A pdb=" N HISBJ 101 " --> pdb=" O HISBJ 150 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N HISBJ 150 " --> pdb=" O HISBJ 101 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'BK' and resid 17 through 24 Processing sheet with id= 38, first strand: chain 'BL' and resid 169 through 172 removed outlier: 6.836A pdb=" N VALBL 132 " --> pdb=" O ILEBL 172 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THRBL 194 " --> pdb=" O THRBL 135 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'BN' and resid 55 through 60 removed outlier: 3.770A pdb=" N GLUBN 143 " --> pdb=" O TRPBN 18 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASPBN 22 " --> pdb=" O LEUBN 145 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'BN' and resid 77 through 81 removed outlier: 7.415A pdb=" N GLYBN 86 " --> pdb=" O THRBN 81 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'BO' and resid 55 through 58 removed outlier: 6.551A pdb=" N LEUBO 74 " --> pdb=" O ILEBO 58 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASPBO 71 " --> pdb=" O ILEBO 86 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N SERBO 102 " --> pdb=" O ARGBO 90 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARGBO 90 " --> pdb=" O SERBO 102 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLYBO 88 " --> pdb=" O ASNBO 104 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'BP' and resid 93 through 96 Processing sheet with id= 43, first strand: chain 'BP' and resid 273 through 277 Processing sheet with id= 44, first strand: chain 'BQ' and resid 93 through 97 removed outlier: 6.812A pdb=" N GLYBQ 93 " --> pdb=" O ALABQ 156 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'BQ' and resid 118 through 123 removed outlier: 5.953A pdb=" N ILEBQ 160 " --> pdb=" O ARGBQ 123 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VALBQ 161 " --> pdb=" O ILEBQ 89 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'BR' and resid 41 through 44 removed outlier: 4.391A pdb=" N METBR 121 " --> pdb=" O ILEBR 110 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'BS' and resid 79 through 85 removed outlier: 6.543A pdb=" N ILEBS 90 " --> pdb=" O THRBS 107 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VALBS 103 " --> pdb=" O VALBS 94 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'BT' and resid 129 through 135 removed outlier: 4.663A pdb=" N LYSBT 129 " --> pdb=" O ASPBT 123 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILEBT 116 " --> pdb=" O VALBT 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLUBT 173 " --> pdb=" O THRBT 120 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'BT' and resid 139 through 142 removed outlier: 4.123A pdb=" N GLNBT 139 " --> pdb=" O ILEBT 150 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'BV' and resid 109 through 113 removed outlier: 7.293A pdb=" N LEUBV 138 " --> pdb=" O GLYBV 149 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'BV' and resid 116 through 121 removed outlier: 6.594A pdb=" N VALBV 196 " --> pdb=" O ILEBV 165 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLUBV 161 " --> pdb=" O ASNBV 200 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VALBV 160 " --> pdb=" O LEUBV 134 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLUBV 130 " --> pdb=" O VALBV 164 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'BV' and resid 166 through 169 Processing sheet with id= 53, first strand: chain 'BV' and resid 172 through 179 removed outlier: 4.285A pdb=" N TYRBV 184 " --> pdb=" O GLNBV 179 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'BW' and resid 69 through 76 removed outlier: 4.734A pdb=" N ALABW 69 " --> pdb=" O GLUBW 178 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYSBW 175 " --> pdb=" O ALABW 141 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'BX' and resid 26 through 29 removed outlier: 4.521A pdb=" N GLNBX 41 " --> pdb=" O VALBX 29 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASPBX 38 " --> pdb=" O LEUBX 99 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYSBX 93 " --> pdb=" O ILEBX 44 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLYBX 75 " --> pdb=" O PROBX 90 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'BY' and resid 92 through 97 removed outlier: 5.307A pdb=" N ASNBY 92 " --> pdb=" O ALABY 113 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'BY' and resid 132 through 135 removed outlier: 7.078A pdb=" N ASPBY 132 " --> pdb=" O THRBY 148 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARGBY 145 " --> pdb=" O ILEBY 154 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARGBY 152 " --> pdb=" O SERBY 147 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'Ba' and resid 126 through 130 Processing sheet with id= 59, first strand: chain 'Ba' and resid 200 through 205 removed outlier: 8.942A pdb=" N ARGBa 200 " --> pdb=" O LYSBa 233 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEUBa 230 " --> pdb=" O HISBa 289 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Ba' and resid 208 through 214 removed outlier: 4.903A pdb=" N LEUBa 219 " --> pdb=" O ALABa 103 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Ba' and resid 350 through 353 removed outlier: 8.281A pdb=" N ARGBa 350 " --> pdb=" O LEUBa 382 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Bb' and resid 183 through 187 removed outlier: 6.224A pdb=" N ASPBb 183 " --> pdb=" O VALBb 179 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VALBb 175 " --> pdb=" O VALBb 187 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Bb' and resid 190 through 193 removed outlier: 3.907A pdb=" N ASNBb 191 " --> pdb=" O PHEBb 318 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ARGBb 322 " --> pdb=" O VALBb 193 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARGBb 267 " --> pdb=" O LEUBb 221 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEUBb 213 " --> pdb=" O GLNBb 275 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEUBb 218 " --> pdb=" O HISBb 234 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Bb' and resid 215 through 218 Processing sheet with id= 65, first strand: chain 'Bb' and resid 272 through 275 removed outlier: 6.301A pdb=" N LEUBb 272 " --> pdb=" O ALABb 314 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Bc' and resid 74 through 79 removed outlier: 4.718A pdb=" N THRBc 74 " --> pdb=" O HISBc 66 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYSBc 120 " --> pdb=" O GLUBc 63 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHEBc 124 " --> pdb=" O VALBc 67 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'Bc' and resid 161 through 164 removed outlier: 6.848A pdb=" N GLNBc 294 " --> pdb=" O SERBc 278 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'Bc' and resid 214 through 218 Processing sheet with id= 69, first strand: chain 'Be' and resid 40 through 43 removed outlier: 5.002A pdb=" N LYSBe 47 " --> pdb=" O GLYBe 43 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Bg' and resid 61 through 68 removed outlier: 4.077A pdb=" N ALABg 83 " --> pdb=" O TYRBg 79 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Bh' and resid 254 through 258 removed outlier: 6.659A pdb=" N PHEBh 271 " --> pdb=" O THRBh 258 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALABh 282 " --> pdb=" O LEUBh 274 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'Bi' and resid 192 through 195 removed outlier: 6.900A pdb=" N THRBi 213 " --> pdb=" O VALBi 195 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Bi' and resid 199 through 203 removed outlier: 3.765A pdb=" N SERBi 200 " --> pdb=" O TYRBi 209 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYRBi 209 " --> pdb=" O SERBi 200 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Bj' and resid 158 through 162 removed outlier: 4.698A pdb=" N HISBj 251 " --> pdb=" O ARGBj 162 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Bj' and resid 174 through 177 Processing sheet with id= 76, first strand: chain 'Bj' and resid 210 through 217 removed outlier: 3.754A pdb=" N PHEBj 217 " --> pdb=" O LEUBj 227 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEUBj 227 " --> pdb=" O PHEBj 217 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Bk' and resid 123 through 127 removed outlier: 3.941A pdb=" N GLUBk 123 " --> pdb=" O GLNBk 158 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLUBk 154 " --> pdb=" O METBk 127 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Bl' and resid 95 through 101 removed outlier: 5.434A pdb=" N VALBl 137 " --> pdb=" O LYSBl 150 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'Bp' and resid 49 through 56 removed outlier: 3.695A pdb=" N SERBp 50 " --> pdb=" O LYSBp 14 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLYBp 78 " --> pdb=" O PROBp 62 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'Bu' and resid 78 through 85 removed outlier: 3.909A pdb=" N GLYBu 85 " --> pdb=" O LYSBu 93 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYSBu 93 " --> pdb=" O GLYBu 85 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'Bw' and resid 90 through 93 Processing sheet with id= 82, first strand: chain 'Bw' and resid 112 through 116 removed outlier: 4.792A pdb=" N PHEBw 363 " --> pdb=" O THRBw 390 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'Bw' and resid 359 through 362 removed outlier: 8.852A pdb=" N LYSBw 359 " --> pdb=" O LEUBw 395 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'Bx' and resid 35 through 42 removed outlier: 4.677A pdb=" N PHEBx 35 " --> pdb=" O THRBx 54 " (cutoff:3.500A) 2915 hydrogen bonds defined for protein. 8616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1042 hydrogen bonds 1782 hydrogen bond angles 0 basepair planarities 435 basepair parallelities 873 stacking parallelities Total time for adding SS restraints: 64.68 Time building geometry restraints manager: 38.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 25454 1.33 - 1.47: 40370 1.47 - 1.60: 48979 1.60 - 1.73: 1673 1.73 - 1.87: 442 Bond restraints: 116918 Sorted by residual: bond pdb=" CA ILEBx 162 " pdb=" CB ILEBx 162 " ideal model delta sigma weight residual 1.533 1.582 -0.049 1.13e-02 7.83e+03 1.87e+01 bond pdb=" CA PROBh 188 " pdb=" C PROBh 188 " ideal model delta sigma weight residual 1.517 1.556 -0.039 9.30e-03 1.16e+04 1.75e+01 bond pdb=" CA PROBd 102 " pdb=" C PROBd 102 " ideal model delta sigma weight residual 1.517 1.554 -0.037 9.30e-03 1.16e+04 1.60e+01 bond pdb=" CA ILEBL 149 " pdb=" CB ILEBL 149 " ideal model delta sigma weight residual 1.539 1.579 -0.040 1.11e-02 8.12e+03 1.30e+01 bond pdb=" CA ILEBi 67 " pdb=" CB ILEBi 67 " ideal model delta sigma weight residual 1.539 1.557 -0.018 5.40e-03 3.43e+04 1.12e+01 ... (remaining 116913 not shown) Histogram of bond angle deviations from ideal: 96.55 - 104.48: 8615 104.48 - 112.40: 62898 112.40 - 120.33: 49313 120.33 - 128.26: 42394 128.26 - 136.18: 3059 Bond angle restraints: 166279 Sorted