Starting phenix.real_space_refine on Tue Apr 16 19:24:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eri_3941/04_2024/6eri_3941_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eri_3941/04_2024/6eri_3941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eri_3941/04_2024/6eri_3941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eri_3941/04_2024/6eri_3941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eri_3941/04_2024/6eri_3941_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eri_3941/04_2024/6eri_3941_neut.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4401 5.49 5 Mg 343 5.21 5 S 182 5.16 5 C 73742 2.51 5 N 27120 2.21 5 O 39236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AC ARG 33": "NH1" <-> "NH2" Residue "AC ARG 34": "NH1" <-> "NH2" Residue "AC ARG 48": "NH1" <-> "NH2" Residue "AC ARG 59": "NH1" <-> "NH2" Residue "AC ARG 104": "NH1" <-> "NH2" Residue "AC ARG 178": "NH1" <-> "NH2" Residue "AC ARG 200": "NH1" <-> "NH2" Residue "AC ARG 203": "NH1" <-> "NH2" Residue "AC ARG 208": "NH1" <-> "NH2" Residue "AC ARG 256": "NH1" <-> "NH2" Residue "AC ARG 269": "NH1" <-> "NH2" Residue "AD PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD ARG 214": "NH1" <-> "NH2" Residue "AD ARG 219": "NH1" <-> "NH2" Residue "AE ARG 81": "NH1" <-> "NH2" Residue "AE ARG 105": "NH1" <-> "NH2" Residue "AE ARG 158": "NH1" <-> "NH2" Residue "AE ARG 221": "NH1" <-> "NH2" Residue "AF ARG 18": "NH1" <-> "NH2" Residue "AF ARG 79": "NH1" <-> "NH2" Residue "AF ARG 107": "NH1" <-> "NH2" Residue "AF ARG 117": "NH1" <-> "NH2" Residue "AF ARG 125": "NH1" <-> "NH2" Residue "AF ARG 127": "NH1" <-> "NH2" Residue "AF ARG 148": "NH1" <-> "NH2" Residue "AG ARG 78": "NH1" <-> "NH2" Residue "AG ARG 91": "NH1" <-> "NH2" Residue "AG ARG 93": "NH1" <-> "NH2" Residue "AG ARG 100": "NH1" <-> "NH2" Residue "AG ARG 109": "NH1" <-> "NH2" Residue "AG ARG 154": "NH1" <-> "NH2" Residue "AG ARG 189": "NH1" <-> "NH2" Residue "AG ARG 192": "NH1" <-> "NH2" Residue "AG ARG 203": "NH1" <-> "NH2" Residue "AG ARG 211": "NH1" <-> "NH2" Residue "AJ ARG 82": "NH1" <-> "NH2" Residue "AJ ARG 136": "NH1" <-> "NH2" Residue "AJ ARG 179": "NH1" <-> "NH2" Residue "AJ ARG 242": "NH1" <-> "NH2" Residue "AJ ARG 247": "NH1" <-> "NH2" Residue "AK ARG 54": "NH1" <-> "NH2" Residue "AK ARG 71": "NH1" <-> "NH2" Residue "AL ARG 100": "NH1" <-> "NH2" Residue "AL ARG 120": "NH1" <-> "NH2" Residue "AL TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AL ARG 139": "NH1" <-> "NH2" Residue "AL ARG 144": "NH1" <-> "NH2" Residue "AL ARG 151": "NH1" <-> "NH2" Residue "AL ARG 163": "NH1" <-> "NH2" Residue "AL ARG 215": "NH1" <-> "NH2" Residue "AL ARG 238": "NH1" <-> "NH2" Residue "AL ARG 247": "NH1" <-> "NH2" Residue "AL ARG 252": "NH1" <-> "NH2" Residue "AM ARG 10": "NH1" <-> "NH2" Residue "AM ARG 23": "NH1" <-> "NH2" Residue "AM ARG 31": "NH1" <-> "NH2" Residue "AM ARG 45": "NH1" <-> "NH2" Residue "AM ARG 51": "NH1" <-> "NH2" Residue "AM ARG 56": "NH1" <-> "NH2" Residue "AM ARG 59": "NH1" <-> "NH2" Residue "AM ARG 60": "NH1" <-> "NH2" Residue "AM ARG 115": "NH1" <-> "NH2" Residue "AN ARG 22": "NH1" <-> "NH2" Residue "AN ARG 27": "NH1" <-> "NH2" Residue "AN ARG 28": "NH1" <-> "NH2" Residue "AN ARG 32": "NH1" <-> "NH2" Residue "AN ARG 73": "NH1" <-> "NH2" Residue "AN ARG 74": "NH1" <-> "NH2" Residue "AN ARG 96": "NH1" <-> "NH2" Residue "AN ARG 106": "NH1" <-> "NH2" Residue "AN ARG 114": "NH1" <-> "NH2" Residue "AO ARG 49": "NH1" <-> "NH2" Residue "AO ARG 50": "NH1" <-> "NH2" Residue "AP ARG 116": "NH1" <-> "NH2" Residue "AP ARG 144": "NH1" <-> "NH2" Residue "AP ARG 161": "NH1" <-> "NH2" Residue "AP ARG 182": "NH1" <-> "NH2" Residue "AP ARG 184": "NH1" <-> "NH2" Residue "AP TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AP ARG 223": "NH1" <-> "NH2" Residue "AQ ARG 3": "NH1" <-> "NH2" Residue "AQ ARG 6": "NH1" <-> "NH2" Residue "AQ TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ ARG 13": "NH1" <-> "NH2" Residue "AQ ARG 18": "NH1" <-> "NH2" Residue "AQ ARG 33": "NH1" <-> "NH2" Residue "AQ ARG 48": "NH1" <-> "NH2" Residue "AQ ARG 70": "NH1" <-> "NH2" Residue "AQ ARG 88": "NH1" <-> "NH2" Residue "AR ARG 77": "NH1" <-> "NH2" Residue "AR ARG 146": "NH1" <-> "NH2" Residue "AR ARG 207": "NH1" <-> "NH2" Residue "AS ARG 71": "NH1" <-> "NH2" Residue "AS ARG 117": "NH1" <-> "NH2" Residue "AS ARG 168": "NH1" <-> "NH2" Residue "AS ARG 170": "NH1" <-> "NH2" Residue "AS ARG 176": "NH1" <-> "NH2" Residue "AS ARG 178": "NH1" <-> "NH2" Residue "AT ARG 106": "NH1" <-> "NH2" Residue "AT ARG 107": "NH1" <-> "NH2" Residue "AU ARG 51": "NH1" <-> "NH2" Residue "AU ARG 147": "NH1" <-> "NH2" Residue "AU ARG 160": "NH1" <-> "NH2" Residue "AW ARG 97": "NH1" <-> "NH2" Residue "AW ARG 153": "NH1" <-> "NH2" Residue "AX ARG 73": "NH1" <-> "NH2" Residue "AX ARG 107": "NH1" <-> "NH2" Residue "AX ARG 120": "NH1" <-> "NH2" Residue "AY ARG 91": "NH1" <-> "NH2" Residue "AY ARG 94": "NH1" <-> "NH2" Residue "AY ARG 97": "NH1" <-> "NH2" Residue "AY ARG 107": "NH1" <-> "NH2" Residue "AY ARG 111": "NH1" <-> "NH2" Residue "AY ARG 114": "NH1" <-> "NH2" Residue "AY ARG 134": "NH1" <-> "NH2" Residue "AZ ARG 37": "NH1" <-> "NH2" Residue "AZ ARG 46": "NH1" <-> "NH2" Residue "Aa ARG 7": "NH1" <-> "NH2" Residue "Ab ARG 8": "NH1" <-> "NH2" Residue "Ab ARG 20": "NH1" <-> "NH2" Residue "Ab ARG 39": "NH1" <-> "NH2" Residue "Ac ARG 103": "NH1" <-> "NH2" Residue "Ac ARG 110": "NH1" <-> "NH2" Residue "Ac ARG 115": "NH1" <-> "NH2" Residue "Ac ARG 117": "NH1" <-> "NH2" Residue "Ac ARG 129": "NH1" <-> "NH2" Residue "Ad ARG 101": "NH1" <-> "NH2" Residue "Ad ARG 112": "NH1" <-> "NH2" Residue "Ad ARG 113": "NH1" <-> "NH2" Residue "Ad ARG 128": "NH1" <-> "NH2" Residue "Ae ARG 8": "NH1" <-> "NH2" Residue "Ae ARG 20": "NH1" <-> "NH2" Residue "Ae ARG 22": "NH1" <-> "NH2" Residue "Af ARG 50": "NH1" <-> "NH2" Residue "Aw ARG 113": "NH1" <-> "NH2" Residue "Aw ARG 115": "NH1" <-> "NH2" Residue "Aw ARG 128": "NH1" <-> "NH2" Residue "BB ARG 25": "NH1" <-> "NH2" Residue "BB ARG 30": "NH1" <-> "NH2" Residue "BB ARG 52": "NH1" <-> "NH2" Residue "BB ARG 90": "NH1" <-> "NH2" Residue "BB ARG 92": "NH1" <-> "NH2" Residue "BB ARG 114": "NH1" <-> "NH2" Residue "BB ARG 129": "NH1" <-> "NH2" Residue "BB ARG 132": "NH1" <-> "NH2" Residue "BB ARG 136": "NH1" <-> "NH2" Residue "BB ARG 143": "NH1" <-> "NH2" Residue "BB ARG 178": "NH1" <-> "NH2" Residue "BB ARG 215": "NH1" <-> "NH2" Residue "BB ARG 229": "NH1" <-> "NH2" Residue "BC ARG 88": "NH1" <-> "NH2" Residue "BC ARG 138": "NH1" <-> "NH2" Residue "BC ARG 142": "NH1" <-> "NH2" Residue "BC ARG 183": "NH1" <-> "NH2" Residue "BD ARG 3": "NH1" <-> "NH2" Residue "BD ARG 33": "NH1" <-> "NH2" Residue "BD ARG 199": "NH1" <-> "NH2" Residue "BE ARG 175": "NH1" <-> "NH2" Residue "BE ARG 299": "NH1" <-> "NH2" Residue "BG ARG 78": "NH1" <-> "NH2" Residue "BG ARG 111": "NH1" <-> "NH2" Residue "BH ARG 20": "NH1" <-> "NH2" Residue "BH ARG 25": "NH1" <-> "NH2" Residue "BH ARG 84": "NH1" <-> "NH2" Residue "BJ ARG 104": "NH1" <-> "NH2" Residue "BK ARG 47": "NH1" <-> "NH2" Residue "BK ARG 90": "NH1" <-> "NH2" Residue "BK ARG 120": "NH1" <-> "NH2" Residue "BK ARG 136": "NH1" <-> "NH2" Residue "BL ARG 12": "NH1" <-> "NH2" Residue "BL ARG 56": "NH1" <-> "NH2" Residue "BM ARG 75": "NH1" <-> "NH2" Residue "BM ARG 124": "NH1" <-> "NH2" Residue "BM ARG 156": "NH1" <-> "NH2" Residue "BN ARG 14": "NH1" <-> "NH2" Residue "BN ARG 24": "NH1" <-> "NH2" Residue "BN ARG 32": "NH1" <-> "NH2" Residue "BN ARG 52": "NH1" <-> "NH2" Residue "BN ARG 58": "NH1" <-> "NH2" Residue "BN ARG 70": "NH1" <-> "NH2" Residue "BN ARG 97": "NH1" <-> "NH2" Residue "BO ARG 35": "NH1" <-> "NH2" Residue "BO ARG 51": "NH1" <-> "NH2" Residue "BP ARG 27": "NH1" <-> "NH2" Residue "BP ARG 28": "NH1" <-> "NH2" Residue "BR ARG 27": "NH1" <-> "NH2" Residue "BR ARG 50": "NH1" <-> "NH2" Residue "BU ARG 109": "NH1" <-> "NH2" Residue "BV ARG 82": "NH1" <-> "NH2" Residue "BV ARG 140": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 145026 Number of models: 1 Model: "" Number of chains: 66 Chain: "AA" Number of atoms: 57902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2696, 57902 Classifications: {'RNA': 2696} Modifications used: {'rna2p_pur': 284, 'rna2p_pyr': 124, 'rna3p_pur': 1285, 'rna3p_pyr': 1003} Link IDs: {'rna2p': 408, 'rna3p': 2287} Chain breaks: 4 Chain: "AB" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 2277 Classifications: {'RNA': 106} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 53, 'rna3p_pyr': 36} Link IDs: {'rna2p': 17, 'rna3p': 88} Chain: "AC" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1896 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 232} Chain: "AD" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1686 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 210} Chain: "AE" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1676 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 12, 'TRANS': 199} Chain: "AF" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1328 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain breaks: 1 Chain: "AG" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1343 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "AH" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 367 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "AJ" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1619 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 12, 'TRANS': 187} Chain: "AK" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "AL" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1405 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 10, 'TRANS': 173} Chain: "AM" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1071 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 8, 'TRANS': 125} Chain: "AN" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "AO" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 952 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "AP" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 953 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "AQ" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 994 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain: "AR" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1326 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 16, 'TRANS': 148} Chain: "AS" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1388 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain: "AT" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 743 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "AU" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1015 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "AW" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "AX" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 625 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "AY" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 832 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "AZ" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 536 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "Aa" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 396 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "Ab" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 489 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "Ac" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 471 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "Ad" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 588 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "Ae" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 305 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "Af" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 375 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 38} Chain: "Aw" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 423 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "Ax" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2522 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 59, 'rna3p_pyr': 47} Link IDs: {'rna2p': 12, 'rna3p': 105} Chain: "Az" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1512 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "BA" Number of atoms: 31806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1481, 31806 Classifications: {'RNA': 1481} Modifications used: {'rna2p_pur': 122, 'rna2p_pyr': 80, 'rna3p_pur': 729, 'rna3p_pyr': 550} Link IDs: {'rna2p': 202, 'rna3p': 1278} Chain: "BB" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1639 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "BC" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1745 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "BD" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1633 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain: "BE" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1189 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "BF" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 911 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "BG" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1178 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "BH" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1004 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain breaks: 1 Chain: "BI" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1091 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "BJ" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 796 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "BK" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 828 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "BL" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 959 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} Chain: "BM" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 913 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain: "BN" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 824 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "BO" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 606 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "BP" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 675 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "BQ" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 6, 'TRANS': 77} Chain: "BR" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 440 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "BS" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 653 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "BT" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 818 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "BU" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 514 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "BV" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 836 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "BW" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 289 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "BY" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 850 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'TRANS': 169} Chain breaks: 2 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 510 Unresolved non-hydrogen dihedrals: 170 Planarities with less than four sites: {'UNK:plan-1': 170} Unresolved non-hydrogen planarities: 170 Chain: "AA" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 247 Unusual residues: {' MG': 247} Classifications: {'undetermined': 247} Link IDs: {None: 246} Chain: "AB" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' MG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "Ab" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Ae" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Af" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Aw" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Ax" 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: "BA" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Unusual residues: {' MG': 82} Classifications: {'undetermined': 82} Link IDs: {None: 81} Chain: "BN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 85202 SG CYSAb 15 135.628 44.304 133.211 1.00 93.02 S ATOM 85219 SG CYSAb 18 138.398 43.078 134.956 1.00 96.48 S ATOM 85500 SG CYSAb 52 138.718 42.224 131.576 1.00 91.27 S ATOM 85525 SG CYSAb 55 137.187 39.963 133.913 1.00 93.46 S ATOM 86756 SG CYSAe 11 148.268 123.029 47.823 1.00 99.92 S ATOM 86780 SG CYSAe 14 151.291 121.752 48.934 1.00 98.74 S ATOM 86892 SG CYSAe 27 151.408 124.969 46.883 1.00101.88 S Time building chain proxies: 55.72, per 1000 atoms: 0.38 Number of scatterers: 145026 At special positions: 0 Unit cell: (283.02, 262.88, 223.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 182 16.00 P 4401 15.00 Mg 343 11.99 O 39236 8.00 N 27120 7.00 C 73742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 55.95 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNAb 101 " pdb="ZN ZNAb 101 " - pdb=" SG CYSAb 15 " pdb="ZN ZNAb 101 " - pdb=" SG CYSAb 55 " pdb="ZN ZNAb 101 " - pdb=" SG CYSAb 52 " pdb="ZN ZNAb 101 " - pdb=" SG CYSAb 18 " pdb=" ZNAe 501 " pdb="ZN ZNAe 501 " - pdb=" ND1 HISAe 32 " pdb="ZN ZNAe 501 " - pdb=" SG CYSAe 14 " pdb="ZN ZNAe 501 " - pdb=" SG CYSAe 27 " pdb="ZN ZNAe 501 " - pdb=" SG CYSAe 11 " Number of angles added : 9 12140 Ramachandran restraints generated. 