by residual: angle pdb=" C GLYBh 284 " pdb=" N PROBh 285 " pdb=" CA PROBh 285 " ideal model delta sigma weight residual 120.31 132.96 -12.65 9.80e-01 1.04e+00 1.67e+02 angle pdb=" C VALBi 89 " pdb=" N PROBi 90 " pdb=" CA PROBi 90 " ideal model delta sigma weight residual 120.38 130.11 -9.73 1.03e+00 9.43e-01 8.92e+01 angle pdb=" C GLUB4 71 " pdb=" N PROB4 72 " pdb=" CA PROB4 72 " ideal model delta sigma weight residual 119.82 128.56 -8.74 9.80e-01 1.04e+00 7.95e+01 angle pdb=" C ARGBt 23 " pdb=" N PROBt 24 " pdb=" CA PROBt 24 " ideal model delta sigma weight residual 119.84 130.55 -10.71 1.25e+00 6.40e-01 7.34e+01 angle pdb=" C LYSBD 119 " pdb=" N PROBD 120 " pdb=" CA PROBD 120 " ideal model delta sigma weight residual 119.56 128.10 -8.54 1.01e+00 9.80e-01 7.15e+01 ... (remaining 166274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 65332 35.82 - 71.65: 4459 71.65 - 107.47: 552 107.47 - 143.29: 15 143.29 - 179.11: 34 Dihedral angle restraints: 70392 sinusoidal: 43312 harmonic: 27080 Sorted by residual: dihedral pdb=" CA PHEBE 316 " pdb=" C PHEBE 316 " pdb=" N PROBE 317 " pdb=" CA PROBE 317 " ideal model delta harmonic sigma weight residual 180.00 93.45 86.55 0 5.00e+00 4.00e-02 3.00e+02 dihedral pdb=" O4' CBA 404 " pdb=" C1' CBA 404 " pdb=" N1 CBA 404 " pdb=" C2 CBA 404 " ideal model delta sinusoidal sigma weight residual -160.00 19.11 -179.11 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' CBA 64 " pdb=" C1' CBA 64 " pdb=" N1 CBA 64 " pdb=" C2 CBA 64 " ideal model delta sinusoidal sigma weight residual -160.00 17.83 -177.83 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 70389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 17902 0.080 - 0.161: 1628 0.161 - 0.241: 106 0.241 - 0.322: 6 0.322 - 0.402: 2 Chirality restraints: 19644 Sorted by residual: chirality pdb=" C3' UBA 48 " pdb=" C4' UBA 48 " pdb=" O3' UBA 48 " pdb=" C2' UBA 48 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA ASNBx 164 " pdb=" N ASNBx 164 " pdb=" C ASNBx 164 " pdb=" CB ASNBx 164 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA PHEBb 78 " pdb=" N PHEBb 78 " pdb=" C PHEBb 78 " pdb=" CB PHEBb 78 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 19641 not shown) Planarity restraints: 15128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' UBA 693 " -0.045 2.00e-02 2.50e+03 2.44e-02 1.34e+01 pdb=" N1 UBA 693 " 0.056 2.00e-02 2.50e+03 pdb=" C2 UBA 693 " 0.001 2.00e-02 2.50e+03 pdb=" O2 UBA 693 " 0.003 2.00e-02 2.50e+03 pdb=" N3 UBA 693 " -0.004 2.00e-02 2.50e+03 pdb=" C4 UBA 693 " -0.008 2.00e-02 2.50e+03 pdb=" O4 UBA 693 " -0.009 2.00e-02 2.50e+03 pdb=" C5 UBA 693 " -0.003 2.00e-02 2.50e+03 pdb=" C6 UBA 693 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ABA 243 " 0.044 2.00e-02 2.50e+03 1.92e-02 1.02e+01 pdb=" N9 ABA 243 " -0.041 2.00e-02 2.50e+03 pdb=" C8 ABA 243 " -0.005 2.00e-02 2.50e+03 pdb=" N7 ABA 243 " 0.004 2.00e-02 2.50e+03 pdb=" C5 ABA 243 " -0.001 2.00e-02 2.50e+03 pdb=" C6 ABA 243 " 0.007 2.00e-02 2.50e+03 pdb=" N6 ABA 243 " 0.009 2.00e-02 2.50e+03 pdb=" N1 ABA 243 " 0.005 2.00e-02 2.50e+03 pdb=" C2 ABA 243 " -0.001 2.00e-02 2.50e+03 pdb=" N3 ABA 243 " -0.007 2.00e-02 2.50e+03 pdb=" C4 ABA 243 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ABA 52 " 0.042 2.00e-02 2.50e+03 1.88e-02 9.73e+00 pdb=" N9 ABA 52 " -0.042 2.00e-02 2.50e+03 pdb=" C8 ABA 52 " -0.006 2.00e-02 2.50e+03 pdb=" N7 ABA 52 " -0.000 2.00e-02 2.50e+03 pdb=" C5 ABA 52 " 0.001 2.00e-02 2.50e+03 pdb=" C6 ABA 52 " 0.009 2.00e-02 2.50e+03 pdb=" N6 ABA 52 " 0.008 2.00e-02 2.50e+03 pdb=" N1 ABA 52 " 0.006 2.00e-02 2.50e+03 pdb=" C2 ABA 52 " -0.005 2.00e-02 2.50e+03 pdb=" N3 ABA 52 " -0.008 2.00e-02 2.50e+03 pdb=" C4 ABA 52 " -0.005 2.00e-02 2.50e+03 ... (remaining 15125 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 424 2.47 - 3.08: 69791 3.08 - 3.69: 181521 3.69 - 4.29: 280059 4.29 - 4.90: 415744 Nonbonded interactions: 947539 Sorted by model distance: nonbonded pdb=" O6 GBA 187 " pdb="MG MGBA3004 " model vdw 1.865 2.170 nonbonded pdb=" OP1 UBA1373 " pdb="MG MGBA3105 " model vdw 1.887 2.170 nonbonded pdb=" OP1 ABA 52 " pdb="MG MGBA3137 " model vdw 1.939 2.170 nonbonded pdb=" OP1 ABA 298 " pdb="MG MGBA3070 " model vdw 1.942 2.170 nonbonded pdb=" OP1 ABA 762 " pdb="MG MGBA3070 " model vdw 1.950 2.170 ... (remaining 947534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'DL' and resid 64 through 89) selection = (chain 'EL' and resid 64 through 89) selection = (chain 'FL' and resid 64 through 89) selection = (chain 'GL' and resid 64 through 89) selection = chain 'HL' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 9.200 Check model and map are aligned: 1.180 Set scattering table: 0.760 Process input model: 299.450 Find NCS groups from input model: 2.940 Set up NCS constraints: 0.280 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 317.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 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 : 0.007 0.071 116918 Z= 0.432 Angle : 1.141 15.803 166279 Z= 0.734 Chirality : 0.047 0.402 19644 Planarity : 0.005 0.069 15128 Dihedral : 20.434 179.113 52830 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.98 % Favored : 95.86 % Rotamer: Outliers : 10.13 % Allowed : 9.29 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.16 % Twisted General : 0.05 % 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: -2.82 (0.07), residues: 9175 helix: -2.80 (0.07), residues: 3163 sheet: -0.82 (0.12), residues: 1202 loop : -1.40 (0.07), residues: 4810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRPBn 47 HIS 0.012 0.002 HISBb 189 PHE 0.034 0.002 PHEBe 66 TYR 0.039 0.002 TYRBo 40 ARG 0.006 0.001 ARGB3 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3275 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 810 poor density : 2465 time to evaluate : 7.