6070 Oldfield, 0 Emsley, 6070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11768 Finding SS restraints... Secondary structure from input PDB file: 209 helices and 0 sheets defined 40.0% alpha, 0.0% beta 1305 base pairs and 2566 stacking pairs defined. Time for finding SS restraints: 53.03 Creating SS restraints... Processing helix chain 'AC' and resid 204 through 210 removed outlier: 3.818A pdb=" N LEUAC 210 " --> pdb=" O SERAC 206 " (cutoff:3.500A) Processing helix chain 'AC' and resid 217 through 221 Processing helix chain 'AD' and resid 145 through 149 Processing helix chain 'AD' and resid 150 through 159 Processing helix chain 'AD' and resid 210 through 215 Processing helix chain 'AE' and resid 79 through 94 removed outlier: 3.864A pdb=" N HISAE 85 " --> pdb=" O ARGAE 81 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THRAE 90 " --> pdb=" O ARGAE 86 " (cutoff:3.500A) Processing helix chain 'AE' and resid 153 through 168 Processing helix chain 'AE' and resid 178 through 182 removed outlier: 3.623A pdb=" N PHEAE 182 " --> pdb=" O ALAAE 179 " (cutoff:3.500A) Processing helix chain 'AE' and resid 186 through 198 Processing helix chain 'AE' and resid 213 through 218 Processing helix chain 'AE' and resid 235 through 242 removed outlier: 4.075A pdb=" N VALAE 239 " --> pdb=" O ASNAE 235 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEUAE 240 " --> pdb=" O LEUAE 236 " (cutoff:3.500A) Processing helix chain 'AE' and resid 248 through 259 removed outlier: 3.533A pdb=" N GLNAE 253 " --> pdb=" O GLUAE 249 " (cutoff:3.500A) Processing helix chain 'AF' and resid 17 through 26 removed outlier: 3.664A pdb=" N THRAF 21 " --> pdb=" O ASNAF 17 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILEAF 24 " --> pdb=" O LYSAF 20 " (cutoff:3.500A) Processing helix chain 'AF' and resid 26 through 36 removed outlier: 3.538A pdb=" N PHEAF 35 " --> pdb=" O LEUAF 31 " (cutoff:3.500A) Processing helix chain 'AF' and resid 39 through 43 Processing helix chain 'AF' and resid 56 through 60 removed outlier: 4.371A pdb=" N SERAF 59 " --> pdb=" O GLYAF 56 " (cutoff:3.500A) Processing helix chain 'AF' and resid 62 through 77 removed outlier: 3.731A pdb=" N ASNAF 70 " --> pdb=" O ASPAF 66 " (cutoff:3.500A) Processing helix chain 'AF' and resid 109 through 120 removed outlier: 3.584A pdb=" N ASNAF 120 " --> pdb=" O ASPAF 116 " (cutoff:3.500A) Processing helix chain 'AF' and resid 133 through 137 removed outlier: 3.714A pdb=" N SERAF 136 " --> pdb=" O ASNAF 133 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHEAF 137 " --> pdb=" O PROAF 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'AF' and resid 133 through 137' Processing helix chain 'AF' and resid 177 through 188 removed outlier: 4.037A pdb=" N ALAAF 181 " --> pdb=" O THRAF 177 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEUAF 187 " --> pdb=" O LYSAF 183 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N METAF 188 " --> pdb=" O LEUAF 184 " (cutoff:3.500A) Processing helix chain 'AG' and resid 98 through 121 removed outlier: 4.251A pdb=" N GLYAG 106 " --> pdb=" O ASNAG 102 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEUAG 107 " --> pdb=" O GLNAG 103 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHEAG 108 " --> pdb=" O METAG 104 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARGAG 109 " --> pdb=" O HISAG 105 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THRAG 110 " --> pdb=" O GLYAG 106 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VALAG 119 " --> pdb=" O METAG 115 " (cutoff:3.500A) Processing helix chain 'AG' and resid 177 through 192 removed outlier: 3.663A pdb=" N TRPAG 191 " --> pdb=" O THRAG 187 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARGAG 192 " --> pdb=" O ILEAG 188 " (cutoff:3.500A) Processing helix chain 'AH' and resid 70 through 77 removed outlier: 3.503A pdb=" N PHEAH 77 " --> pdb=" O PHEAH 73 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 52 through 72 removed outlier: 3.602A pdb=" N ARGAJ 62 " --> pdb=" O THRAJ 58 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLNAJ 63 " --> pdb=" O GLUAJ 59 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHEAJ 72 " --> pdb=" O VALAJ 68 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 88 through 92 Processing helix chain 'AJ' and resid 108 through 112 removed outlier: 3.773A pdb=" N LYSAJ 112 " --> pdb=" O PROAJ 109 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 123 through 136 removed outlier: 3.515A pdb=" N THRAJ 130 " --> pdb=" O ARGAJ 126 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 157 through 161 Processing helix chain 'AJ' and resid 166 through 171 Processing helix chain 'AJ' and resid 188 through 195 Processing helix chain 'AJ' and resid 196 through 208 removed outlier: 4.262A pdb=" N ILEAJ 200 " --> pdb=" O PROAJ 196 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLYAJ 206 " --> pdb=" O HISAJ 202 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N METAJ 207 " --> pdb=" O ALAAJ 203 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 211 through 219 removed outlier: 4.324A pdb=" N ASNAJ 219 " --> pdb=" O ARGAJ 215 " (cutoff:3.500A) Processing helix chain 'AK' and resid 103 through 109 removed outlier: 3.555A pdb=" N LEUAK 106 " --> pdb=" O ALAAK 103 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARGAK 107 " --> pdb=" O ARGAK 104 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLNAK 108 " --> pdb=" O GLUAK 105 " (cutoff:3.500A) Processing helix chain 'AK' and resid 110 through 117 removed outlier: 3.831A pdb=" N VALAK 114 " --> pdb=" O PHEAK 110 " (cutoff:3.500A) Processing helix chain 'AL' and resid 161 through 169 removed outlier: 4.153A pdb=" N ILEAL 165 " --> pdb=" O ASNAL 161 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLUAL 166 " --> pdb=" O LEUAL 162 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLYAL 169 " --> pdb=" O ILEAL 165 " (cutoff:3.500A) Processing helix chain 'AL' and resid 177 through 185 removed outlier: 3.550A pdb=" N ALAAL 183 " --> pdb=" O GLUAL 179 " (cutoff:3.500A) Processing helix chain 'AL' and resid 190 through 196 removed outlier: 3.599A pdb=" N GLUAL 193 " --> pdb=" O SERAL 190 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEUAL 196 " --> pdb=" O GLUAL 193 " (cutoff:3.500A) Processing helix chain 'AL' and resid 218 through 228 removed outlier: 3.503A pdb=" N GLUAL 223 " --> pdb=" O GLYAL 219 " (cutoff:3.500A) Processing helix chain 'AL' and resid 243 through 261 removed outlier: 3.595A pdb=" N LYSAL 248 " --> pdb=" O GLUAL 244 " (cutoff:3.500A) Processing helix chain 'AM' and resid 44 through 58 removed outlier: 3.616A pdb=" N ASNAM 57 " --> pdb=" O ALAAM 53 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALAAM 58 " --> pdb=" O METAM 54 " (cutoff:3.500A) Processing helix chain 'AM' and resid 110 through 125 removed outlier: 3.792A pdb=" N ILEAM 120 " --> pdb=" O ARGAM 116 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYSAM 124 " --> pdb=" O ILEAM 120 " (cutoff:3.500A) Processing helix chain 'AN' and resid 23 through 42 removed outlier: 3.804A pdb=" N ARGAN 32 " --> pdb=" O ARGAN 28 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THRAN 36 " --> pdb=" O ARGAN 32 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLNAN 37 " --> pdb=" O GLYAN 33 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYSAN 40 " --> pdb=" O THRAN 36 " (cutoff:3.500A) Processing helix chain 'AN' and resid 48 through 67 removed outlier: 3.646A pdb=" N ARGAN 55 " --> pdb=" O ALAAN 51 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYSAN 56 " --> pdb=" O SERAN 52 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYRAN 57 " --> pdb=" O ALAAN 53 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYSAN 60 " --> pdb=" O LYSAN 56 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLUAN 67 " --> pdb=" O THRAN 63 " (cutoff:3.500A) Processing helix chain 'AN' and resid 69 through 80 removed outlier: 3.742A pdb=" N GLNAN 75 " --> pdb=" O HISAN 71 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALAAN 76 " --> pdb=" O LYSAN 72 " (cutoff:3.500A) Processing helix chain 'AN' and resid 83 through 97 removed outlier: 3.674A pdb=" N HISAN 87 " --> pdb=" O LYSAN 83 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALAAN 91 " --> pdb=" O HISAN 87 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLUAN 92 " --> pdb=" O ALAAN 88 " (cutoff:3.500A) Proline residue: AN 94 - end of helix Processing helix chain 'AO' and resid 48 through 62 removed outlier: 3.686A pdb=" N ILEAO 60 " --> pdb=" O ARGAO 56 " (cutoff:3.500A) Processing helix chain 'AO' and resid 102 through 107 removed outlier: 3.724A pdb=" N GLUAO 107 " --> pdb=" O LYSAO 103 " (cutoff:3.500A) Processing helix chain 'AO' and resid 116 through 133 removed outlier: 3.626A pdb=" N GLUAO 133 " --> pdb=" O LYSAO 129 " (cutoff:3.500A) Processing helix chain 'AO' and resid 150 through 161 Processing helix chain 'AP' and resid 118 through 120 No H-bonds generated for 'chain 'AP' and resid 118 through 120' Processing helix chain 'AP' and resid 121 through 138 removed outlier: 3.664A pdb=" N VALAP 131 " --> pdb=" O ASNAP 127 " (cutoff:3.500A) Processing helix chain 'AP' and resid 175 through 178 removed outlier: 3.689A pdb=" N HISAP 178 " --> pdb=" O ALAAP 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'AP' and resid 175 through 178' Processing helix chain 'AP' and resid 220 through 224 Processing helix chain 'AP' and resid 226 through 230 removed outlier: 3.665A pdb=" N LEUAP 229 " --> pdb=" O LEUAP 226 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 8 through 21 removed outlier: 3.600A pdb=" N LYSAQ 16 " --> pdb=" O ARGAQ 12 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALAAQ 21 " --> pdb=" O ILEAQ 17 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 25 through 30 Processing helix chain 'AQ' and resid 31 through 68 removed outlier: 4.129A pdb=" N GLNAQ 37 " --> pdb=" O ARGAQ 33 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILEAQ 40 " --> pdb=" O ALAAQ 36 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARGAQ 41 " --> pdb=" O GLNAQ 37 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASPAQ 51 " --> pdb=" O HISAQ 47 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYSAQ 54 " --> pdb=" O ARGAQ 50 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARGAQ 55 " --> pdb=" O ASPAQ 51 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THRAQ 63 " --> pdb=" O ARGAQ 59 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 77 through 89 removed outlier: 3.509A pdb=" N TYRAQ 86 " --> pdb=" O ILEAQ 82 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 93 through 104 removed outlier: 3.775A pdb=" N ILEAQ 102 " --> pdb=" O ALAAQ 98 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 104 through 116 removed outlier: 4.283A pdb=" N ILEAQ 108 " --> pdb=" O ASNAQ 104 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYRAQ 109 " --> pdb=" O PROAQ 105 " (cutoff:3.500A) Processing helix chain 'AR' and resid 73 through 77 removed outlier: 4.048A pdb=" N ARGAR 77 " --> pdb=" O GLUAR 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'AR' and resid 73 through 77' Processing helix chain 'AR' and resid 84 through 89 removed outlier: 4.052A pdb=" N VALAR 88 " --> pdb=" O GLNAR 84 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEUAR 89 " --> pdb=" O LEUAR 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'AR' and resid 84 through 89' Processing helix chain 'AR' and resid 100 through 111 removed outlier: 3.600A pdb=" N ASNAR 104 " --> pdb=" O THRAR 100 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILEAR 107 " --> pdb=" O TYRAR 103 " (cutoff:3.500A) Processing helix chain 'AS' and resid 26 through 31 removed outlier: 4.027A pdb=" N GLUAS 31 " --> pdb=" O GLYAS 27 " (cutoff:3.500A) Processing helix chain 'AS' and resid 42 through 54 removed outlier: 3.516A pdb=" N ARGAS 48 " --> pdb=" O ASPAS 44 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VALAS 49 " --> pdb=" O LYSAS 45 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLNAS 52 " --> pdb=" O ARGAS 48 " (cutoff:3.500A) Processing helix chain 'AS' and resid 57 through 66 removed outlier: 3.528A pdb=" N GLUAS 66 " --> pdb=" O LEUAS 62 " (cutoff:3.500A) Processing helix chain 'AS' and resid 72 through 91 removed outlier: 3.633A pdb=" N ILEAS 76 " --> pdb=" O ALAAS 72 " (cutoff:3.500A) Processing helix chain 'AS' and resid 94 through 96 No H-bonds generated for 'chain 'AS' and resid 94 through 96' Processing helix chain 'AS' and resid 118 through 120 No H-bonds generated for 'chain 'AS' and resid 118 through 120' Processing helix chain 'AS' and resid 142 through 152 removed outlier: 4.431A pdb=" N PHEAS 148 " --> pdb=" O SERAS 144 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SERAS 151 " --> pdb=" O LYSAS 147 " (cutoff:3.500A) Processing helix chain 'AS' and resid 153 through 164 removed outlier: 3.942A pdb=" N ALAAS 159 " --> pdb=" O LYSAS 155 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEUAS 160 " --> pdb=" O LYSAS 156 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N METAS 164 " --> pdb=" O LEUAS 160 " (cutoff:3.500A) Processing helix chain 'AS' and resid 165 through 173 removed outlier: 3.676A pdb=" N GLUAS 171 " --> pdb=" O GLYAS 167 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEUAS 172 " --> pdb=" O ARGAS 168 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEUAS 173 " --> pdb=" O ARGAS 169 " (cutoff:3.500A) Processing helix chain 'AS' and resid 176 through 182 Processing helix chain 'AS' and resid 185 through 190 removed outlier: 3.985A pdb=" N LYSAS 189 " --> pdb=" O SERAS 185 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILEAS 190 " --> pdb=" O PHEAS 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'AS' and resid 185 through 190' Processing helix chain 'AT' and resid 110 through 113 Processing helix chain 'AT' and resid 121 through 132 removed outlier: 3.906A pdb=" N ALAAT 129 " --> pdb=" O ILEAT 125 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASPAT 130 " --> pdb=" O LYSAT 126 " (cutoff:3.500A) Processing helix chain 'AT' and resid 143 through 155 removed outlier: 3.509A pdb=" N PHEAT 155 " --> pdb=" O ILEAT 151 " (cutoff:3.500A) Processing helix chain 'AT' and resid 183 through 192 Processing helix chain 'AU' and resid 50 through 54 removed outlier: 3.796A pdb=" N ARGAU 54 " --> pdb=" O ARGAU 51 " (cutoff:3.500A) Processing helix chain 'AW' and resid 149 through 172 removed outlier: 3.579A pdb=" N ARGAW 159 " --> pdb=" O ARGAW 155 " (cutoff:3.500A) Processing helix chain 'AX' and resid 123 through 133 removed outlier: 3.553A pdb=" N LYSAX 127 " --> pdb=" O THRAX 123 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THRAX 128 " --> pdb=" O LYSAX 124 " (cutoff:3.500A) Processing helix chain 'AX' and resid 133 through 142 Processing helix chain 'AY' and resid 61 through 71 removed outlier: 3.562A pdb=" N LEUAY 65 " --> pdb=" O LYSAY 61 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEUAY 68 " --> pdb=" O GLUAY 64 " (cutoff:3.500A) Processing helix chain 'AY' and resid 72 through 97 removed outlier: 3.763A pdb=" N PHEAY 88 " --> pdb=" O LYSAY 84 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N METAY 89 " --> pdb=" O GLYAY 85 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SERAY 95 " --> pdb=" O ARGAY 91 " (cutoff:3.500A) Processing helix chain 'AY' and resid 102 through 127 removed outlier: 4.083A pdb=" N GLYAY 106 " --> pdb=" O PROAY 102 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALAAY 113 " --> pdb=" O ARGAY 109 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N METAY 115 " --> pdb=" O ARGAY 111 " (cutoff:3.500A) Processing helix chain 'AY' and resid 129 through 143 removed outlier: 3.708A pdb=" N LYSAY 135 " --> pdb=" O ARGAY 131 " (cutoff:3.500A) Processing helix chain 'AY' and resid 149 through 157 removed outlier: 4.217A pdb=" N GLUAY 157 " --> pdb=" O LYSAY 153 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 77 through 82 removed outlier: 4.023A pdb=" N LEUAZ 81 " --> pdb=" O HISAZ 77 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 93 through 102 removed outlier: 3.727A pdb=" N LYSAZ 100 " --> pdb=" O LYSAZ 96 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYRAZ 101 " --> pdb=" O PHEAZ 97 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 9 through 37 removed outlier: 3.639A pdb=" N ILEAa 19 " --> pdb=" O ILEAa 15 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRPAa 20 " --> pdb=" O ARGAa 16 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYSAa 23 " --> pdb=" O ILEAa 19 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLYAa 24 " --> pdb=" O TRPAa 20 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYRAa 25 " --> pdb=" O LYSAa 21 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRPAa 26 " --> pdb=" O LYSAa 22 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYSAa 30 " --> pdb=" O TRPAa 26 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 104 through 113 Processing helix chain 'Ac' and resid 113 through 118 Processing helix chain 'Ac' and resid 120 through 134 Processing helix chain 'Ad' and resid 95 through 100 Processing helix chain 'Ad' and resid 125 through 134 removed outlier: 3.559A pdb=" N LYSAd 134 " --> pdb=" O ASNAd 130 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 139 through 141 No H-bonds generated for 'chain 'Ad' and resid 139 through 141' Processing helix chain 'Ad' and resid 142 through 150 removed outlier: 3.689A pdb=" N GLYAd 148 " --> pdb=" O ASPAd 144 " (cutoff:3.500A) Processing helix chain 'Af' and resid 56 through 63 Processing helix chain 'Af' and resid 68 through 73 Processing helix chain 'Aw' and resid 95 through 129 Processing helix chain 'Aw' and resid 132 through 137 Processing helix chain 'Aw' and resid 138 through 140 No H-bonds generated for 'chain 'Aw' and resid 138 through 