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 810 outliers final: 201 residues processed: 2993 average time/residue: 1.1623 time to fit residues: 5730.2966 Evaluate side-chains 1685 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1484 time to evaluate : 7.408 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 201 outliers final: 1 residues processed: 201 average time/residue: 0.8998 time to fit residues: 344.3534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 902 optimal weight: 0.0030 chunk 810 optimal weight: 0.7980 chunk 449 optimal weight: 20.0000 chunk 276 optimal weight: 9.9990 chunk 546 optimal weight: 4.9990 chunk 432 optimal weight: 7.9990 chunk 837 optimal weight: 0.9990 chunk 324 optimal weight: 20.0000 chunk 509 optimal weight: 0.9990 chunk 623 optimal weight: 3.9990 chunk 970 optimal weight: 4.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B0 41 ASN B0 59 HIS B0 76 HIS B1 42 HIS B1 89 HIS B2 90 GLN B3 67 HIS B4 60 GLN B5 83 ASN B5 118 GLN B8 118 HIS B8 154 GLN B9 97 GLN BC 215 GLN BC 268 GLN BC 453 GLN BC 514 ASN BC 649 GLN BC 679 HIS BD 183 HIS BD 234 GLN BD 254 ASN ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 197 HIS BE 281 ASN BE 292 HIS ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 97 HIS ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 257 GLN BI 88 HIS BI 126 GLN BI 136 ASN BJ 41 HIS ** BJ 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 48 GLN BK 126 GLN ** BN 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 74 GLN BN 80 HIS BN 140 ASN ** BO 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 89 HIS BO 142 GLN BP 53 HIS BP 84 ASN BP 87 HIS BP 170 ASN BP 219 ASN BQ 110 ASN BR 27 HIS BR 112 ASN BR 116 GLN BR 147 ASN ** BS 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 79 HIS BS 115 HIS BS 162 GLN BT 153 ASN BT 158 GLN BT 185 ASN BT 253 GLN ** BV 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 122 ASN BV 144 ASN BV 175 ASN BW 73 HIS BW 149 GLN BW 157 HIS BW 171 HIS BW 203 ASN BX 14 ASN BX 77 ASN BY 55 HIS BY 84 ASN Ba 108 HIS Ba 119 GLN Ba 156 ASN Ba 221 GLN Ba 223 HIS Ba 266 GLN Ba 274 ASN Ba 343 GLN Ba 358 GLN Bb 220 ASN Bb 224 HIS Bb 275 GLN Bb 308 GLN Bb 354 GLN Bc 243 GLN Bc 274 GLN Bc 294 GLN ** Bc 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bc 310 ASN Be 42 HIS Bf 62 HIS ** Bf 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bf 121 HIS Bf 130 HIS Bg 17 ASN Bg 24 GLN Bg 127 GLN Bg 129 GLN Bg 131 HIS Bg 135 ASN Bh 118 ASN Bh 128 GLN Bh 172 ASN ** Bi 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 161 HIS Bj 54 GLN Bj 76 GLN Bj 251 HIS ** Bk 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 111 HIS Bk 177 ASN Bm 111 HIS Bn 33 HIS ** Bn 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 109 ASN Bn 122 ASN Bo 63 GLN Bo 82 GLN Bp 35 GLN ** Bp 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 124 HIS Bq 125 ASN Bt 34 ASN Bt 85 HIS Bu 95 ASN Bu 103 HIS Bu 145 ASN Bv 107 GLN ** Bv 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 65 GLN Bw 96 GLN Bw 148 HIS Bw 201 HIS ** Bw 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 271 GLN ** Bw 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 379 GLN Bw 381 ASN Bw 385 ASN ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 403 ASN ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bx 164 ASN Bx 170 ASN Bx 184 ASN Bx 196 HIS Total number of N/Q/H flips: 132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 116918 Z= 0.211 Angle : 0.683 12.333 166279 Z= 0.351 Chirality : 0.041 0.355 19644 Planarity : 0.006 0.087 15128 Dihedral : 20.734 179.563 33689 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.70 % Favored : 97.18 % Rotamer: Outliers : 3.33 % Allowed : 16.36 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.16 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.08), residues: 9175 helix: -0.31 (0.09), residues: 3181 sheet: -0.33 (0.12), residues: 1341 loop : -0.68 (0.08), residues: 4653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRPBj 178 HIS 0.013 0.001 HISBe 111 PHE 0.030 0.002 PHEBp 68 TYR 0.038 0.002 TYRBk 86 ARG 0.014 0.001 ARGBK 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1952 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1686 time to evaluate : 7.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 266 outliers final: 124 residues processed: 1860 average time/residue: 1.0377 time to fit residues: 3237.6540 Evaluate side-chains 1536 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1412 time to evaluate : 7.344 Switching outliers to nearest non-outliers outliers start: 124 outliers final: 0 residues processed: 124 average time/residue: 0.7730 time to fit residues: 189.3441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 539 optimal weight: 7.9990 chunk 301 optimal weight: 7.9990 chunk 807 optimal weight: 4.9990 chunk 661 optimal weight: 10.0000 chunk 267 optimal weight: 30.0000 chunk 972 optimal weight: 6.9990 chunk 1050 optimal weight: 0.0870 chunk 866 optimal weight: 10.0000 chunk 964 optimal weight: 10.0000 chunk 331 optimal weight: 0.9980 chunk 780 optimal weight: 20.0000 overall best weight: 4.