140' Processing helix chain 'Az' and resid 80 through 112 removed outlier: 3.826A pdb=" N LYSAz 101 " --> pdb=" O GLNAz 97 " (cutoff:3.500A) Processing helix chain 'Az' and resid 121 through 125 removed outlier: 3.802A pdb=" N ARGAz 125 " --> pdb=" O METAz 122 " (cutoff:3.500A) Processing helix chain 'Az' and resid 137 through 140 No H-bonds generated for 'chain 'Az' and resid 137 through 140' Processing helix chain 'Az' and resid 158 through 172 removed outlier: 4.157A pdb=" N LYSAz 162 " --> pdb=" O LYSAz 158 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALAAz 163 " --> pdb=" O SERAz 159 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLNAz 172 " --> pdb=" O ILEAz 168 " (cutoff:3.500A) Processing helix chain 'Az' and resid 192 through 231 removed outlier: 3.637A pdb=" N VALAz 202 " --> pdb=" O GLUAz 198 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYSAz 223 " --> pdb=" O ARGAz 219 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SERAz 224 " --> pdb=" O ASPAz 220 " (cutoff:3.500A) Processing helix chain 'Az' and resid 235 through 268 removed outlier: 3.808A pdb=" N LYSAz 248 " --> pdb=" O ALAAz 244 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEUAz 249 " --> pdb=" O ASPAz 245 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYSAz 256 " --> pdb=" O GLUAz 252 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VALAz 257 " --> pdb=" O TYRAz 253 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLUAz 267 " --> pdb=" O GLNAz 263 " (cutoff:3.500A) Processing helix chain 'BB' and resid 28 through 33 removed outlier: 3.540A pdb=" N METBB 31 " --> pdb=" O ASNBB 28 " (cutoff:3.500A) Proline residue: BB 33 - end of helix Processing helix chain 'BB' and resid 47 through 67 removed outlier: 3.626A pdb=" N ALABB 51 " --> pdb=" O LEUBB 47 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARGBB 52 " --> pdb=" O THRBB 48 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHEBB 53 " --> pdb=" O ARGBB 49 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SERBB 66 " --> pdb=" O PHEBB 62 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARGBB 67 " --> pdb=" O ASPBB 63 " (cutoff:3.500A) Processing helix chain 'BB' and resid 77 through 79 No H-bonds generated for 'chain 'BB' and resid 77 through 79' Processing helix chain 'BB' and resid 80 through 90 removed outlier: 3.673A pdb=" N VALBB 84 " --> pdb=" O ALABB 80 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALABB 85 " --> pdb=" O ALABB 81 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILEBB 89 " --> pdb=" O ALABB 85 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARGBB 90 " --> pdb=" O ARGBB 86 " (cutoff:3.500A) Processing helix chain 'BB' and resid 107 through 125 removed outlier: 3.701A pdb=" N ARGBB 122 " --> pdb=" O PHEBB 118 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N METBB 123 " --> pdb=" O ARGBB 119 " (cutoff:3.500A) Processing helix chain 'BB' and resid 127 through 131 removed outlier: 4.436A pdb=" N LEUBB 130 " --> pdb=" O ALABB 127 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALABB 131 " --> pdb=" O GLYBB 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'BB' and resid 127 through 131' Processing helix chain 'BB' and resid 134 through 152 removed outlier: 3.760A pdb=" N TYRBB 151 " --> pdb=" O HISBB 147 " (cutoff:3.500A) Processing helix chain 'BB' and resid 173 through 184 removed outlier: 3.650A pdb=" N LEUBB 177 " --> pdb=" O GLUBB 173 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARGBB 178 " --> pdb=" O TYRBB 174 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYSBB 180 " --> pdb=" O ALABB 176 " (cutoff:3.500A) Processing helix chain 'BB' and resid 196 through 200 removed outlier: 3.820A pdb=" N LEUBB 199 " --> pdb=" O ASNBB 196 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALABB 200 " --> pdb=" O PROBB 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'BB' and resid 196 through 200' Processing helix chain 'BB' and resid 210 through 230 removed outlier: 3.667A pdb=" N ILEBB 217 " --> pdb=" O SERBB 213 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYSBB 220 " --> pdb=" O LEUBB 216 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYSBB 226 " --> pdb=" O VALBB 222 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLUBB 227 " --> pdb=" O PHEBB 223 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SERBB 230 " --> pdb=" O CYSBB 226 " (cutoff:3.500A) Processing helix chain 'BC' and resid 6 through 11 Processing helix chain 'BC' and resid 25 through 51 removed outlier: 4.371A pdb=" N ALABC 30 " --> pdb=" O PROBC 26 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLUBC 31 " --> pdb=" O LYSBC 27 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYSBC 42 " --> pdb=" O LYSBC 38 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYSBC 44 " --> pdb=" O ARGBC 40 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYSBC 49 " --> pdb=" O ASNBC 45 " (cutoff:3.500A) Processing helix chain 'BC' and resid 80 through 84 Processing helix chain 'BC' and resid 90 through 104 removed outlier: 3.967A pdb=" N LYSBC 96 " --> pdb=" O VALBC 92 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYSBC 101 " --> pdb=" O ILEBC 97 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLUBC 102 " --> pdb=" O ASNBC 98 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASNBC 104 " --> pdb=" O GLNBC 100 " (cutoff:3.500A) Processing helix chain 'BC' and resid 123 through 137 removed outlier: 3.799A pdb=" N LEUBC 127 " --> pdb=" O ASPBC 123 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLNBC 134 " --> pdb=" O PHEBC 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SERBC 137 " --> pdb=" O GLYBC 133 " (cutoff:3.500A) Processing helix chain 'BC' and resid 141 through 153 removed outlier: 3.709A pdb=" N GLUBC 153 " --> pdb=" O ILEBC 149 " (cutoff:3.500A) Processing helix chain 'BD' and resid 8 through 13 Processing helix chain 'BD' and resid 31 through 39 removed outlier: 3.671A pdb=" N GLNBD 35 " --> pdb=" O ASPBD 31 " (cutoff:3.500A) Processing helix chain 'BD' and resid 42 through 58 removed outlier: 4.110A pdb=" N LEUBD 54 " --> pdb=" O GLUBD 50 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARGBD 55 " --> pdb=" O LYSBD 51 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYRBD 58 " --> pdb=" O LEUBD 54 " (cutoff:3.500A) Processing helix chain 'BD' and resid 61 through 75 removed outlier: 3.763A pdb=" N TYRBD 68 " --> pdb=" O GLNBD 64 " (cutoff:3.500A) Processing helix chain 'BD' and resid 78 through 89 removed outlier: 3.631A pdb=" N LEUBD 84 " --> pdb=" O GLYBD 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N METBD 89 " --> pdb=" O GLNBD 85 " (cutoff:3.500A) Processing helix chain 'BD' and resid 90 through 98 removed outlier: 3.676A pdb=" N PHEBD 96 " --> pdb=" O ASPBD 92 " (cutoff:3.500A) Processing helix chain 'BD' and resid 103 through 113 Processing helix chain 'BD' and resid 141 through 154 removed outlier: 3.605A pdb=" N ILEBD 148 " --> pdb=" O SERBD 144 " (cutoff:3.500A) Processing helix chain 'BD' and resid 180 through 184 removed outlier: 3.812A pdb=" N VALBD 184 " --> pdb=" O SERBD 181 " (cutoff:3.500A) Processing helix chain 'BD' and resid 189 through 197 removed outlier: 3.896A pdb=" N VALBD 193 " --> pdb=" O ASNBD 189 " (cutoff:3.500A) Processing helix chain 'BE' and resid 196 through 210 Processing helix chain 'BE' and resid 250 through 259 removed outlier: 3.519A pdb=" N THRBE 255 " --> pdb=" O GLYBE 251 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VALBE 256 " --> pdb=" O ALABE 252 " (cutoff:3.500A) Processing helix chain 'BE' and resid 274 through 288 removed outlier: 3.738A pdb=" N THRBE 288 " --> pdb=" O VALBE 284 " (cutoff:3.500A) Processing helix chain 'BE' and resid 291 through 298 removed outlier: 3.615A pdb=" N VALBE 295 " --> pdb=" O GLNBE 291 " (cutoff:3.500A) Processing helix chain 'BE' and resid 302 through 308 removed outlier: 3.669A pdb=" N LEUBE 306 " --> pdb=" O PROBE 302 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYSBE 308 " --> pdb=" O GLUBE 304 " (cutoff:3.500A) Processing helix chain 'BF' and resid 76 through 94 removed outlier: 3.583A pdb=" N ARGBF 80 " --> pdb=" O THRBF 76 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLYBF 94 " --> pdb=" O LEUBF 90 " (cutoff:3.500A) Processing helix chain 'BF' and resid 139 through 141 No H-bonds generated for 'chain 'BF' and resid 139 through 141' Processing helix chain 'BF' and resid 142 through 152 removed outlier: 3.625A pdb=" N VALBF 150 " --> pdb=" O GLUBF 146 " (cutoff:3.500A) Processing helix chain 'BG' and resid 20 through 28 removed outlier: 4.139A pdb=" N ASNBG 24 " --> pdb=" O ASNBG 20 " (cutoff:3.500A) Processing helix chain 'BG' and resid 36 through 55 removed outlier: 3.656A pdb=" N TYRBG 40 " --> pdb=" O LYSBG 36 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLNBG 41 " --> pdb=" O SERBG 37 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARGBG 45 " --> pdb=" O GLNBG 41 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALABG 46 " --> pdb=" O ILEBG 42 " (cutoff:3.500A) Processing helix chain 'BG' and resid 57 through 70 removed outlier: 3.960A pdb=" N VALBG 61 " --> pdb=" O ASNBG 57 " (cutoff:3.500A) Processing helix chain 'BG' and resid 92 through 111 removed outlier: 3.650A pdb=" N TRPBG 103 " --> pdb=" O LEUBG 99 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYSBG 110 " --> pdb=" O GLYBG 106 " (cutoff:3.500A) Processing helix chain 'BG' and resid 115 through 129 Processing helix chain 'BG' and resid 132 through 148 Processing helix chain 'BH' and resid 4 through 20 removed outlier: 3.703A pdb=" N ASPBH 8 " --> pdb=" O ASPBH 4 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THRBH 11 " --> pdb=" O ALABH 7 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILEBH 13 " --> pdb=" O ILEBH 9 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALABH 16 " --> pdb=" O CYSBH 12 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASPBH 17 " --> pdb=" O ILEBH 13 " (cutoff:3.500A) Processing helix chain 'BH' and resid 29 through 42 removed outlier: 3.967A pdb=" N ASNBH 34 " --> pdb=" O ASNBH 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUBH 39 " --> pdb=" O ILEBH 35 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARGBH 41 " --> pdb=" O LYSBH 37 " (cutoff:3.500A) Processing helix chain 'BH' and resid 98 through 103 removed outlier: 3.636A pdb=" N GLYBH 101 " --> pdb=" O ARGBH 98 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N METBH 103 " --> pdb=" O LEUBH 100 " (cutoff:3.500A) Processing helix chain 'BH' and resid 117 through 124 Processing helix chain 'BI' and resid 57 through 63 Processing helix chain 'BI' and resid 101 through 106 Processing helix chain 'BI' and resid 108 through 115 removed outlier: 3.830A pdb=" N VALBI 115 " --> pdb=" O TRPBI 111 " (cutoff:3.500A) Processing helix chain 'BI' and resid 116 through 121 removed outlier: 3.706A pdb=" N THRBI 121 " --> pdb=" O THRBI 117 " (cutoff:3.500A) Processing helix chain 'BI' and resid 122 through 124 No H-bonds generated for 'chain 'BI' and resid 122 through 124' Processing helix chain 'BI' and resid 138 through 158 removed outlier: 3.533A pdb=" N LEUBI 154 " --> pdb=" O VALBI 150 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEUBI 155 " --> pdb=" O ALABI 151 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYSBI 156 " --> pdb=" O ARGBI 152 " (cutoff:3.500A) Processing helix chain 'BI' and resid 161 through 168 removed outlier: 4.105A pdb=" N LEUBI 165 " --> pdb=" O HISBI 161 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 107 through 124 removed outlier: 3.620A pdb=" N ASPBJ 113 " --> pdb=" O PROBJ 109 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THRBJ 124 " --> pdb=" O ASPBJ 120 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 173 through 183 Processing helix chain 'BK' and resid 56 through 60 Processing helix chain 'BK' and resid 62 through 67 removed outlier: 3.589A pdb=" N LYSBK 65 " --> pdb=" O ARGBK 62 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARGBK 66 " --> pdb=" O GLYBK 63 " (cutoff:3.500A) Processing helix chain 'BK' and resid 68 through 86 removed outlier: 3.663A pdb=" N ALABK 72 " --> pdb=" O THRBK 68 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THRBK 82 " --> pdb=" O ASNBK 78 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VALBK 83 " --> pdb=" O ALABK 79 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLUBK 85 " --> pdb=" O ARGBK 81 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLNBK 86 " --> pdb=" O THRBK 82 " (cutoff:3.500A) Processing helix chain 'BK' and resid 100 through 111 removed outlier: 4.120A pdb=" N ALABK 104 " --> pdb=" O LEUBK 100 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEUBK 106 " --> pdb=" O ARGBK 102 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARGBK 107 " --> pdb=" O ASPBK 103 " (cutoff:3.500A) Processing helix chain 'BL' and resid 3 through 9 Processing helix chain 'BM' and resid 64 through 68 removed outlier: 3.647A pdb=" N TYRBM 67 " --> pdb=" O SERBM 64 " (cutoff:3.500A) Processing helix chain 'BM' and resid 72 through 84 removed outlier: 3.506A pdb=" N ALABM 76 " --> pdb=" O GLYBM 72 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARGBM 77 " --> pdb=" O ARGBM 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEUBM 80 " --> pdb=" O ALABM 76 " (cutoff:3.500A) Processing helix chain 'BM' and resid 94 through 105 removed outlier: 3.675A pdb=" N GLUBM 104 " --> pdb=" O GLNBM 100 " (cutoff:3.500A) Processing helix chain 'BM' and resid 106 through 108 No H-bonds generated for 'chain 'BM' and resid 106 through 108' Processing helix chain 'BM' and resid 112 through 129 Processing helix chain 'BM' and resid 130 through 139 removed outlier: 3.597A pdb=" N HISBM 136 " --> pdb=" O ARGBM 132 " (cutoff:3.500A) Processing helix chain 'BM' and resid 151 through 157 Processing helix chain 'BN' and resid 3 through 20 removed outlier: 3.587A pdb=" N ARGBN 13 " --> pdb=" O ARGBN 9 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLNBN 18 " --> pdb=" O ARGBN 14 " (cutoff:3.500A) Processing helix chain 'BN' and resid 21 through 34 removed outlier: 3.629A pdb=" N ARGBN 25 " --> pdb=" O HISBN 21 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARGBN 32 " --> pdb=" O LYSBN 28 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALBN 34 " --> pdb=" O GLUBN 30 " (cutoff:3.500A) Processing helix chain 'BN' and resid 39 through 49 removed outlier: 3.556A pdb=" N GLNBN 48 " --> pdb=" O HISBN 44 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SERBN 49 " --> pdb=" O GLYBN 45 " (cutoff:3.500A) Processing helix chain 'BN' and resid 51 through 55 Processing helix chain 'BN' and resid 79 through 89 Processing helix chain 'BO' and resid 21 through 41 removed outlier: 3.607A pdb=" N LEUBO 38 " --> pdb=" O ARGBO 34 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HISBO 39 " --> pdb=" O ARGBO 35 " (cutoff:3.500A) Processing helix chain 'BO' and resid 46 through 71 removed outlier: 3.788A pdb=" N LYSBO 55 " --> pdb=" O ARGBO 51 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THRBO 56 " --> pdb=" O GLYBO 52 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLNBO 61 " --> pdb=" O LEUBO 57 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYSBO 69 " --> pdb=" O ALABO 65 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILEBO 70 " --> pdb=" O TYRBO 66 " (cutoff:3.500A) Processing helix chain 'BO' and resid 71 through 83 removed outlier: 3.789A pdb=" N TYRBO 75 " --> pdb=" O ASNBO 71 " (cutoff:3.500A) Processing helix chain 'BP' and resid 49 through 58 removed outlier: 3.817A pdb=" N ILEBP 53 " --> pdb=" O ASNBP 49 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASPBP 55 " --> pdb=" O PROBP 51 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHEBP 56 " --> pdb=" O ALABP 52 " (cutoff:3.500A) Processing helix chain 'BP' and resid 64 through 74 Processing helix chain 'BP' and resid 75 through 81 removed outlier: 3.851A pdb=" N GLUBP 79 " --> pdb=" O GLUBP 75 " (cutoff:3.500A) Processing helix chain 'BR' and resid 32 through 38 removed outlier: 3.772A pdb=" N ILEBR 36 " --> pdb=" O ASNBR 32 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARGBR 38 " --> pdb=" O SERBR 34 " (cutoff:3.500A) Processing helix chain 'BR' and resid 48 through 53 Processing helix chain 'BR' and resid 55 through 72 removed outlier: 3.704A pdb=" N LEUBR 61 " --> pdb=" O LYSBR 57 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEBR 71 " --> pdb=" O LYSBR 67 " (cutoff:3.500A) Processing helix chain 'BS' and resid 12 through 26 removed outlier: 3.753A pdb=" N LYSBS 18 " --> pdb=" O HISBS 14 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYSBS 24 " --> pdb=" O GLUBS 20 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYSBS 25 " --> pdb=" O LYSBS 21 " (cutoff:3.500A) Processing helix chain 'BS' and resid 41 through 45 Processing helix chain 'BS' and resid 63 through 67 removed outlier: 4.203A pdb=" N VALBS 67 " --> pdb=" O ASPBS 64 " (cutoff:3.500A) Processing helix chain 'BS' and resid 70 through 75 removed outlier: 3.747A pdb=" N GLUBS 73 " --> pdb=" O LYSBS 70 " (cutoff:3.500A) Processing helix chain 'BT' and resid 88 through 128 removed outlier: 3.826A pdb=" N VALBT 111 " --> pdb=" O ARGBT 107 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N METBT 115 " --> pdb=" O VALBT 111 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VALBT 118 " --> pdb=" O ARGBT 114 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYSBT 127 " --> pdb=" O ASPBT 123 " (cutoff:3.500A) Processing helix chain 'BT' and resid 133 through 135 No H-bonds generated