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 56 ASN ** B1 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 149 GLN B2 237 GLN B4 60 GLN B5 144 GLN ** B5 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 154 GLN B8 185 ASN BC 514 ASN BC 562 ASN BC 580 ASN BC 649 GLN BC 679 HIS BE 138 HIS ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 105 ASN BF 153 HIS BF 241 ASN ** BF 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 93 ASN BI 100 GLN BI 126 GLN ** BJ 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 208 ASN ** BS 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BV 80 HIS ** BV 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 185 GLN BW 131 ASN BY 35 ASN Ba 65 HIS Ba 221 GLN Ba 289 HIS Ba 360 ASN Bb 239 ASN Bc 252 HIS Bc 274 GLN ** Bc 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 127 GLN Bh 65 ASN Bh 69 HIS Bh 77 HIS ** Bi 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 235 GLN ** Bj 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 179 GLN ** Bk 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 68 GLN ** Bn 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 30 GLN Bt 78 GLN Bu 181 ASN Bv 60 GLN ** Bv 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 67 GLN ** Bw 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bx 131 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 116918 Z= 0.356 Angle : 0.693 12.565 166279 Z= 0.356 Chirality : 0.043 0.374 19644 Planarity : 0.006 0.088 15128 Dihedral : 20.541 178.983 33689 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.28 % Favored : 96.63 % Rotamer: Outliers : 3.31 % Allowed : 17.39 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.16 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.08), residues: 9175 helix: 0.56 (0.09), residues: 3193 sheet: -0.02 (0.13), residues: 1299 loop : -0.52 (0.09), residues: 4683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRPBj 178 HIS 0.017 0.002 HISBp 72 PHE 0.036 0.002 PHEBp 68 TYR 0.035 0.002 TYRBb 51 ARG 0.021 0.001 ARGBd 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1729 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1464 time to evaluate : 7.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 265 outliers final: 139 residues processed: 1640 average time/residue: 1.0078 time to fit residues: 2795.0375 Evaluate side-chains 1470 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1331 time to evaluate : 7.313 Switching outliers to nearest non-outliers outliers start: 139 outliers final: 0 residues processed: 139 average time/residue: 0.8129 time to fit residues: 219.7771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 960 optimal weight: 10.0000 chunk 731 optimal weight: 0.0980 chunk 504 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 464 optimal weight: 6.9990 chunk 653 optimal weight: 8.9990 chunk 976 optimal weight: 8.9990 chunk 1033 optimal weight: 0.9990 chunk 509 optimal weight: 0.9980 chunk 925 optimal weight: 10.0000 chunk 278 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 56 ASN B1 239 GLN B2 149 GLN B2 237 GLN ** B4 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 185 ASN ** BC 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 236 GLN BD 254 ASN BE 128 HIS BE 138 HIS ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 138 HIS ** BF 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 241 ASN ** BF 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 126 GLN BI 136 ASN BJ 73 GLN ** BJ 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 217 GLN ** BK 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 49 GLN BQ 208 ASN ** BU 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 185 GLN ** Bc 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Be 50 GLN Bh 69 HIS Bh 172 ASN ** Bi 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 235 GLN Bj 87 HIS ** Bk 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bp 84 GLN ** Bp 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 78 GLN Bu 181 ASN Bv 60 GLN ** Bv 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 67 GLN ** Bw 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 116918 Z= 0.220 Angle : 0.608 12.666 166279 Z= 0.310 Chirality : 0.039 0.311 19644 Planarity : 0.005 0.080 15128 Dihedral : 20.483 179.422 33689 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.12 % Favored : 96.78 % Rotamer: Outliers : 1.99 % Allowed : 18.90 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.16 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.09), residues: 9175 helix: 1.09 (0.09), residues: 3189 sheet: 0.01 (0.13), residues: 1326 loop : -0.39 (0.09), residues: 4660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRPBj 178 HIS 0.011 0.001 HISBe 111 PHE 0.028 0.001 PHEBp 68 TYR 0.022 0.001 TYRBb 51 ARG 0.006 0.001 ARGBk 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1593 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1434 time to evaluate : 8.