for 'chain 'BT' and resid 133 through 135' Processing helix chain 'BT' and resid 136 through 156 removed outlier: 3.797A pdb=" N ALABT 144 " --> pdb=" O ASPBT 140 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYSBT 156 " --> pdb=" O LYSBT 152 " (cutoff:3.500A) Processing helix chain 'BT' and resid 160 through 182 removed outlier: 3.887A pdb=" N VALBT 178 " --> pdb=" O ASNBT 174 " (cutoff:3.500A) Processing helix chain 'BU' and resid 97 through 111 removed outlier: 4.086A pdb=" N ASNBU 101 " --> pdb=" O GLUBU 97 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARGBU 102 " --> pdb=" O ARGBU 98 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARGBU 105 " --> pdb=" O ASNBU 101 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLUBU 106 " --> pdb=" O ARGBU 102 " (cutoff:3.500A) Processing helix chain 'BU' and resid 111 through 121 removed outlier: 3.735A pdb=" N GLUBU 115 " --> pdb=" O GLYBU 111 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYRBU 121 " --> pdb=" O LYSBU 117 " (cutoff:3.500A) Processing helix chain 'BU' and resid 124 through 141 Processing helix chain 'BV' and resid 87 through 105 removed outlier: 3.575A pdb=" N LYSBV 100 " --> pdb=" O ASPBV 96 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYSBV 104 " --> pdb=" O LYSBV 100 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N HISBV 105 " --> pdb=" O SERBV 101 " (cutoff:3.500A) Processing helix chain 'BV' and resid 106 through 109 removed outlier: 3.709A pdb=" N VALBV 109 " --> pdb=" O SERBV 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'BV' and resid 106 through 109' Processing helix chain 'BV' and resid 152 through 176 removed outlier: 3.845A pdb=" N LYSBV 172 " --> pdb=" O LEUBV 168 " (cutoff:3.500A) Processing helix chain 'BW' and resid 61 through 69 removed outlier: 3.566A pdb=" N PHEBW 67 " --> pdb=" O LYSBW 63 " (cutoff:3.500A) Processing helix chain 'BY' and resid 1028 through 1033 Processing helix chain 'BY' and resid 1102 through 1122 Processing helix chain 'BY' and resid 1122 through 1127 removed outlier: 3.853A pdb=" N UNKBY1126 " --> pdb=" O UNKBY1122 " (cutoff:3.500A) Processing helix chain 'BY' and resid 1134 through 1141 Processing helix chain 'BY' and resid 1228 through 1233 removed outlier: 3.744A pdb=" N UNKBY1233 " --> pdb=" O UNKBY1229 " (cutoff:3.500A) Processing helix chain 'BY' and resid 1237 through 1245 Processing helix chain 'BY' and resid 1246 through 1258 removed outlier: 3.731A pdb=" N UNKBY1258 " --> pdb=" O UNKBY1254 " (cutoff:3.500A) 1374 hydrogen bonds defined for protein. 4005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3270 hydrogen bonds 5376 hydrogen bond angles 0 basepair planarities 1305 basepair parallelities 2566 stacking parallelities Total time for adding SS restraints: 196.02 Time building geometry restraints manager: 61.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 22660 1.33 - 1.45: 61882 1.45 - 1.57: 63158 1.57 - 1.69: 8795 1.69 - 1.81: 301 Bond restraints: 156796 Sorted by residual: bond pdb=" CA THRAJ 51 " pdb=" CB THRAJ 51 " ideal model delta sigma weight residual 1.528 1.574 -0.046 2.61e-02 1.47e+03 3.05e+00 bond pdb=" N METAe 1 " pdb=" CA METAe 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.52e+00 bond pdb=" N METAM 1 " pdb=" CA METAM 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.49e+00 bond pdb=" N METBP 1 " pdb=" CA METBP 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.48e+00 bond pdb=" N METAK 1 " pdb=" CA METAK 1 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.32e+00 ... (remaining 156791 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.45: 26953 106.45 - 113.35: 91324 113.35 - 120.25: 58693 120.25 - 127.15: 46297 127.15 - 134.06: 10191 Bond angle restraints: 233458 Sorted by residual: angle pdb=" C ASPAZ 90 " pdb=" N ALAAZ 91 " pdb=" CA ALAAZ 91 " ideal model delta sigma weight residual 120.82 126.37 -5.55 1.50e+00 4.44e-01 1.37e+01 angle pdb=" C GLYAC 192 " pdb=" N ASNAC 193 " pdb=" CA ASNAC 193 " ideal model delta sigma weight residual 121.54 128.48 -6.94 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C PHEAR 93 " pdb=" N GLNAR 94 " pdb=" CA GLNAR 94 " ideal model delta sigma weight residual 120.82 126.14 -5.32 1.50e+00 4.44e-01 1.26e+01 angle pdb=" N ILEBF 156 " pdb=" CA ILEBF 156 " pdb=" C ILEBF 156 " ideal model delta sigma weight residual 111.48 108.37 3.11 9.40e-01 1.13e+00 1.09e+01 angle pdb=" C PROAM 70 " pdb=" N ASPAM 71 " pdb=" CA ASPAM 71 " ideal model delta sigma weight residual 121.54 127.65 -6.11 1.91e+00 2.74e-01 1.02e+01 ... (remaining 233453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 89734 35.85 - 71.71: 9396 71.71 - 107.56: 1167 107.56 - 143.41: 7 143.41 - 179.27: 25 Dihedral angle restraints: 100329 sinusoidal: 82093 harmonic: 18236 Sorted by residual: dihedral pdb=" O4' UAB 27 " pdb=" C1' UAB 27 " pdb=" N1 UAB 27 " pdb=" C2 UAB 27 " ideal model delta sinusoidal sigma weight residual -160.00 14.28 -174.28 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' UBA 547 " pdb=" C1' UBA 547 " pdb=" N1 UBA 547 " pdb=" C2 UBA 547 " ideal model delta sinusoidal sigma weight residual 200.00 28.34 171.66 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' CAx 37 " pdb=" C1' CAx 37 " pdb=" N1 CAx 37 " pdb=" C2 CAx 37 " ideal model delta sinusoidal sigma weight residual 200.00 32.08 167.92 1 1.50e+01 4.44e-03 8.44e+01 ... (remaining 100326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 25818 0.039 - 0.077: 3046 0.077 - 0.116: 564 0.116 - 0.154: 168 0.154 - 0.193: 13 Chirality restraints: 29609 Sorted by residual: chirality pdb=" C3' AAA1399 " pdb=" C4' AAA1399 " pdb=" O3' AAA1399 " pdb=" C2' AAA1399 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" C3' AAA1200 " pdb=" C4' AAA1200 " pdb=" O3' AAA1200 " pdb=" C2' AAA1200 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" C1' ABA 512 " pdb=" O4' ABA 512 " pdb=" C2' ABA 512 " pdb=" N9 ABA 512 " both_signs ideal model delta sigma weight residual False 2.46 2.28 0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 29606 not shown) Planarity restraints: 13145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THRAR 174 " -0.066 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PROAR 175 " 0.174 5.00e-02 4.00e+02 pdb=" CA PROAR 175 " -0.052 5.00e-02 4.00e+02 pdb=" CD PROAR 175 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARGAR 77 " 0.060 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PROAR 78 " -0.155 5.00e-02 4.00e+02 pdb=" CA PROAR 78 " 0.046 5.00e-02 4.00e+02 pdb=" CD PROAR 78 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALAG 50 " -0.055 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PROAG 51 " 0.147 5.00e-02 4.00e+02 pdb=" CA PROAG 51 " -0.045 5.00e-02 4.00e+02 pdb=" CD PROAG 51 " -0.047 5.00e-02 4.00e+02 ... (remaining 13142 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 115 1.98 - 2.71: 12016 2.71 - 3.44: 184519 3.44 - 4.17: 457775 4.17 - 4.90: 640457 Nonbonded interactions: 1294882 Sorted by model distance: nonbonded pdb=" NZ LYSBB 40 " pdb=" O UNKBY1202 " model vdw 1.251 2.520 nonbonded pdb=" O LYSBB 38 " pdb=" N UNKBY1206 " model vdw 1.307 2.520 nonbonded pdb=" OD2 ASPBB 201 " pdb=" CB UNKBY1117 " model vdw 1.374 3.440 nonbonded pdb=" NH1 ARGBB 92 " pdb=" CB UNKBY1257 " model vdw 1.431 3.520 nonbonded pdb=" NZ LYSBB 40 " pdb=" C UNKBY1202 " model vdw 1.433 3.350 ... (remaining 1294877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.360 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: 0.100 Extract box with map and model: 20.250 Check model and map are aligned: 1.630 Set scattering table: 1.050 Process input model: 483.040 Find NCS groups from input model: 2.990 Set up NCS constraints: 0.380 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: 0.040 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 528.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.003 0.052 156796 Z= 0.165 Angle : 0.449 7.879 233458 Z= 0.235 Chirality : 0.029 0.193 29609 Planarity : 0.004 0.101 13145 Dihedral : 21.564 179.268 88561 Min Nonbonded Distance : 1.251 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.38 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.09), residues: 6070 helix: -2.55 (0.08), residues: 1969 sheet: -2.74 (0.14), residues: 1000 loop : -2.37 (0.10), residues: 3101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPAQ 61 HIS 0.011 0.001 HISAM 13 PHE 0.012 0.001 PHEAT 154 TYR 0.011 0.001 TYRAK 32 ARG 0.009 0.001 ARGAM 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12140 Ramachandran restraints generated. 6070 Oldfield, 0 Emsley, 6070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12140 Ramachandran restraints generated. 