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 159 outliers final: 87 residues processed: 1534 average time/residue: 1.0574 time to fit residues: 2739.6826 Evaluate side-chains 1390 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1303 time to evaluate : 7.343 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 0.8158 time to fit residues: 144.7894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 860 optimal weight: 8.9990 chunk 586 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 769 optimal weight: 7.9990 chunk 426 optimal weight: 10.0000 chunk 881 optimal weight: 5.9990 chunk 714 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 527 optimal weight: 8.9990 chunk 927 optimal weight: 4.9990 chunk 260 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B0 59 HIS B1 94 ASN B2 149 GLN B2 181 HIS B2 218 GLN B2 237 GLN B4 60 GLN B7 87 HIS BC 352 ASN ** BC 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 157 ASN BE 138 HIS ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 241 ASN ** BF 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 136 ASN ** BJ 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 54 ASN ** BN 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 94 GLN BQ 208 ASN ** BS 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 162 GLN ** BU 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 185 GLN BY 73 GLN Ba 338 GLN Bc 305 HIS Be 88 GLN ** Bf 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 69 HIS ** Bh 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bk 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 116 HIS Bn 69 HIS ** Bp 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 33 GLN Bu 122 HIS Bu 181 ASN ** Bv 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 116918 Z= 0.469 Angle : 0.737 14.115 166279 Z= 0.374 Chirality : 0.045 0.293 19644 Planarity : 0.006 0.083 15128 Dihedral : 20.499 179.520 33689 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.99 % Favored : 95.90 % Rotamer: Outliers : 2.63 % Allowed : 19.53 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.16 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.09), residues: 9175 helix: 1.05 (0.09), residues: 3189 sheet: -0.06 (0.13), residues: 1318 loop : -0.51 (0.09), residues: 4668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRPBj 178 HIS 0.012 0.002 HISB0 132 PHE 0.029 0.002 PHEBp 68 TYR 0.039 0.002 TYRBb 51 ARG 0.013 0.001 ARGBP 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1564 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1354 time to evaluate : 7.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 210 outliers final: 134 residues processed: 1490 average time/residue: 1.0316 time to fit residues: 2596.4442 Evaluate side-chains 1426 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1292 time to evaluate : 7.362 Switching outliers to nearest non-outliers outliers start: 134 outliers final: 0 residues processed: 134 average time/residue: 0.8057 time to fit residues: 210.6576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 347 optimal weight: 0.8980 chunk 930 optimal weight: 4.9990 chunk 204 optimal weight: 20.0000 chunk 606 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 1034 optimal weight: 1.9990 chunk 858 optimal weight: 7.9990 chunk 478 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 342 optimal weight: 2.9990 chunk 542 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 149 GLN B2 237 GLN B4 60 GLN ** BC 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 241 ASN ** BF 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 276 HIS BI 126 GLN ** BJ 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 94 GLN BQ 208 ASN BS 115 HIS ** BT 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 185 GLN ** BY 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 116 ASN Be 50 GLN Bh 172 ASN Bh 310 ASN ** Bi 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 199 ASN Bk 94 HIS Bu 40 GLN Bu 95 ASN Bu 122 HIS Bu 181 ASN ** Bv 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 185 HIS ** Bw 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 116918 Z= 0.173 Angle : 0.590 13.890 166279 Z= 0.299 Chirality : 0.038 0.289 19644 Planarity : 0.005 0.074 15128 Dihedral : 20.431 179.364 33689 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.23 % Favored : 96.68 % Rotamer: Outliers : 1.06 % Allowed : 20.44 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.16 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.09), residues: 9175 helix: 1.43 (0.09), residues: 3201 sheet: 0.05 (0.13), residues: 1315 loop : -0.37 (0.09), residues: 4659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRPBj 178 HIS 0.008 0.001 HISBe 111 PHE 0.029 0.001 PHEBm 141 TYR 0.023 0.001 TYRBc 178 ARG 0.020 0.000 ARGBd 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1486 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1401 time to evaluate : 7.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 40 residues processed: 1453 average time/residue: 1.0572 time to fit residues: 2593.9311 Evaluate side-chains 1333 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1293 time to evaluate : 7.371 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.8229 time to fit residues: 71.3203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 997 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 589 optimal weight: 0.4980 chunk 755 optimal weight: 3.9990 chunk 585 optimal weight: 0.8980 chunk 870 optimal weight: 7.9990 chunk 577 optimal weight: 9.9990 chunk 1030 optimal weight: 3.9990 chunk 644 optimal weight: 0.7980 chunk 628 optimal weight: 3.9990 chunk 475 optimal weight: 7.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 149 GLN B2 237 GLN B4 60 GLN BC 575 ASN ** BC 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 280 HIS ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 241 ASN ** BF 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 126 GLN ** BJ 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 185 GLN BY 35 ASN BY 119 GLN BY 205 GLN Bb 116 ASN Bc 50 ASN Be 50 GLN Be 88 GLN Bh 69 HIS ** Bh 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 310 ASN ** Bi 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bk 94 HIS ** Bm 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 120 GLN ** Bp 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 135 ASN Bt 33 GLN Bu 95 ASN ** Bw 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 116918 Z= 0.178 Angle : 0.578 13.143 166279 Z= 0.293 Chirality : 0.037 0.266 19644 Planarity : 0.005 0.111 15128 Dihedral : 20.267 179.846 33689 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.40 % Rotamer: Outliers : 0.93 % Allowed : 21.39 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.16 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.09), residues: 9175 helix: 1.59 (0.09), residues: 3193 sheet: 0.08 (0.13), residues: 1353 loop : -0.26 (0.09), residues: 4629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRPBc 189 HIS 0.008 0.001 HISBe 111 PHE 0.033 0.001 PHEBp 68 TYR 0.024 0.001 TYRBb 51 ARG 0.013 0.000 ARGBI 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1470 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1396 time to evaluate : 7.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 44 residues processed: 1429 average time/residue: 1.0722 time to fit residues: 2579.4212 Evaluate side-chains 1355 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1311 time to evaluate : 7.337 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.8171 time to fit residues: 76.5950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 637 optimal weight: 4.9990 chunk 411 optimal weight: 8.9990 chunk 615 optimal weight: 1.9990 chunk 310 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 655 optimal weight: 10.0000 chunk 701 optimal weight: 0.4980 chunk 509 optimal weight: 0.0870 chunk 96 optimal weight: 10.0000 chunk 809 optimal weight: 0.7980 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 237 GLN B4 60 GLN ** BC 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 241 ASN ** BF 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 126 GLN ** BI 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 160 GLN ** BN 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 138 GLN BS 162 GLN ** BT 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 185 GLN BY 35 ASN BY 119 GLN Bb 116 ASN Bb 332 HIS Bf 130 HIS Bh 69 HIS ** Bh 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 310 ASN ** Bi 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 199 ASN ** Bk 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 96 HIS Bm 120 GLN Bq 135 ASN Bt 33 GLN Bt 46 GLN Bu 95 ASN ** Bv 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 352 GLN ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 116918 Z= 0.185 Angle : 0.574 13.666 166279 Z= 0.291 Chirality : 0.037 0.281 19644 Planarity : 0.005 0.093 15128 Dihedral : 20.192 179.589 33689 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.46 % Favored : 96.46 % Rotamer: Outliers : 0.91 % Allowed : 21.38 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.16 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.09), residues: 9175 helix: 1.71 (0.09), residues: 3176 sheet: 0.13 (0.13), residues: 1343 loop : -0.23 (0.09), residues: 4656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRPBj 178 HIS 0.013 0.001 HISBd 158 PHE 0.032 0.001 PHEBp 68 TYR 0.024 0.001 TYRBb 51 ARG 0.017 0.000 ARGBd 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1350 time to evaluate : 6.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 46 residues processed: 1390 average time/residue: 1.0658 time to fit residues: 2493.1045 Evaluate side-chains 1335 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1289 time to evaluate : 7.286 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.8936 time to fit residues: 85.0239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 937 optimal weight: 0.8980 chunk 987 optimal weight: 0.3980 chunk 900 optimal weight: 0.7980 chunk 960 optimal weight: 0.5980 chunk 986 optimal weight: 4.9990 chunk 577 optimal weight: 6.9990 chunk 418 optimal weight: 5.9990 chunk 753 optimal weight: 1.9990 chunk 294 optimal weight: 5.9990 chunk 867 optimal weight: 4.9990 chunk 908 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 237 GLN B5 168 GLN ** BC 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 102 GLN ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 74 GLN ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 241 ASN ** BF 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 126 GLN BL 160 GLN ** BN 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 162 GLN ** BT 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 185 GLN BX 103 GLN Ba 195 HIS Bb 116 ASN Be 50 GLN Bh 69 HIS ** Bh 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 310 ASN ** Bi 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 161 HIS ** Bi 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bk 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 120 GLN Bp 84 GLN Bq 135 ASN Bt 33 GLN ** Bu 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bv 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 67 GLN ** Bw 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 116918 Z= 0.151 Angle : 0.562 12.006 166279 Z= 0.284 Chirality : 0.036 0.325 19644 Planarity : 0.005 0.109 15128 Dihedral : 20.133 179.970 33689 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 0.54 % Allowed : 21.85 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.16 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.09), residues: 9175 helix: 1.77 (0.09), residues: 3184 sheet: 0.23 (0.14), residues: 1332 loop : -0.21 (0.09), residues: 4659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.001 TRPBj 178 HIS 0.010 0.001 HISBk 175 PHE 0.029 0.001 PHEBm 101 TYR 0.022 0.001 TYRBk 125 ARG 0.013 0.000 ARGBp 7 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1419 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1376 time to evaluate : 7.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 22 residues processed: 1396 average time/residue: 1.0550 time to fit residues: 2472.3174 Evaluate side-chains 1309 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1287 time to evaluate : 7.132 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.8378 time to fit residues: 43.4729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 956 optimal weight: 2.9990 chunk 630 optimal weight: 9.9990 chunk 1015 optimal weight: 2.9990 chunk 619 optimal weight: 2.9990 chunk 481 optimal weight: 10.0000 chunk 705 optimal weight: 7.9990 chunk 1064 optimal weight: 30.0000 chunk 980 optimal weight: 2.9990 chunk 848 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 655 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 237 GLN B3 47 GLN ** BC 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 56 HIS BO 62 ASN BO 142 GLN BQ 138 GLN ** BS 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 162 GLN ** BT 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 185 GLN BX 103 GLN Bb 116 ASN Bh 69 HIS ** Bh 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 310 ASN ** Bi 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 217 HIS ** Bk 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 96 HIS Bm 120 GLN Bp 84 GLN Bq 135 ASN Bt 33 GLN Bu 40 GLN ** Bv 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 67 GLN ** Bw 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 116918 Z= 0.240 Angle : 0.593 15.306 166279 Z= 0.300 Chirality : 0.038 0.280 19644 Planarity : 0.005 0.111 15128 Dihedral : 20.085 179.839 33689 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.67 % Favored : 96.24 % Rotamer: Outliers : 0.31 % Allowed : 22.15 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.16 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.09), residues: 9175 helix: 1.73 (0.09), residues: 3208 sheet: 0.20 (0.14), residues: 1321 loop : -0.24 (0.09), residues: 4646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.002 TRPBj 178 HIS 0.008 0.001 HISBq 129 PHE 0.023 0.002 PHEBJ 134 TYR 0.026 0.001 TYRBb 51 ARG 0.015 0.001 ARGBJ 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18350 Ramachandran restraints generated. 9175 Oldfield, 0 Emsley, 9175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1300 time to evaluate : 7.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 1306 average time/residue: 1.0875 time to fit residues: 2385.6055 Evaluate side-chains 1289 residues out of total 8097 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1273 time to evaluate : 7.385 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.8698 time to fit residues: 34.9627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1069 random chunks: chunk 520 optimal weight: 0.9980 chunk 673 optimal weight: 0.0030 chunk 903 optimal weight: 8.9990 chunk 259 optimal weight: 10.0000 chunk 781 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 chunk 849 optimal weight: 6.9990 chunk 355 optimal weight: 3.9990 chunk 872 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 237 GLN B3 47 GLN B4 60 GLN B5 168 GLN B6 31 ASN ** BC 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 142 GLN ** BS 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 162 GLN ** BT 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 185 GLN BX 103 GLN Bb 116 ASN Bh 69 HIS ** Bh 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 310 ASN ** Bi 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bk 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 57 GLN Bm 120 GLN Bp 84 GLN Bq 135 ASN Bt 33 GLN Bt 46 GLN ** Bv 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bx 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.118864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.087993 restraints weight = 206894.712| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.52 r_work: 0.2829 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 116918 Z= 0.167 Angle : 0.565 10.651 166279 Z= 0.285 Chirality : 0.036 0.265 19644 Planarity : 0.005 0.110 15128 Dihedral : 20.087 179.827 33689 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 0.24 % Allowed : 22.57 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.16 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.09), residues: 9175 helix: 1.80 (0.09), residues: 3191 sheet: 0.25 (0.14), residues: 1321 loop : -0.19 (0.09), residues: 4663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.001 TRPBj 178 HIS 0.008 0.001 HISBq 129 PHE 0.023 0.001 PHEBp 68 TYR 0.022 0.001 TYRBb 51 ARG 0.014 0.000 ARGBp 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40555.21 seconds wall clock time: 701 minutes 11.92 seconds (42071.92 seconds total)