6070 Oldfield, 0 Emsley, 6070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1676 residues out of total 5288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1676 time to evaluate : 6.515 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: AC 60 LYS cc_start: 0.7912 (ttmp) cc_final: 0.7031 (tttm) REVERT: AC 118 VAL cc_start: 0.7572 (t) cc_final: 0.7318 (t) REVERT: AC 121 LYS cc_start: 0.7357 (ptmt) cc_final: 0.7112 (pttp) REVERT: AC 137 ILE cc_start: 0.7264 (mm) cc_final: 0.6929 (pt) REVERT: AC 253 ARG cc_start: 0.7495 (ttm-80) cc_final: 0.7178 (ttp80) REVERT: AC 259 ASN cc_start: 0.8012 (m-40) cc_final: 0.7706 (m110) REVERT: AC 264 ASN cc_start: 0.7855 (m-40) cc_final: 0.7585 (t0) REVERT: AC 266 ILE cc_start: 0.8315 (mm) cc_final: 0.8115 (mm) REVERT: AD 101 SER cc_start: 0.8590 (p) cc_final: 0.8326 (m) REVERT: AD 213 LYS cc_start: 0.8384 (tttp) cc_final: 0.8072 (ttmt) REVERT: AD 249 LYS cc_start: 0.8473 (mttt) cc_final: 0.8097 (mttp) REVERT: AD 258 LYS cc_start: 0.8128 (tttt) cc_final: 0.7766 (ttpt) REVERT: AD 265 LYS cc_start: 0.7655 (ttpt) cc_final: 0.7240 (tttp) REVERT: AE 73 LYS cc_start: 0.7848 (ttmp) cc_final: 0.7607 (ttpt) REVERT: AE 95 LYS cc_start: 0.7746 (ttmt) cc_final: 0.7469 (tttp) REVERT: AE 227 LYS cc_start: 0.8494 (ttmp) cc_final: 0.7686 (ttpt) REVERT: AF 26 LYS cc_start: 0.7404 (tttt) cc_final: 0.7097 (mppt) REVERT: AF 72 LEU cc_start: 0.7056 (tm) cc_final: 0.6790 (tt) REVERT: AF 83 THR cc_start: 0.7470 (m) cc_final: 0.7097 (p) REVERT: AF 167 MET cc_start: 0.6731 (ptp) cc_final: 0.6229 (ptp) REVERT: AG 64 LYS cc_start: 0.6413 (mttp) cc_final: 0.6117 (mptp) REVERT: AG 132 VAL cc_start: 0.7613 (p) cc_final: 0.7281 (m) REVERT: AG 174 SER cc_start: 0.6568 (t) cc_final: 0.6141 (m) REVERT: AG 213 GLU cc_start: 0.6763 (pt0) cc_final: 0.6346 (mp0) REVERT: AK 92 ASN cc_start: 0.8238 (m110) cc_final: 0.7766 (m-40) REVERT: AL 94 LYS cc_start: 0.6979 (mmtt) cc_final: 0.6528 (mmmt) REVERT: AL 156 LYS cc_start: 0.7657 (mppt) cc_final: 0.7373 (mptt) REVERT: AL 190 SER cc_start: 0.8220 (m) cc_final: 0.7981 (m) REVERT: AL 213 LYS cc_start: 0.6881 (mmmm) cc_final: 0.6656 (mptt) REVERT: AM 6 ARG cc_start: 0.7322 (tmt170) cc_final: 0.7098 (ttm170) REVERT: AM 12 GLN cc_start: 0.7854 (mt0) cc_final: 0.7028 (mm-40) REVERT: AM 37 LEU cc_start: 0.8352 (mt) cc_final: 0.8116 (mt) REVERT: AM 63 LYS cc_start: 0.7180 (tptm) cc_final: 0.6961 (tptm) REVERT: AM 64 ILE cc_start: 0.7369 (mm) cc_final: 0.6637 (tp) REVERT: AM 106 ILE cc_start: 0.8621 (mt) cc_final: 0.8187 (tt) REVERT: AO 92 MET cc_start: 0.6991 (mtm) cc_final: 0.6718 (mtm) REVERT: AO 116 THR cc_start: 0.8142 (p) cc_final: 0.7823 (t) REVERT: AO 126 MET cc_start: 0.7548 (ptm) cc_final: 0.7201 (ptp) REVERT: AO 151 ARG cc_start: 0.7283 (mtm180) cc_final: 0.6405 (mtm-85) REVERT: AO 165 VAL cc_start: 0.8251 (t) cc_final: 0.7896 (m) REVERT: AP 161 ARG cc_start: 0.6627 (ptm-80) cc_final: 0.6381 (ptm-80) REVERT: AQ 16 LYS cc_start: 0.8440 (mttm) cc_final: 0.7823 (mtpt) REVERT: AQ 17 ILE cc_start: 0.8812 (mm) cc_final: 0.8435 (mm) REVERT: AQ 51 ASP cc_start: 0.7707 (m-30) cc_final: 0.7398 (m-30) REVERT: AR 154 ASP cc_start: 0.8189 (t70) cc_final: 0.7890 (t0) REVERT: AR 176 ILE cc_start: 0.7244 (pt) cc_final: 0.6568 (mt) REVERT: AR 218 ARG cc_start: 0.7599 (ttt180) cc_final: 0.7321 (ttt180) REVERT: AR 228 GLU cc_start: 0.7696 (mp0) cc_final: 0.7437 (mp0) REVERT: AS 102 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7927 (mttp) REVERT: AS 164 MET cc_start: 0.7468 (ptp) cc_final: 0.7057 (ptp) REVERT: AT 158 LYS cc_start: 0.7657 (mttp) cc_final: 0.7394 (mtpp) REVERT: AU 89 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6671 (pp20) REVERT: AW 106 ASN cc_start: 0.8941 (m-40) cc_final: 0.8670 (m-40) REVERT: AX 97 ARG cc_start: 0.7597 (ptm-80) cc_final: 0.6992 (ptt90) REVERT: AY 60 LYS cc_start: 0.5533 (mmtt) cc_final: 0.5243 (mmtp) REVERT: AY 138 LYS cc_start: 0.7792 (mtpp) cc_final: 0.7569 (mtpp) REVERT: AY 147 ARG cc_start: 0.7247 (ptm160) cc_final: 0.7038 (ptp-110) REVERT: Ab 21 LYS cc_start: 0.7433 (mtmm) cc_final: 0.6687 (mmmt) REVERT: Ab 40 HIS cc_start: 0.6882 (m90) cc_final: 0.6194 (t-170) REVERT: Ab 57 LYS cc_start: 0.7573 (ptpt) cc_final: 0.7352 (pttm) REVERT: Ac 106 LYS cc_start: 0.8344 (ttpm) cc_final: 0.7883 (ttmt) REVERT: Ae 22 ARG cc_start: 0.6951 (mtt180) cc_final: 0.6695 (mtm110) REVERT: Af 69 ARG cc_start: 0.7579 (mtm-85) cc_final: 0.6898 (mmp-170) REVERT: Az 83 GLU cc_start: 0.6513 (mt-10) cc_final: 0.5937 (mm-30) REVERT: Az 103 ILE cc_start: 0.7173 (mm) cc_final: 0.6763 (tp) REVERT: Az 140 ILE cc_start: 0.6951 (mm) cc_final: 0.6738 (pt) REVERT: Az 199 LEU cc_start: 0.6552 (tt) cc_final: 0.6121 (tp) REVERT: Az 206 LEU cc_start: 0.6726 (mt) cc_final: 0.6321 (mt) REVERT: Az 226 GLU cc_start: 0.6511 (mt-10) cc_final: 0.5972 (mm-30) REVERT: Az 230 LYS cc_start: 0.5076 (mttp) cc_final: 0.4437 (ttmm) REVERT: Az 268 LEU cc_start: 0.5416 (mm) cc_final: 0.5103 (mm) REVERT: BB 49 ARG cc_start: 0.5418 (mmt180) cc_final: 0.4725 (mmp80) REVERT: BB 52 ARG cc_start: 0.4679 (tpm-80) cc_final: 0.3694 (ttt180) REVERT: BB 86 ARG cc_start: 0.5420 (mmp-170) cc_final: 0.4769 (mtt180) REVERT: BB 158 MET cc_start: 0.4631 (ttm) cc_final: 0.4332 (ttm) REVERT: BB 193 THR cc_start: 0.4365 (p) cc_final: 0.3349 (m) REVERT: BC 38 LYS cc_start: 0.6727 (mptm) cc_final: 0.5961 (mttt) REVERT: BC 78 MET cc_start: 0.5846 (mtp) cc_final: 0.5003 (mmm) REVERT: BC 102 GLU cc_start: 0.5455 (pm20) cc_final: 0.4917 (tt0) REVERT: BC 129 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7286 (mm-30) REVERT: BC 134 GLN cc_start: 0.6866 (mt0) cc_final: 0.5955 (mm110) REVERT: BC 158 LYS cc_start: 0.7821 (mptp) cc_final: 0.6724 (mmmt) REVERT: BC 172 GLU cc_start: 0.6123 (mt-10) cc_final: 0.5267 (mm-30) REVERT: BC 173 ILE cc_start: 0.7664 (tt) cc_final: 0.6964 (mm) REVERT: BC 196 CYS cc_start: 0.7132 (t) cc_final: 0.6336 (m) REVERT: BC 207 LEU cc_start: 0.7159 (mm) cc_final: 0.6729 (mm) REVERT: BD 89 MET cc_start: 0.6447 (mmt) cc_final: 0.6233 (mmm) REVERT: BD 172 LYS cc_start: 0.5184 (ptmt) cc_final: 0.4751 (pttp) REVERT: BD 187 LYS cc_start: 0.7727 (ttmt) cc_final: 0.7238 (mptp) REVERT: BE 235 ARG cc_start: 0.7262 (ttm170) cc_final: 0.6941 (ttp80) REVERT: BE 291 GLN cc_start: 0.7422 (mm110) cc_final: 0.7212 (mm-40) REVERT: BE 308 LYS cc_start: 0.6010 (mtpp) cc_final: 0.5280 (mmpt) REVERT: BF 97 MET cc_start: 0.5015 (mtt) cc_final: 0.4776 (mmm) REVERT: BF 123 ASN cc_start: 0.6584 (m110) cc_final: 0.6041 (m-40) REVERT: BG 45 ARG cc_start: 0.7084 (mtt-85) cc_final: 0.6268 (mmm-85) REVERT: BG 53 LYS cc_start: 0.7235 (mtpm) cc_final: 0.7035 (mtmm) REVERT: BG 129 LYS cc_start: 0.6101 (mtmt) cc_final: 0.5868 (mtmm) REVERT: BH 20 ARG cc_start: 0.6677 (ttp-110) cc_final: 0.6298 (mmm-85) REVERT: BH 122 LEU cc_start: 0.7529 (mt) cc_final: 0.7112 (pp) REVERT: BJ 118 ILE cc_start: 0.8143 (mm) cc_final: 0.7830 (pp) REVERT: BK 88 MET cc_start: 0.2941 (mmt) cc_final: 0.1238 (mmp) REVERT: BK 93 VAL cc_start: 0.6615 (m) cc_final: 0.6409 (p) REVERT: BL 57 LEU cc_start: 0.8164 (mt) cc_final: 0.7844 (mp) REVERT: BL 70 ILE cc_start: 0.7318 (mt) cc_final: 0.7050 (mp) REVERT: BL 79 VAL cc_start: 0.7842 (t) cc_final: 0.7541 (p) REVERT: BN 14 ARG cc_start: 0.7361 (ttt90) cc_final: 0.7123 (tmt-80) REVERT: BO 42 LEU cc_start: 0.6194 (mm) cc_final: 0.5633 (tp) REVERT: BQ 77 GLU cc_start: 0.7216 (tt0) cc_final: 0.6872 (tp30) REVERT: BQ 107 LYS cc_start: 0.6873 (ptpp) cc_final: 0.6466 (mmtt) REVERT: BR 53 ARG cc_start: 0.6566 (mtm180) cc_final: 0.6340 (mtt180) REVERT: BS 44 MET cc_start: 0.7025 (ptm) cc_final: 0.6735 (ptp) REVERT: BS 71 LEU cc_start: 0.6990 (mt) cc_final: 0.6631 (mm) REVERT: BT 105 LYS cc_start: 0.6651 (tttm) cc_final: 0.6003 (tppt) REVERT: BV 80 GLN cc_start: 0.6662 (tp-100) cc_final: 0.6228 (tt0) REVERT: BV 124 SER cc_start: 0.8452 (t) cc_final: 0.8014 (p) outliers start: 0 outliers final: 6 residues processed: 1676 average time/residue: 2.2272 time to fit residues: 5174.5501 Evaluate side-chains 968 residues out of total 5288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 962 time to evaluate : 5.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AE residue 211 ASP Chi-restraints excluded: chain AF residue 40 ILE Chi-restraints excluded: chain AJ residue 159 ASP Chi-restraints excluded: chain BB residue 216 LEU Chi-restraints excluded: chain BC residue 176 ILE Chi-restraints excluded: chain BD residue 12 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 887 optimal weight: 8.9990 chunk 796 optimal weight: 10.0000 chunk 442 optimal weight: 0.5980 chunk 272 optimal weight: 10.0000 chunk 537 optimal weight: 7.9990 chunk 425 optimal weight: 8.9990 chunk 823 optimal weight: 2.9990 chunk 318 optimal weight: 5.9990 chunk 500 optimal weight: 0.8980 chunk 613 optimal weight: 10.0000 chunk 954 optimal weight: 0.0060 overall best weight: 2.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: