Starting phenix.real_space_refine on Fri Mar 22 07:23:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj5_16905/03_2024/8oj5_16905.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj5_16905/03_2024/8oj5_16905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj5_16905/03_2024/8oj5_16905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj5_16905/03_2024/8oj5_16905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj5_16905/03_2024/8oj5_16905.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj5_16905/03_2024/8oj5_16905.pdb" } resolution = 2.9 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= 0.005 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 5 6.06 5 P 3740 5.49 5 Mg 220 5.21 5 S 279 5.16 5 C 76580 2.51 5 N 27088 2.21 5 O 37129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 34": "OE1" <-> "OE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 36": "OE1" <-> "OE2" Residue "LB PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD GLU 186": "OE1" <-> "OE2" Residue "LE PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG ASP 231": "OD1" <-> "OD2" Residue "LH GLU 66": "OE1" <-> "OE2" Residue "LI ASP 28": "OD1" <-> "OD2" Residue "LI ASP 83": "OD1" <-> "OD2" Residue "LI ASP 193": "OD1" <-> "OD2" Residue "LM PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO ASP 100": "OD1" <-> "OD2" Residue "LO GLU 162": "OE1" <-> "OE2" Residue "LO GLU 186": "OE1" <-> "OE2" Residue "LP GLU 89": "OE1" <-> "OE2" Residue "LP GLU 103": "OE1" <-> "OE2" Residue "LP ASP 110": "OD1" <-> "OD2" Residue "LP GLU 115": "OE1" <-> "OE2" Residue "LQ GLU 76": "OE1" <-> "OE2" Residue "LQ TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LR GLU 31": "OE1" <-> "OE2" Residue "LR ASP 47": "OD1" <-> "OD2" Residue "LR GLU 111": "OE1" <-> "OE2" Residue "LR GLU 140": "OE1" <-> "OE2" Residue "LR ASP 148": "OD1" <-> "OD2" Residue "LT GLU 137": "OE1" <-> "OE2" Residue "LU ASP 98": "OD1" <-> "OD2" Residue "LU GLU 111": "OE1" <-> "OE2" Residue "LV GLU 99": "OE1" <-> "OE2" Residue "LV GLU 124": "OE1" <-> "OE2" Residue "LX GLU 84": "OE1" <-> "OE2" Residue "LX GLU 91": "OE1" <-> "OE2" Residue "LX ASP 143": "OD1" <-> "OD2" Residue "LY ASP 10": "OD1" <-> "OD2" Residue "LY ASP 112": "OD1" <-> "OD2" Residue "LY GLU 120": "OE1" <-> "OE2" Residue "LZ PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ ASP 88": "OD1" <-> "OD2" Residue "LZ ASP 99": "OD1" <-> "OD2" Residue "LZ GLU 120": "OE1" <-> "OE2" Residue "La GLU 84": "OE1" <-> "OE2" Residue "La ASP 102": "OD1" <-> "OD2" Residue "Lc GLU 80": "OE1" <-> "OE2" Residue "Lc ASP 101": "OD1" <-> "OD2" Residue "Lc ASP 103": "OD1" <-> "OD2" Residue "Ld PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ld ASP 61": "OD1" <-> "OD2" Residue "Le GLU 86": "OE1" <-> "OE2" Residue "Lh ASP 8": "OD1" <-> "OD2" Residue "Lh GLU 16": "OE1" <-> "OE2" Residue "Li GLU 89": "OE1" <-> "OE2" Residue "Lk ASP 10": "OD1" <-> "OD2" Residue "Lm TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lp GLU 88": "OE1" <-> "OE2" Residue "Lz GLU 88": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 145041 Number of models: 1 Model: "" Number of chains: 61 Chain: "5" Number of atoms: 74502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3474, 74502 Classifications: {'RNA': 3474} Modifications used: {'5*END': 1, 'rna2p_pur': 348, 'rna2p_pyr': 203, 'rna3p_pur': 1567, 'rna3p_pyr': 1356} Link IDs: {'rna2p': 550, 'rna3p': 2923} Chain breaks: 22 Chain: "7" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2561 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 52} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "8" Number of atoms: 3152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3152 Classifications: {'RNA': 148} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 10, 'rna3p_pur': 61, 'rna3p_pyr': 63} Link IDs: {'rna2p': 23, 'rna3p': 124} Chain breaks: 2 Chain: "A" Number of atoms: 5479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5479 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 14, 'TRANS': 677} Chain breaks: 3 Chain: "B" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3234 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 390} Chain breaks: 2 Chain: "C" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 1, 'TRANS': 186} Chain: "D" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 588 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 7, 'TRANS': 70} Chain: "LA" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1898 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 233} Chain: "LB" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3239 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 386} Chain: "LC" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2927 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 18, 'TRANS': 349} Chain: "LD" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2382 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LE" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1765 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 206} Chain breaks: 2 Chain: "LF" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "LG" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1927 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 226} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "LH" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "LI" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1634 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "LJ" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1401 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Chain: "LL" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1573 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 179} Chain: "LM" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1120 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "LN" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "LO" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1650 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "LP" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "LQ" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "LR" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1294 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 3, 'TRANS': 151} Chain: "LS" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1453 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "LT" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "LU" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 825 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "LV" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 979 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "LW" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 519 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "LX" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "LY" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "LZ" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "La" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "Lb" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Lc" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 764 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "Ld" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "Le" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "Lf" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "Lg" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Lh" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Li" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Lj" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 82} Chain: "Lk" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "Ll" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Lm" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "Lo" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 863 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "Lp" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "Lr" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "Lz" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1744 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 208} Chain: "5" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 207 Unusual residues: {' MG': 207} Classifications: {'undetermined': 207} Link IDs: {None: 206} Chain: "7" 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: "8" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "LP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Le" 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: "Lf" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Lg" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lj" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Lm" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lo" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0RR1 SG CYSLg 46 84.999 101.130 67.779 1.00 66.43 S ATOM A0RRI SG CYSLg 49 82.942 97.928 67.286 1.00 68.44 S ATOM A0RYT SG CYSLg 83 85.520 98.890 64.720 1.00 53.64 S ATOM A0RZD SG CYSLg 86 82.407 101.050 65.106 1.00 60.77 S ATOM A0TP8 SG CYSLj 19 123.229 119.973 108.028 1.00 38.87 S ATOM A0TQ0 SG CYSLj 22 124.927 120.393 111.399 1.00 42.66 S ATOM A0TSJ SG CYSLj 34 121.135 120.110 111.161 1.00 43.82 S ATOM A0TT2 SG CYSLj 37 122.831 123.255 109.951 1.00 42.71 S ATOM A0V1K SG CYSLm 96 79.138 71.120 203.825 1.00 47.65 S ATOM A0V2A SG CYSLm 99 81.691 69.214 201.782 1.00 59.81 S ATOM A0V4S SG CYSLm 110 81.698 68.857 205.567 1.00 62.19 S ATOM A0V60 SG CYSLm 115 82.854 72.075 204.020 1.00 52.83 S ATOM A0VBI SG CYSLo 12 75.110 177.296 168.301 1.00 36.05 S ATOM A0VC6 SG CYSLo 15 73.985 180.889 168.677 1.00 66.16 S ATOM A0VP7 SG CYSLo 72 71.647 178.305 167.020 1.00 46.82 S ATOM A0VQ8 SG CYSLo 77 74.837 179.508 165.277 1.00 60.16 S ATOM A0W5A SG CYSLp 39 69.160 97.932 74.938 1.00 66.76 S ATOM A0W5X SG CYSLp 42 69.973 95.175 72.505 1.00 43.51 S ATOM A0W9B SG CYSLp 57 72.052 95.577 75.665 1.00 60.49 S ATOM A0W9R SG CYSLp 60 72.402 98.163 72.956 1.00 55.50 S Residues with excluded nonbonded symmetry interactions: 248 residue: pdb=" P A 51765 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A 51765 " occ=0.00 residue: pdb=" P A 51766 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A 51766 " occ=0.00 residue: pdb=" P A 51767 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A 51767 " occ=0.00 residue: pdb=" N SER A 743 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER A 743 " occ=0.00 residue: pdb=" N LYS A 744 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 744 " occ=0.00 residue: pdb=" N LYS A 745 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 745 " occ=0.00 residue: pdb=" N THR A 746 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A 746 " occ=0.00 residue: pdb=" N GLY A 747 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 747 " occ=0.00 residue: pdb=" N LEU A 757 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 757 " occ=0.00 residue: pdb=" N ASP A 758 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A 758 " occ=0.00 residue: pdb=" N LYS A 759 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 759 " occ=0.00 residue: pdb=" N GLU A 760 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 760 " occ=0.00 ... (remaining 236 not shown) Time building chain proxies: 57.45, per 1000 atoms: 0.40 Number of scatterers: 145041 At special positions: 0 Unit cell: (231.288, 254.752, 284.082, 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 5 29.99 S 279 16.00 P 3740 15.00 Mg 220 11.99 O 37129 8.00 N 27088 7.00 C 76580 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: 59.79 Conformation dependent library (CDL) restraints added in 9.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLg 201 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 86 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 83 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 46 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 49 " pdb=" ZNLj 102 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 37 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 22 " pdb=" ZNLm 201 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 110 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 99 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 115 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 96 " pdb=" ZNLo 201 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 77 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 12 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 15 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 72 " pdb=" ZNLp 101 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 39 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 57 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 60 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 42 " Number of angles added : 30 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14978 Finding SS restraints... Secondary structure from input PDB file: 321 helices and 89 sheets defined 46.4% alpha, 14.2% beta 1151 base pairs and 2121 stacking pairs defined. Time for finding SS restraints: 49.57 Creating SS restraints... Processing helix chain 'A' and resid 29 through 43 removed outlier: 3.554A pdb=" N ALA A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 79 through 87 Processing helix chain 'A' and resid 89 through 104 removed outlier: 3.559A pdb=" N ILE A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 135 removed outlier: 3.560A pdb=" N GLU A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 179 through 197 removed outlier: 3.674A pdb=" N ILE A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 246 through 265 Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 303 through 320 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 334 through 347 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 365 through 375 Processing helix chain 'A' and resid 376 through 389 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 480 through 487 removed outlier: 4.611A pdb=" N PHE A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 523 removed outlier: 4.607A pdb=" N LYS A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 530 through 560 removed outlier: 3.943A pdb=" N LYS A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 577 removed outlier: 3.934A pdb=" N LEU A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.510A pdb=" N ASP A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.570A pdb=" N LYS A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 632 removed outlier: 4.416A pdb=" N ALA A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN A 631 " --> pdb=" O HIS A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 649 Processing helix chain 'A' and resid 657 through 679 removed outlier: 3.820A pdb=" N ALA A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 674 " --> pdb=" O GLN A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 699 Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.587A pdb=" N ALA A 714 " --> pdb=" O PRO A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 747 removed outlier: 4.106A pdb=" N GLN A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 removed outlier: 3.829A pdb=" N GLU A 762 " --> pdb=" O ASP A 758 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 765 " --> pdb=" O GLN A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 783 removed outlier: 3.576A pdb=" N GLU A 771 " --> pdb=" O THR A 767 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 13 through 18 removed outlier: 4.173A pdb=" N LEU B 17 " --> pdb=" O SER B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 46 removed outlier: 3.861A pdb=" N LEU B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN B 46 " --> pdb=" O ASN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 removed outlier: 4.348A pdb=" N ALA B 55 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 74 Processing helix chain 'B' and resid 96 through 105 Processing helix chain 'B' and resid 108 through 124 removed outlier: 4.290A pdb=" N VAL B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 169 removed outlier: 3.520A pdb=" N TYR B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.693A pdb=" N LEU B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 removed outlier: 3.585A pdb=" N GLN B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 226 through 233 Processing helix chain 'B' and resid 237 through 243 removed outlier: 3.587A pdb=" N TRP B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 372 Processing helix chain 'B' and resid 376 through 385 removed outlier: 4.266A pdb=" N LEU B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 392 Processing helix chain 'B' and resid 394 through 414 removed outlier: 3.728A pdb=" N MET B 401 " --> pdb=" O LYS B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.829A pdb=" N PHE B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET B 422 " --> pdb=" O GLN B 418 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE B 423 " --> pdb=" O HIS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 493 removed outlier: 3.945A pdb=" N LYS B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Proline residue: B 470 - end of helix removed outlier: 3.791A pdb=" N LYS B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 226 removed outlier: 3.573A pdb=" N SER C 226 " --> pdb=" O TYR C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 239 removed outlier: 4.098A pdb=" N VAL C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 272 through 287 Processing helix chain 'C' and resid 291 through 302 removed outlier: 3.612A pdb=" N SER C 300 " --> pdb=" O GLN C 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 41 removed outlier: 3.841A pdb=" N VAL D 32 " --> pdb=" O PRO D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 Processing helix chain 'LA' and resid 8 through 17 removed outlier: 3.634A pdb=" N GLYLA 11 " --> pdb=" O GLNLA 8 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SERLA 14 " --> pdb=" O GLYLA 11 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VALLA 15 " --> pdb=" O ALALA 12 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARGLA 17 " --> pdb=" O SERLA 14 " (cutoff:3.500A) Processing helix chain 'LA' and resid 33 through 39 Processing helix chain 'LA' and resid 173 through 177 removed outlier: 3.531A pdb=" N LYSLA 177 " --> pdb=" O ARGLA 174 " (cutoff:3.500A) Processing helix chain 'LA' and resid 181 through 191 removed outlier: 3.554A pdb=" N ALALA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) Processing helix chain 'LA' and resid 200 through 204 Processing helix chain 'LB' and resid 13 through 17 removed outlier: 3.695A pdb=" N PHELB 16 " --> pdb=" O SERLB 13 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEULB 17 " --> pdb=" O LEULB 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 13 through 17' Processing helix chain 'LB' and resid 111 through 117 removed outlier: 3.932A pdb=" N ARGLB 117 " --> pdb=" O GLULB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 132 through 138 Processing helix chain 'LB' and resid 139 through 157 Processing helix chain 'LB' and resid 167 through 171 Processing helix chain 'LB' and resid 189 through 200 removed outlier: 3.540A pdb=" N ARGLB 200 " --> pdb=" O TRPLB 196 " (cutoff:3.500A) Processing helix chain 'LB' and resid 206 through 210 Processing helix chain 'LB' and resid 230 through 235 Processing helix chain 'LB' and resid 356 through 361 Processing helix chain 'LB' and resid 381 through 390 Processing helix chain 'LB' and resid 392 through 403 Processing helix chain 'LC' and resid 25 through 30 Processing helix chain 'LC' and resid 33 through 45 Processing helix chain 'LC' and resid 46 through 49 removed outlier: 3.628A pdb=" N ARGLC 49 " --> pdb=" O LYSLC 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 46 through 49' Processing helix chain 'LC' and resid 116 through 131 Processing helix chain 'LC' and resid 133 through 140 Processing helix chain 'LC' and resid 156 through 161 Processing helix chain 'LC' and resid 163 through 174 Processing helix chain 'LC' and resid 176 through 187 removed outlier: 3.769A pdb=" N ILELC 180 " --> pdb=" O ALALC 176 " (cutoff:3.500A) Processing helix chain 'LC' and resid 192 through 198 removed outlier: 3.533A pdb=" N LYSLC 195 " --> pdb=" O GLYLC 192 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASNLC 198 " --> pdb=" O LYSLC 195 " (cutoff:3.500A) Processing helix chain 'LC' and resid 216 through 222 Processing helix chain 'LC' and resid 233 through 235 No H-bonds generated for 'chain 'LC' and resid 233 through 235' Processing helix chain 'LC' and resid 236 through 241 Processing helix chain 'LC' and resid 254 through 259 Processing helix chain 'LC' and resid 259 through 265 Processing helix chain 'LC' and resid 288 through 295 Processing helix chain 'LC' and resid 295 through 301 removed outlier: 3.797A pdb=" N ALALC 301 " --> pdb=" O GLULC 297 " (cutoff:3.500A) Processing helix chain 'LC' and resid 321 through 329 Processing helix chain 'LC' and resid 331 through 368 Processing helix chain 'LD' and resid 9 through 16 Processing helix chain 'LD' and resid 20 through 25 Processing helix chain 'LD' and resid 29 through 38 removed outlier: 3.944A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILELD 38 " --> pdb=" O LYSLD 34 " (cutoff:3.500A) Processing helix chain 'LD' and resid 40 through 44 Processing helix chain 'LD' and resid 81 through 87 Proline residue: LD 84 - end of helix Processing helix chain 'LD' and resid 94 through 114 Processing helix chain 'LD' and resid 157 through 170 removed outlier: 3.654A pdb=" N GLYLD 161 " --> pdb=" O ASNLD 157 " (cutoff:3.500A) Processing helix chain 'LD' and resid 191 through 200 Processing helix chain 'LD' and resid 201 through 215 Processing helix chain 'LD' and resid 215 through 223 Processing helix chain 'LD' and resid 223 through 229 Processing helix chain 'LD' and resid 232 through 250 removed outlier: 4.704A pdb=" N GLULD 237 " --> pdb=" O PROLD 233 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLULD 238 " --> pdb=" O ASPLD 234 " (cutoff:3.500A) Processing helix chain 'LD' and resid 272 through 294 Processing helix chain 'LE' and resid 58 through 66 Processing helix chain 'LE' and resid 132 through 136 Processing helix chain 'LE' and resid 178 through 183 Processing helix chain 'LE' and resid 190 through 192 No H-bonds generated for 'chain 'LE' and resid 190 through 192' Processing helix chain 'LE' and resid 213 through 218 Processing helix chain 'LE' and resid 243 through 264 removed outlier: 3.823A pdb=" N GLNLE 256 " --> pdb=" O ALALE 252 " (cutoff:3.500A) Proline residue: LE 259 - end of helix removed outlier: 3.771A pdb=" N ILELE 264 " --> pdb=" O LYSLE 260 " (cutoff:3.500A) Processing helix chain 'LE' and resid 266 through 273 Processing helix chain 'LF' and resid 25 through 79 removed outlier: 3.674A pdb=" N ILELF 69 " --> pdb=" O TYRLF 65 " (cutoff:3.500A) Processing helix chain 'LF' and resid 102 through 112 Processing helix chain 'LF' and resid 126 through 136 Processing helix chain 'LF' and resid 146 through 158 Processing helix chain 'LF' and resid 171 through 180 removed outlier: 4.233A pdb=" N ILELF 175 " --> pdb=" O ASPLF 171 " (cutoff:3.500A) Processing helix chain 'LF' and resid 181 through 183 No H-bonds generated for 'chain 'LF' and resid 181 through 183' Processing helix chain 'LF' and resid 186 through 197 Processing helix chain 'LF' and resid 200 through 208 Processing helix chain 'LF' and resid 239 through 248 removed outlier: 3.507A pdb=" N LEULF 243 " --> pdb=" O GLNLF 239 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARGLF 246 " --> pdb=" O ARGLF 242 " (cutoff:3.500A) Processing helix chain 'LG' and resid 51 through 55 removed outlier: 3.646A pdb=" N VALLG 55 " --> pdb=" O THRLG 52 " (cutoff:3.500A) Processing helix chain 'LG' and resid 58 through 74 Processing helix chain 'LG' and resid 77 through 82 Processing helix chain 'LG' and resid 83 through 85 No H-bonds generated for 'chain 'LG' and resid 83 through 85' Processing helix chain 'LG' and resid 88 through 101 removed outlier: 3.763A pdb=" N LYSLG 101 " --> pdb=" O LYSLG 97 " (cutoff:3.500A) Processing helix chain 'LG' and resid 106 through 124 Processing helix chain 'LG' and resid 139 through 149 Processing helix chain 'LG' and resid 163 through 167 Processing helix chain 'LG' and resid 168 through 178 removed outlier: 4.666A pdb=" N ALALG 172 " --> pdb=" O VALLG 168 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYSLG 176 " --> pdb=" O ALALG 172 " (cutoff:3.500A) Processing helix chain 'LG' and resid 186 through 194 removed outlier: 3.643A pdb=" N LEULG 190 " --> pdb=" O GLYLG 186 " (cutoff:3.500A) Processing helix chain 'LG' and resid 208 through 226 removed outlier: 4.434A pdb=" N GLYLG 213 " --> pdb=" O SERLG 209 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALALG 214 " --> pdb=" O GLULG 210 " (cutoff:3.500A) Processing helix chain 'LG' and resid 229 through 235 removed outlier: 3.858A pdb=" N ARGLG 235 " --> pdb=" O ASPLG 231 " (cutoff:3.500A) Processing helix chain 'LG' and resid 243 through 265 Processing helix chain 'LH' and resid 63 through 68 Processing helix chain 'LH' and resid 68 through 86 removed outlier: 3.872A pdb=" N THRLH 72 " --> pdb=" O ALALH 68 " (cutoff:3.500A) Processing helix chain 'LH' and resid 116 through 120 Processing helix chain 'LH' and resid 150 through 165 Processing helix chain 'LI' and resid 5 through 10 removed outlier: 3.627A pdb=" N ARGLI 10 " --> pdb=" O ARGLI 7 " (cutoff:3.500A) Processing helix chain 'LI' and resid 42 through 46 removed outlier: 3.512A pdb=" N PHELI 46 " --> pdb=" O VALLI 43 " (cutoff:3.500A) Processing helix chain 'LI' and resid 62 through 81 Processing helix chain 'LI' and resid 144 through 157 removed outlier: 4.161A pdb=" N PHELI 157 " --> pdb=" O ARGLI 153 " (cutoff:3.500A) Processing helix chain 'LI' and resid 177 through 187 removed outlier: 4.579A pdb=" N GLULI 182 " --> pdb=" O ALALI 178 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ASPLI 183 " --> pdb=" O ASPLI 179 " (cutoff:3.500A) Processing helix chain 'LI' and resid 205 through 214 removed outlier: 3.938A pdb=" N TRPLI 209 " --> pdb=" O PROLI 205 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 10 through 14 removed outlier: 3.539A pdb=" N GLULJ 14 " --> pdb=" O PROLJ 11 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 30 through 45 Processing helix chain 'LJ' and resid 76 through 91 Processing helix chain 'LJ' and resid 97 through 99 No H-bonds generated for 'chain 'LJ' and resid 97 through 99' Processing helix chain 'LJ' and resid 111 through 115 Processing helix chain 'LJ' and resid 138 through 143 removed outlier: 3.693A pdb=" N ALALJ 142 " --> pdb=" O PHELJ 139 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 158 through 171 Processing helix chain 'LL' and resid 17 through 20 removed outlier: 3.529A pdb=" N ARGLL 20 " --> pdb=" O ASPLL 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'LL' and resid 17 through 20' Processing helix chain 'LL' and resid 27 through 47 Processing helix chain 'LL' and resid 77 through 85 Processing helix chain 'LL' and resid 87 through 92 removed outlier: 4.201A pdb=" N ARGLL 92 " --> pdb=" O LYSLL 88 " (cutoff:3.500A) Processing helix chain 'LL' and resid 93 through 95 No H-bonds generated for 'chain 'LL' and resid 93 through 95' Processing helix chain 'LL' and resid 106 through 123 Processing helix chain 'LL' and resid 139 through 146 removed outlier: 3.866A pdb=" N LEULL 146 " --> pdb=" O GLULL 142 " (cutoff:3.500A) Processing helix chain 'LL' and resid 170 through 176 Processing helix chain 'LL' and resid 177 through 188 Processing helix chain 'LM' and resid 69 through 81 Processing helix chain 'LM' and resid 81 through 89 Processing helix chain 'LM' and resid 89 through 103 Processing helix chain 'LM' and resid 105 through 137 Processing helix chain 'LN' and resid 3 through 12 Processing helix chain 'LN' and resid 16 through 32 Processing helix chain 'LN' and resid 44 through 51 Processing helix chain 'LN' and resid 75 through 79 Processing helix chain 'LN' and resid 83 through 87 Processing helix chain 'LN' and resid 97 through 110 Processing helix chain 'LN' and resid 139 through 144 Processing helix chain 'LN' and resid 145 through 157 removed outlier: 4.870A pdb=" N TRPLN 150 " --> pdb=" O ASPLN 147 " (cutoff:3.500A) Proline residue: LN 154 - end of helix Processing helix chain 'LN' and resid 159 through 163 removed outlier: 3.634A pdb=" N GLYLN 163 " --> pdb=" O GLULN 160 " (cutoff:3.500A) Processing helix chain 'LN' and resid 165 through 170 Processing helix chain 'LN' and resid 171 through 173 No H-bonds generated for 'chain 'LN' and resid 171 through 173' Processing helix chain 'LN' and resid 177 through 184 removed outlier: 4.250A pdb=" N HISLN 181 " --> pdb=" O HISLN 178 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N HISLN 182 " --> pdb=" O LYSLN 179 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THRLN 183 " --> pdb=" O PHELN 180 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILELN 184 " --> pdb=" O HISLN 181 " (cutoff:3.500A) Processing helix chain 'LN' and resid 187 through 196 Processing helix chain 'LO' and resid 15 through 29 Processing helix chain 'LO' and resid 37 through 40 Processing helix chain 'LO' and resid 46 through 60 removed outlier: 3.615A pdb=" N LYSLO 60 " --> pdb=" O ALALO 56 " (cutoff:3.500A) Processing helix chain 'LO' and resid 65 through 69 Processing helix chain 'LO' and resid 75 through 87 removed outlier: 3.608A pdb=" N METLO 87 " --> pdb=" O THRLO 83 " (cutoff:3.500A) Processing helix chain 'LO' and resid 92 through 101 Processing helix chain 'LO' and resid 109 through 114 removed outlier: 4.177A pdb=" N LYSLO 114 " --> pdb=" O PROLO 110 " (cutoff:3.500A) Processing helix chain 'LO' and resid 120 through 123 Processing helix chain 'LO' and resid 124 through 129 Processing helix chain 'LO' and resid 138 through 145 Processing helix chain 'LO' and resid 149 through 185 removed outlier: 3.590A pdb=" N GLULO 162 " --> pdb=" O GLULO 158 " (cutoff:3.500A) Processing helix chain 'LO' and resid 189 through 199 Processing helix chain 'LP' and resid 10 through 12 No H-bonds generated for 'chain 'LP' and resid 10 through 12' Processing helix chain 'LP' and resid 25 through 37 Processing helix chain 'LP' and resid 40 through 53 Processing helix chain 'LP' and resid 70 through 76 Processing helix chain 'LP' and resid 84 through 105 Processing helix chain 'LP' and resid 108 through 110 No H-bonds generated for 'chain 'LP' and resid 108 through 110' Processing helix chain 'LQ' and resid 22 through 39 Processing helix chain 'LQ' and resid 41 through 53 removed outlier: 3.969A pdb=" N GLNLQ 45 " --> pdb=" O SERLQ 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N METLQ 53 " --> pdb=" O LYSLQ 49 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 63 through 71 Processing helix chain 'LQ' and resid 106 through 116 Processing helix chain 'LQ' and resid 122 through 130 removed outlier: 3.557A pdb=" N LEULQ 128 " --> pdb=" O ASPLQ 124 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 147 through 152 removed outlier: 4.088A pdb=" N HISLQ 151 " --> pdb=" O GLULQ 147 " (cutoff:3.500A) Processing helix chain 'LR' and resid 4 through 16 Processing helix chain 'LR' and resid 18 through 20 No H-bonds generated for 'chain 'LR' and resid 18 through 20' Processing helix chain 'LR' and resid 28 through 34 Processing helix chain 'LR' and resid 37 through 48 Processing helix chain 'LR' and resid 60 through 72 Processing helix chain 'LR' and resid 77 through 81 removed outlier: 3.502A pdb=" N ARGLR 81 " --> pdb=" O ILELR 78 " (cutoff:3.500A) Processing helix chain 'LR' and resid 84 through 89 Processing helix chain 'LR' and resid 90 through 112 Processing helix chain 'LR' and resid 116 through 129 Processing helix chain 'LR' and resid 134 through 156 Processing helix chain 'LS' and resid 36 through 52 Processing helix chain 'LS' and resid 55 through 57 No H-bonds generated for 'chain 'LS' and resid 55 through 57' Processing helix chain 'LS' and resid 101 through 118 Processing helix chain 'LS' and resid 120 through 122 No H-bonds generated for 'chain 'LS' and resid 120 through 122' Processing helix chain 'LS' and resid 133 through 137 Processing helix chain 'LS' and resid 139 through 144 Processing helix chain 'LT' and resid 27 through 32 removed outlier: 3.517A pdb=" N ARGLT 32 " --> pdb=" O ALALT 28 " (cutoff:3.500A) Processing helix chain 'LT' and resid 54 through 58 Processing helix chain 'LT' and resid 99 through 123 removed outlier: 3.628A pdb=" N ASPLT 103 " --> pdb=" O SERLT 99 " (cutoff:3.500A) Processing helix chain 'LU' and resid 25 through 32 Processing helix chain 'LU' and resid 35 through 47 Processing helix chain 'LU' and resid 55 through 60 Processing helix chain 'LU' and resid 79 through 94 removed outlier: 3.845A pdb=" N LEULU 83 " --> pdb=" O SERLU 79 " (cutoff:3.500A) Processing helix chain 'LV' and resid 69 through 73 Processing helix chain 'LV' and resid 122 through 129 removed outlier: 3.581A pdb=" N LEULV 128 " --> pdb=" O GLULV 124 " (cutoff:3.500A) Processing helix chain 'LV' and resid 129 through 136 removed outlier: 3.511A pdb=" N ASNLV 135 " --> pdb=" O ARGLV 131 " (cutoff:3.500A) Processing helix chain 'LW' and resid 33 through 42 Processing helix chain 'LW' and resid 45 through 49 Processing helix chain 'LW' and resid 52 through 60 Processing helix chain 'LX' and resid 72 through 76 Processing helix chain 'LX' and resid 83 through 93 Processing helix chain 'LX' and resid 105 through 118 Processing helix chain 'LX' and resid 145 through 154 Processing helix chain 'LY' and resid 10 through 20 Processing helix chain 'LY' and resid 22 through 30 removed outlier: 4.098A pdb=" N LYSLY 28 " --> pdb=" O HISLY 24 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 100 through 102 No H-bonds generated for 'chain 'LY' and resid 100 through 102' Processing helix chain 'LY' and resid 112 through 134 Processing helix chain 'LZ' and resid 58 through 66 Processing helix chain 'LZ' and resid 97 through 102 removed outlier: 3.849A pdb=" N PHELZ 101 " --> pdb=" O LYSLZ 98 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARGLZ 102 " --> pdb=" O ASPLZ 99 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 103 through 123 Processing helix chain 'LZ' and resid 124 through 126 No H-bonds generated for 'chain 'LZ' and resid 124 through 126' Processing helix chain 'La' and resid 2 through 5 Processing helix chain 'La' and resid 6 through 12 removed outlier: 3.962A pdb=" N LYSLa 10 " --> pdb=" O ARGLa 6 " (cutoff:3.500A) Processing helix chain 'La' and resid 41 through 49 Processing helix chain 'La' and resid 77 through 82 Processing helix chain 'La' and resid 83 through 93 Processing helix chain 'La' and resid 103 through 107 Processing helix chain 'La' and resid 130 through 140 Processing helix chain 'Lb' and resid 11 through 19 removed outlier: 4.276A pdb=" N ASNLb 19 " --> pdb=" O LYSLb 15 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 36 through 49 Processing helix chain 'Lb' and resid 50 through 52 No H-bonds generated for 'chain 'Lb' and resid 50 through 52' Processing helix chain 'Lb' and resid 53 through 75 removed outlier: 3.567A pdb=" N LYSLb 73 " --> pdb=" O ALALb 69 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 91 through 101 Processing helix chain 'Lb' and resid 105 through 118 removed outlier: 3.520A pdb=" N ARGLb 117 " --> pdb=" O ALALb 113 " (cutoff:3.500A) Processing helix chain 'Lc' and resid 10 through 25 Processing helix chain 'Lc' and resid 30 through 40 Processing helix chain 'Lc' and resid 53 through 68 Processing helix chain 'Lc' and resid 77 through 85 Processing helix chain 'Ld' and resid 29 through 33 Processing helix chain 'Ld' and resid 37 through 39 No H-bonds generated for 'chain 'Ld' and resid 37 through 39' Processing helix chain 'Ld' and resid 40 through 57 Processing helix chain 'Ld' and resid 65 through 73 Processing helix chain 'Le' and resid 57 through 61 Processing helix chain 'Le' and resid 63 through 67 removed outlier: 3.701A pdb=" N LYSLe 67 " --> pdb=" O LYSLe 64 " (cutoff:3.500A) Processing helix chain 'Le' and resid 81 through 86 Processing helix chain 'Le' and resid 87 through 89 No H-bonds generated for 'chain 'Le' and resid 87 through 89' Processing helix chain 'Le' and resid 104 through 119 removed outlier: 3.881A pdb=" N ALALe 110 " --> pdb=" O LYSLe 106 " (cutoff:3.500A) Processing helix chain 'Lf' and resid 35 through 40 removed outlier: 3.804A pdb=" N GLULf 40 " --> pdb=" O ASPLf 37 " (cutoff:3.500A) Processing helix chain 'Lf' and resid 93 through 97 Processing helix chain 'Lg' and resid 15 through 18 Processing helix chain 'Lg' and resid 60 through 67 Processing helix chain 'Lg' and resid 68 through 73 removed outlier: 3.907A pdb=" N HISLg 73 " --> pdb=" O THRLg 70 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 83 through 114 removed outlier: 3.740A pdb=" N GLNLg 114 " --> pdb=" O GLNLg 110 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 5 through 10 Processing helix chain 'Lh' and resid 13 through 37 Processing helix chain 'Lh' and resid 40 through 74 removed outlier: 3.652A pdb=" N ILELh 47 " --> pdb=" O LYSLh 43 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARGLh 48 " --> pdb=" O LEULh 44 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VALLh 49 " --> pdb=" O SERLh 45 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 80 through 84 Processing helix chain 'Lh' and resid 88 through 93 Processing helix chain 'Lh' and resid 96 through 101 Processing helix chain 'Lh' and resid 104 through 114 Processing helix chain 'Li' and resid 25 through 30 Processing helix chain 'Li' and resid 34 through 49 Processing helix chain 'Li' and resid 51 through 64 Processing helix chain 'Li' and resid 65 through 78 Processing helix chain 'Li' and resid 79 through 103 Processing helix chain 'Lj' and resid 4 through 9 removed outlier: 3.848A pdb=" N GLYLj 9 " --> pdb=" O THRLj 5 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.654A pdb=" N ASNLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 66 through 75 removed outlier: 3.751A pdb=" N ARGLj 75 " --> pdb=" O TYRLj 71 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 7 through 16 Processing helix chain 'Lk' and resid 49 through 59 Processing helix chain 'Ll' and resid 6 through 20 Processing helix chain 'Ll' and resid 24 through 30 removed outlier: 3.518A pdb=" N ARGLl 28 " --> pdb=" O GLNLl 25 " (cutoff:3.500A) Processing helix chain 'Lm' and resid 79 through 91 removed outlier: 3.797A pdb=" N TYRLm 89 " --> pdb=" O LEULm 85 " (cutoff:3.500A) Processing helix chain 'Lo' and resid 35 through 46 Processing helix chain 'Lp' and resid 8 through 15 removed outlier: 3.757A pdb=" N LYSLp 13 " --> pdb=" O ILELp 10 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 19 through 35 removed outlier: 3.923A pdb=" N LYSLp 28 " --> pdb=" O LYSLp 24 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILELp 29 " --> pdb=" O METLp 25 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 73 through 91 Processing helix chain 'Lr' and resid 3 through 11 Processing helix chain 'Lr' and resid 72 through 75 Processing helix chain 'Lr' and resid 85 through 101 removed outlier: 3.691A pdb=" N ASNLr 100 " --> pdb=" O METLr 96 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 103 through 105 No H-bonds generated for 'chain 'Lr' and resid 103 through 105' Processing helix chain 'Lr' and resid 106 through 122 Processing helix chain 'Lz' and resid 6 through 21 removed outlier: 3.905A pdb=" N ALALz 13 " --> pdb=" O THRLz 9 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASNLz 21 " --> pdb=" O VALLz 17 " (cutoff:3.500A) Processing helix chain 'Lz' and resid 22 through 25 removed outlier: 3.651A pdb=" N ARGLz 25 " --> pdb=" O GLNLz 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lz' and resid 22 through 25' Processing helix chain 'Lz' and resid 70 through 80 Processing helix chain 'Lz' and resid 86 through 93 removed outlier: 4.016A pdb=" N LEULz 93 " --> pdb=" O ALALz 89 " (cutoff:3.500A) Processing helix chain 'Lz' and resid 96 through 107 removed outlier: 3.626A pdb=" N TYRLz 107 " --> pdb=" O LEULz 103 " (cutoff:3.500A) Processing helix chain 'Lz' and resid 114 through 118 removed outlier: 4.394A pdb=" N LYSLz 118 " --> pdb=" O GLULz 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lz' and resid 114 through 118' Processing helix chain 'Lz' and resid 119 through 124 Processing helix chain 'Lz' and resid 126 through 132 Processing helix chain 'Lz' and resid 143 through 153 Processing helix chain 'Lz' and resid 175 through 194 removed outlier: 4.238A pdb=" N TYRLz 181 " --> pdb=" O ASPLz 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.643A pdb=" N ILE A 57 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'A' and resid 201 through 202 removed outlier: 3.631A pdb=" N THR A 201 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 10 removed outlier: 5.652A pdb=" N ILE B 9 " --> pdb=" O ASN B 500 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 197 through 202 removed outlier: 3.733A pdb=" N VAL C 197 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL D 20 " --> pdb=" O GLU C 199 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLU C 201 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N TYR D 18 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 228 through 230 Processing sheet with id=AB1, first strand: chain 'D' and resid 48 through 51 Processing sheet with id=AB2, first strand: chain 'LA' and resid 71 through 77 removed outlier: 3.559A pdb=" N ASPLA 47 " --> pdb=" O LYSLA 60 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VALLA 62 " --> pdb=" O VALLA 45 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VALLA 45 " --> pdb=" O VALLA 62 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ARGLA 64 " --> pdb=" O GLYLA 43 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N GLYLA 43 " --> pdb=" O ARGLA 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'LA' and resid 101 through 103 removed outlier: 6.596A pdb=" N ARGLA 147 " --> pdb=" O ILELA 137 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N HISLA 139 " --> pdb=" O LYSLA 145 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYSLA 145 " --> pdb=" O HISLA 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'LA' and resid 224 through 225 Processing sheet with id=AB5, first strand: chain 'LB' and resid 42 through 43 removed outlier: 4.835A pdb=" N ILELB 160 " --> pdb=" O VALLB 185 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VALLB 159 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLYLB 91 " --> pdb=" O VALLB 159 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARGLB 161 " --> pdb=" O ILELB 89 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILELB 89 " --> pdb=" O ARGLB 161 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILELB 163 " --> pdb=" O VALLB 87 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYSLB 103 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VALLB 93 " --> pdb=" O THRLB 101 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N THRLB 101 " --> pdb=" O VALLB 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'LB' and resid 42 through 43 removed outlier: 4.835A pdb=" N ILELB 160 " --> pdb=" O VALLB 185 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VALLB 159 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLYLB 91 " --> pdb=" O VALLB 159 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARGLB 161 " --> pdb=" O ILELB 89 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILELB 89 " --> pdb=" O ARGLB 161 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILELB 163 " --> pdb=" O VALLB 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'LB' and resid 365 through 368 removed outlier: 6.447A pdb=" N VALLB 57 " --> pdb=" O LYSLB 366 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILELB 368 " --> pdb=" O HISLB 55 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N HISLB 55 " --> pdb=" O ILELB 368 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N VALLB 344 " --> pdb=" O VALLB 222 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VALLB 222 " --> pdb=" O VALLB 344 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VALLB 219 " --> pdb=" O ILELB 280 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILELB 280 " --> pdb=" O VALLB 219 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLYLB 221 " --> pdb=" O THRLB 278 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N THRLB 278 " --> pdb=" O GLYLB 221 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILELB 284 " --> pdb=" O LYSLB 334 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYSLB 334 " --> pdb=" O ILELB 284 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLYLB 52 " --> pdb=" O ILELB 78 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLULB 80 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LYSLB 50 " --> pdb=" O GLULB 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'LB' and resid 225 through 229 removed outlier: 5.740A pdb=" N LYSLB 272 " --> pdb=" O LYSLB 226 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYRLB 228 " --> pdb=" O GLYLB 270 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLYLB 270 " --> pdb=" O TYRLB 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'LB' and resid 292 through 293 Processing sheet with id=AC1, first strand: chain 'LC' and resid 17 through 23 removed outlier: 4.711A pdb=" N LYSLC 20 " --> pdb=" O VALLC 10 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VALLC 153 " --> pdb=" O SERLC 9 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEULC 152 " --> pdb=" O TRPLC 252 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N CYSLC 208 " --> pdb=" O ILELC 251 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THRLC 253 " --> pdb=" O CYSLC 208 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILELC 210 " --> pdb=" O THRLC 253 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILELC 209 " --> pdb=" O LEULC 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'LC' and resid 64 through 66 Processing sheet with id=AC3, first strand: chain 'LC' and resid 188 through 189 Processing sheet with id=AC4, first strand: chain 'LD' and resid 73 through 79 removed outlier: 5.744A pdb=" N ILELD 74 " --> pdb=" O TYRLD 66 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYRLD 66 " --> pdb=" O ILELD 74 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYSLD 76 " --> pdb=" O ILELD 64 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N METLD 51 " --> pdb=" O ASPLD 147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'LD' and resid 183 through 184 Processing sheet with id=AC6, first strand: chain 'LE' and resid 49 through 51 removed outlier: 3.571A pdb=" N VALLE 51 " --> pdb=" O ILELE 54 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'LE' and resid 91 through 95 Processing sheet with id=AC8, first strand: chain 'LE' and resid 187 through 189 removed outlier: 6.548A pdb=" N THRLE 176 " --> pdb=" O PHELE 164 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N PHELE 164 " --> pdb=" O THRLE 176 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THRLE 148 " --> pdb=" O PHELE 164 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILELE 149 " --> pdb=" O THRLE 197 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'LF' and resid 81 through 83 removed outlier: 3.532A pdb=" N HISLT 139 " --> pdb=" O VALLF 83 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'LF' and resid 211 through 212 removed outlier: 4.197A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILELF 140 " --> pdb=" O GLYLF 234 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'LF' and resid 159 through 162 Processing sheet with id=AD3, first strand: chain 'LG' and resid 75 through 76 Processing sheet with id=AD4, first strand: chain 'LG' and resid 137 through 138 removed outlier: 6.352A pdb=" N VALLG 155 " --> pdb=" O CYSLG 182 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILELG 184 " --> pdb=" O VALLG 155 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILELG 157 " --> pdb=" O ILELG 184 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'LH' and resid 3 through 11 removed outlier: 6.943A pdb=" N ILELH 4 " --> pdb=" O TRPLH 61 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARGLH 54 " --> pdb=" O LEULH 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'LH' and resid 17 through 21 removed outlier: 3.506A pdb=" N THRLH 24 " --> pdb=" O LYSLH 21 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'LH' and resid 132 through 136 removed outlier: 6.847A pdb=" N ARGLH 89 " --> pdb=" O LYSLH 184 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYSLH 184 " --> pdb=" O ARGLH 89 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LYSLH 91 " --> pdb=" O SERLH 182 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'LH' and resid 103 through 106 Processing sheet with id=AD9, first strand: chain 'LI' and resid 35 through 37 removed outlier: 6.627A pdb=" N METLI 52 " --> pdb=" O ILELI 135 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SERLI 137 " --> pdb=" O GLYLI 50 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLYLI 50 " --> pdb=" O SERLI 137 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARGLI 139 " --> pdb=" O LEULI 48 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEULI 48 " --> pdb=" O ARGLI 139 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'LI' and resid 58 through 61 removed outlier: 6.714A pdb=" N ILELI 97 " --> pdb=" O GLNLI 123 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THRLI 125 " --> pdb=" O HISLI 95 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N HISLI 95 " --> pdb=" O THRLI 125 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'LI' and resid 190 through 193 Processing sheet with id=AE3, first strand: chain 'LJ' and resid 49 through 52 removed outlier: 6.925A pdb=" N VALLJ 133 " --> pdb=" O ARGLJ 18 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEULJ 20 " --> pdb=" O TYRLJ 131 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYRLJ 131 " --> pdb=" O LEULJ 20 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEULJ 22 " --> pdb=" O ASPLJ 129 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASPLJ 129 " --> pdb=" O LEULJ 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'LJ' and resid 93 through 95 removed outlier: 6.706A pdb=" N LEULJ 94 " --> pdb=" O LEULJ 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'LL' and resid 22 through 24 Processing sheet with id=AE6, first strand: chain 'LL' and resid 58 through 60 Processing sheet with id=AE7, first strand: chain 'LL' and resid 124 through 126 Processing sheet with id=AE8, first strand: chain 'LL' and resid 167 through 168 Processing sheet with id=AE9, first strand: chain 'LM' and resid 7 through 8 Processing sheet with id=AF1, first strand: chain 'LM' and resid 45 through 51 removed outlier: 5.255A pdb=" N ARGLM 46 " --> pdb=" O GLYLM 40 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N GLYLM 40 " --> pdb=" O ARGLM 46 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASPLM 39 " --> pdb=" O ILELM 27 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILELM 27 " --> pdb=" O ASPLM 39 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARGLM 11 " --> pdb=" O ILELM 27 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VALLM 12 " --> pdb=" O THRLM 58 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'LN' and resid 36 through 39 removed outlier: 4.381A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYRLN 127 " --> pdb=" O GLULN 123 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLULN 123 " --> pdb=" O TYRLN 127 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHELN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILELN 135 " --> pdb=" O VALLN 115 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VALLN 115 " --> pdb=" O ILELN 135 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'LO' and resid 6 through 10 removed outlier: 6.181A pdb=" N LEULO 7 " --> pdb=" O VALLO 34 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VALLO 36 " --> pdb=" O LEULO 7 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEULO 9 " --> pdb=" O VALLO 36 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'LO' and resid 42 through 44 Processing sheet with id=AF5, first strand: chain 'LP' and resid 14 through 22 removed outlier: 3.928A pdb=" N ASNLP 21 " --> pdb=" O CYSLP 144 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N CYSLP 144 " --> pdb=" O ASNLP 21 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THRLP 151 " --> pdb=" O ILELP 114 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILELP 114 " --> pdb=" O THRLP 151 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'LP' and resid 58 through 59 Processing sheet with id=AF7, first strand: chain 'LP' and resid 126 through 131 removed outlier: 3.659A pdb=" N ARGLP 135 " --> pdb=" O ARGLP 131 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'LQ' and resid 61 through 62 removed outlier: 3.972A pdb=" N LEULQ 103 " --> pdb=" O VALLQ 82 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLYLQ 84 " --> pdb=" O LEULQ 103 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VALLQ 105 " --> pdb=" O GLYLQ 84 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILELQ 86 " --> pdb=" O VALLQ 105 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'LQ' and resid 61 through 62 removed outlier: 6.342A pdb=" N THRLQ 79 " --> pdb=" O VALLQ 137 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'LQ' and resid 180 through 181 removed outlier: 3.569A pdb=" N TYRLQ 186 " --> pdb=" O ARGLQ 181 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'LR' and resid 22 through 24 Processing sheet with id=AG3, first strand: chain 'LS' and resid 59 through 66 removed outlier: 5.468A pdb=" N ILELS 61 " --> pdb=" O ARGLS 15 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARGLS 15 " --> pdb=" O ILELS 61 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'LS' and resid 90 through 99 removed outlier: 6.667A pdb=" N ARGLS 83 " --> pdb=" O ILELS 126 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ILELS 126 " --> pdb=" O ARGLS 83 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASPLS 85 " --> pdb=" O ILELS 124 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILELS 124 " --> pdb=" O ASPLS 85 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'LT' and resid 84 through 92 removed outlier: 6.300A pdb=" N VALLT 75 " --> pdb=" O VALLT 64 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VALLT 64 " --> pdb=" O VALLT 75 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ASNLT 77 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLYLT 62 " --> pdb=" O ASNLT 77 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'LU' and resid 61 through 66 removed outlier: 6.654A pdb=" N SERLU 109 " --> pdb=" O ASNLU 105 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'LU' and resid 48 through 49 Processing sheet with id=AG8, first strand: chain 'LV' and resid 20 through 21 Processing sheet with id=AG9, first strand: chain 'LV' and resid 25 through 28 removed outlier: 6.770A pdb=" N METLV 62 " --> pdb=" O ILELV 40 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VALLV 42 " --> pdb=" O METLV 60 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N METLV 60 " --> pdb=" O VALLV 42 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALALV 102 " --> pdb=" O ILELV 82 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N GLYLV 103 " --> pdb=" O VALLV 25 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASNLV 27 " --> pdb=" O GLYLV 103 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILELV 105 " --> pdb=" O ASNLV 27 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'LV' and resid 88 through 89 removed outlier: 6.358A pdb=" N PHELV 95 " --> pdb=" O ARGLW 20 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ALALW 22 " --> pdb=" O PHELV 95 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYRLV 97 " --> pdb=" O ALALW 22 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'LV' and resid 120 through 121 Processing sheet with id=AH3, first strand: chain 'LW' and resid 4 through 5 removed outlier: 3.535A pdb=" N GLULW 4 " --> pdb=" O ILELW 13 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'LX' and resid 77 through 80 removed outlier: 3.919A pdb=" N LYSLX 134 " --> pdb=" O VALLX 100 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYSLX 123 " --> pdb=" O ARGLX 139 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'LY' and resid 31 through 33 Processing sheet with id=AH6, first strand: chain 'LY' and resid 79 through 82 removed outlier: 6.847A pdb=" N VALLY 79 " --> pdb=" O VALLY 73 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N VALLY 73 " --> pdb=" O VALLY 79 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYRLY 81 " --> pdb=" O VALLY 71 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLULY 54 " --> pdb=" O THRLY 107 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'LY' and resid 86 through 88 Processing sheet with id=AH8, first strand: chain 'LZ' and resid 69 through 76 removed outlier: 6.442A pdb=" N LYSLZ 69 " --> pdb=" O ASPLZ 47 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N HISLZ 40 " --> pdb=" O ASNLZ 28 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASNLZ 28 " --> pdb=" O HISLZ 40 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEULZ 42 " --> pdb=" O VALLZ 26 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LYSLZ 22 " --> pdb=" O ILELZ 46 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYSLZ 9 " --> pdb=" O ILELZ 25 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VALLZ 10 " --> pdb=" O THRLZ 83 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'La' and resid 72 through 74 removed outlier: 6.401A pdb=" N VALLa 73 " --> pdb=" O LEULa 112 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'La' and resid 100 through 102 removed outlier: 6.365A pdb=" N VALLa 124 " --> pdb=" O VALLa 145 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Lc' and resid 26 through 29 removed outlier: 6.309A pdb=" N LYSLc 26 " --> pdb=" O ILELc 97 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VALLc 46 " --> pdb=" O HISLc 72 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Ld' and resid 62 through 64 removed outlier: 6.753A pdb=" N ARGLd 63 " --> pdb=" O VALLd 106 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N TYRLd 108 " --> pdb=" O ARGLd 63 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Le' and resid 75 through 79 Processing sheet with id=AI5, first strand: chain 'Lf' and resid 6 through 16 removed outlier: 5.683A pdb=" N PHELf 11 " --> pdb=" O LYSLf 29 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYSLf 29 " --> pdb=" O PHELf 11 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THRLf 25 " --> pdb=" O LYSLf 15 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N HISLf 24 " --> pdb=" O PHELf 88 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N PHELf 88 " --> pdb=" O HISLf 24 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYSLf 87 " --> pdb=" O VALLf 74 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VALLf 74 " --> pdb=" O LYSLf 87 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLYLf 62 " --> pdb=" O THRLf 57 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N THRLf 57 " --> pdb=" O GLYLf 62 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N ASNLf 55 " --> pdb=" O PROLf 64 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYSLf 66 " --> pdb=" O ALALf 53 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARGLf 46 " --> pdb=" O METLf 104 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VALLf 50 " --> pdb=" O ARGLf 100 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARGLf 100 " --> pdb=" O VALLf 50 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Lg' and resid 20 through 24 Processing sheet with id=AI7, first strand: chain 'Lj' and resid 16 through 17 Processing sheet with id=AI8, first strand: chain 'Lk' and resid 3 through 5 removed outlier: 4.482A pdb=" N VALLk 46 " --> pdb=" O ILELk 5 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SERLk 22 " --> pdb=" O ARGLk 37 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VALLk 23 " --> pdb=" O LYSLk 67 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Lm' and resid 102 through 103 Processing sheet with id=AJ1, first strand: chain 'Lo' and resid 3 through 4 Processing sheet with id=AJ2, first strand: chain 'Lo' and resid 7 through 12 removed outlier: 3.507A pdb=" N LYSLo 17 " --> pdb=" O CYSLo 12 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILELo 66 " --> pdb=" O ILELo 85 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Lp' and resid 47 through 51 removed outlier: 5.280A pdb=" N ARGLp 49 " --> pdb=" O HISLp 56 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N HISLp 56 " --> pdb=" O ARGLp 49 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Lr' and resid 17 through 20 Processing sheet with id=AJ5, first strand: chain 'Lr' and resid 49 through 53 Processing sheet with id=AJ6, first strand: chain 'Lz' and resid 164 through 171 removed outlier: 6.477A pdb=" N CYSLz 164 " --> pdb=" O LEULz 38 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEULz 38 " --> pdb=" O CYSLz 164 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALALz 166 " --> pdb=" O ILELz 36 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILELz 36 " --> pdb=" O ALALz 166 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ALALz 168 " --> pdb=" O LEULz 34 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEULz 34 " --> pdb=" O ALALz 168 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Lz' and resid 50 through 54 Processing sheet with id=AJ8, first strand: chain 'Lz' and resid 65 through 68 removed outlier: 3.864A pdb=" N SERLz 113 " --> pdb=" O LEULz 68 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHELz 110 " --> pdb=" O SERLz 136 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEULz 138 " --> pdb=" O PHELz 110 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALALz 112 " --> pdb=" O LEULz 138 " (cutoff:3.500A) 2936 hydrogen bonds defined for protein. 8295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2964 hydrogen bonds 5100 hydrogen bond angles 0 basepair planarities 1151 basepair parallelities 2121 stacking parallelities Total time for adding SS restraints: 335.22 Time building geometry restraints manager: 64.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 31912 1.34 - 1.46: 53882 1.46 - 1.58: 61759 1.58 - 1.70: 7455 1.70 - 1.82: 446 Bond restraints: 155454 Sorted by residual: bond pdb=" N ILE A 664 " pdb=" CA ILE A 664 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 6.93e+00 bond pdb=" N GLYLN 2 " pdb=" CA GLYLN 2 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.45e+00 bond pdb=" N GLYLZ 2 " pdb=" CA GLYLZ 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.32e+00 bond pdb=" N GLYLD 2 " pdb=" CA GLYLD 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.30e+00 bond pdb=" N GLYLI 2 " pdb=" CA GLYLI 2 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.02e+00 ... (remaining 155449 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.53: 23287 106.53 - 113.40: 90125 113.40 - 120.26: 56626 120.26 - 127.13: 49469 127.13 - 134.00: 8422 Bond angle restraints: 227929 Sorted by residual: angle pdb=" N VALLR 131 " pdb=" CA VALLR 131 " pdb=" C VALLR 131 " ideal model delta sigma weight residual 112.96 109.44 3.52 1.00e+00 1.00e+00 1.24e+01 angle pdb=" CB LYSLR 144 " pdb=" CG LYSLR 144 " pdb=" CD LYSLR 144 " ideal model delta sigma weight residual 111.30 118.97 -7.67 2.30e+00 1.89e-01 1.11e+01 angle pdb=" N GLN A 670 " pdb=" CA GLN A 670 " pdb=" C GLN A 670 " ideal model delta sigma weight residual 113.50 109.55 3.95 1.23e+00 6.61e-01 1.03e+01 angle pdb=" CB LYSLb 63 " pdb=" CG LYSLb 63 " pdb=" CD LYSLb 63 " ideal model delta sigma weight residual 111.30 118.30 -7.00 2.30e+00 1.89e-01 9.25e+00 angle pdb=" CB METLz 144 " pdb=" CG METLz 144 " pdb=" SD METLz 144 " ideal model delta sigma weight residual 112.70 121.71 -9.01 3.00e+00 1.11e-01 9.03e+00 ... (remaining 227924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 89829 35.92 - 71.84: 9195 71.84 - 107.76: 1206 107.76 - 143.68: 7 143.68 - 179.60: 5 Dihedral angle restraints: 100242 sinusoidal: 77054 harmonic: 23188 Sorted by residual: dihedral pdb=" O4' C 8 1 " pdb=" C1' C 8 1 " pdb=" N1 C 8 1 " pdb=" C2 C 8 1 " ideal model delta sinusoidal sigma weight residual -160.00 -13.12 -146.88 1 1.50e+01 4.44e-03 7.84e+01 dihedral pdb=" O4' C 5 704 " pdb=" C1' C 5 704 " pdb=" N1 C 5 704 " pdb=" C2 C 5 704 " ideal model delta sinusoidal sigma weight residual -128.00 51.60 -179.60 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 54512 " pdb=" C1' U 54512 " pdb=" N1 U 54512 " pdb=" C2 U 54512 " ideal model delta sinusoidal sigma weight residual -128.00 50.08 -178.08 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 100239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 27768 0.098 - 0.197: 503 0.197 - 0.295: 0 0.295 - 0.394: 0 0.394 - 0.492: 6 Chirality restraints: 28277 Sorted by residual: chirality pdb=" P G 51769 " pdb=" OP1 G 51769 " pdb=" OP2 G 51769 " pdb=" O5' G 51769 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" P C 51768 " pdb=" OP1 C 51768 " pdb=" OP2 C 51768 " pdb=" O5' C 51768 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" P A 51766 " pdb=" OP1 A 51766 " pdb=" OP2 A 51766 " pdb=" O5' A 51766 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.75e+00 ... (remaining 28274 not shown) Planarity restraints: 14917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HISLU 27 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PROLU 28 " -0.108 5.00e-02 4.00e+02 pdb=" CA PROLU 28 " 0.032 5.00e-02 4.00e+02 pdb=" CD PROLU 28 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARGLB 358 " 0.207 9.50e-02 1.11e+02 9.27e-02 5.56e+00 pdb=" NE ARGLB 358 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARGLB 358 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARGLB 358 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARGLB 358 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SERLd 98 " 0.031 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PROLd 99 " -0.083 5.00e-02 4.00e+02 pdb=" CA PROLd 99 " 0.024 5.00e-02 4.00e+02 pdb=" CD PROLd 99 " 0.027 5.00e-02 4.00e+02 ... (remaining 14914 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 647 2.45 - 3.06: 86107 3.06 - 3.67: 252292 3.67 - 4.29: 401812 4.29 - 4.90: 563250 Nonbonded interactions: 1304108 Sorted by model distance: nonbonded pdb=" O2' G 51316 " pdb="MG MG 55124 " model vdw 1.833 2.170 nonbonded pdb=" OP2 C 53791 " pdb="MG MG 55301 " model vdw 1.839 2.170 nonbonded pdb=" OP1 U 51622 " pdb="MG MG 55257 " model vdw 1.853 2.170 nonbonded pdb=" O6 G 5 21 " pdb="MG MG 8 201 " model vdw 1.863 2.170 nonbonded pdb=" OE1 GLNLj 30 " pdb="MG MG 55306 " model vdw 1.864 2.170 ... (remaining 1304103 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 5.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 24.430 Check model and map are aligned: 1.630 Set scattering table: 1.030 Process input model: 631.650 Find NCS groups from input model: 3.440 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: 0.020 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 680.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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 : 0.002 0.045 155454 Z= 0.099 Angle : 0.327 9.014 227929 Z= 0.176 Chirality : 0.028 0.492 28277 Planarity : 0.002 0.093 14917 Dihedral : 22.004 179.601 85264 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.43 % Favored : 98.56 % Rotamer: Outliers : 0.39 % Allowed : 13.98 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.10), residues: 7890 helix: 2.82 (0.09), residues: 3221 sheet: 0.83 (0.17), residues: 1001 loop : 0.86 (0.11), residues: 3668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPLj 49 HIS 0.002 0.000 HISLD 81 PHE 0.009 0.001 PHE A 560 TYR 0.007 0.001 TYRLo 34 ARG 0.009 0.000 ARGLB 358 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 783 time to evaluate : 8.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 MET cc_start: 0.5988 (mmm) cc_final: 0.4891 (mmm) REVERT: B 185 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.6746 (t70) REVERT: LC 1 MET cc_start: 0.4122 (ppp) cc_final: 0.3475 (ttp) REVERT: LJ 158 SER cc_start: 0.8724 (p) cc_final: 0.8459 (t) REVERT: LO 180 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8240 (tp40) REVERT: LP 151 THR cc_start: 0.8776 (m) cc_final: 0.8543 (p) REVERT: LR 36 ASN cc_start: 0.8278 (p0) cc_final: 0.7967 (m-40) REVERT: LV 73 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7401 (mtp85) REVERT: LV 138 SER cc_start: 0.7575 (t) cc_final: 0.7168 (p) REVERT: LZ 81 MET cc_start: 0.9357 (tpt) cc_final: 0.9134 (tpp) REVERT: Lb 98 TYR cc_start: 0.8731 (t80) cc_final: 0.8500 (t80) REVERT: Lc 31 TYR cc_start: 0.8909 (t80) cc_final: 0.8644 (t80) REVERT: Lh 20 GLN cc_start: 0.8913 (tt0) cc_final: 0.8625 (tp40) REVERT: Lp 59 SER cc_start: 0.8728 (t) cc_final: 0.8384 (m) outliers start: 27 outliers final: 16 residues processed: 803 average time/residue: 2.0433 time to fit residues: 2401.2198 Evaluate side-chains 670 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 653 time to evaluate : 7.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain LA residue 208 GLU Chi-restraints excluded: chain LB residue 362 LYS Chi-restraints excluded: chain LD residue 109 LEU Chi-restraints excluded: chain LQ residue 14 ARG Chi-restraints excluded: chain LS residue 48 VAL Chi-restraints excluded: chain LT residue 99 SER Chi-restraints excluded: chain LZ residue 89 ILE Chi-restraints excluded: chain Lb residue 66 SER Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lz residue 28 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 972 optimal weight: 9.9990 chunk 873 optimal weight: 20.0000 chunk 484 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 588 optimal weight: 8.9990 chunk 466 optimal weight: 20.0000 chunk 902 optimal weight: 20.0000 chunk 349 optimal weight: 10.0000 chunk 549 optimal weight: 20.0000 chunk 672 optimal weight: 9.9990 chunk 1046 optimal weight: 5.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 549 ASN A 668 HIS A 695 GLN B 140 GLN B 465 GLN ** LB 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 245 GLN LF 110 GLN LG 38 ASN LG 64 GLN LG 149 ASN LG 225 ASN LL 188 ASN LP 10 ASN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 8 ASN LT 112 ASN LT 127 GLN LT 131 GLN LT 144 ASN LU 27 HIS LX 57 GLN ** LX 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 93 ASN LX 94 ASN LY 14 ASN ** LY 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lb 60 ASN Lc 40 GLN Ld 93 ASN Lg 3 GLN Lh 65 GLN Lh 107 GLN Li 12 ASN Lo 102 GLN Lz 84 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 155454 Z= 0.387 Angle : 0.620 10.481 227929 Z= 0.319 Chirality : 0.040 0.250 28277 Planarity : 0.005 0.050 14917 Dihedral : 22.465 179.219 68303 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.08 % Favored : 97.88 % Rotamer: Outliers : 2.32 % Allowed : 14.29 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.10), residues: 7890 helix: 2.12 (0.09), residues: 3242 sheet: 0.51 (0.16), residues: 1004 loop : 0.44 (0.10), residues: 3644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPLj 49 HIS 0.010 0.002 HISLE 128 PHE 0.035 0.002 PHE A 666 TYR 0.020 0.002 TYRLQ 32 ARG 0.008 0.001 ARGLN 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 684 time to evaluate : 7.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 661 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: LB 356 LYS cc_start: 0.8539 (mttt) cc_final: 0.8175 (mttp) REVERT: LC 1 MET cc_start: 0.3907 (ppp) cc_final: 0.3525 (ttp) REVERT: LD 109 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8483 (mt) REVERT: LI 187 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8381 (tptp) REVERT: LJ 65 ASN cc_start: 0.8140 (t0) cc_final: 0.7617 (t0) REVERT: LJ 158 SER cc_start: 0.8670 (p) cc_final: 0.8435 (t) REVERT: LM 125 ASN cc_start: 0.8563 (t0) cc_final: 0.8299 (m110) REVERT: LO 180 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8238 (tp40) REVERT: LV 138 SER cc_start: 0.7703 (t) cc_final: 0.7362 (p) REVERT: LW 47 ARG cc_start: 0.8585 (mtt90) cc_final: 0.8379 (mtt90) REVERT: LX 145 ASP cc_start: 0.8285 (t0) cc_final: 0.7932 (t0) REVERT: LZ 112 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7440 (tpp-160) REVERT: Lb 30 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: Lb 58 GLN cc_start: 0.8106 (pt0) cc_final: 0.7879 (pm20) REVERT: Lb 98 TYR cc_start: 0.8795 (t80) cc_final: 0.8549 (t80) REVERT: Ld 112 THR cc_start: 0.9192 (p) cc_final: 0.8893 (t) REVERT: Ld 118 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7978 (mt0) REVERT: Le 83 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8366 (tmmt) REVERT: Lh 20 GLN cc_start: 0.9007 (tt0) cc_final: 0.8572 (tp40) REVERT: Lp 59 SER cc_start: 0.8800 (t) cc_final: 0.8387 (m) REVERT: Lr 52 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: Lr 56 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6612 (p0) outliers start: 160 outliers final: 55 residues processed: 784 average time/residue: 2.1051 time to fit residues: 2405.2814 Evaluate side-chains 708 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 644 time to evaluate : 7.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain LC residue 189 MET Chi-restraints excluded: chain LD residue 109 LEU Chi-restraints excluded: chain LD residue 136 ASP Chi-restraints excluded: chain LD residue 262 LYS Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LI residue 187 LYS Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 188 ARG Chi-restraints excluded: chain LP residue 110 ASP Chi-restraints excluded: chain LQ residue 14 ARG Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LR residue 30 ASN Chi-restraints excluded: chain LS residue 48 VAL Chi-restraints excluded: chain LT residue 52 MET Chi-restraints excluded: chain LT residue 127 GLN Chi-restraints excluded: chain LT residue 143 THR Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 73 THR Chi-restraints excluded: chain LU residue 98 ASP Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 41 LEU Chi-restraints excluded: chain LX residue 85 SER Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LY residue 105 VAL Chi-restraints excluded: chain LY residue 125 SER Chi-restraints excluded: chain LZ residue 112 ARG Chi-restraints excluded: chain Lb residue 30 GLU Chi-restraints excluded: chain Lb residue 54 LEU Chi-restraints excluded: chain Lc residue 55 LEU Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Ld residue 106 VAL Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 83 LYS Chi-restraints excluded: chain Le residue 123 THR Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 57 THR Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Lh residue 116 LEU Chi-restraints excluded: chain Li residue 18 THR Chi-restraints excluded: chain Li residue 63 VAL Chi-restraints excluded: chain Lk residue 13 LEU Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Lp residue 26 VAL Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 52 GLU Chi-restraints excluded: chain Lr residue 56 ASP Chi-restraints excluded: chain Lz residue 28 PHE Chi-restraints excluded: chain Lz residue 87 ILE Chi-restraints excluded: chain Lz residue 117 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 581 optimal weight: 5.9990 chunk 324 optimal weight: 20.0000 chunk 870 optimal weight: 10.0000 chunk 712 optimal weight: 9.9990 chunk 288 optimal weight: 10.0000 chunk 1048 optimal weight: 20.0000 chunk 1132 optimal weight: 20.0000 chunk 933 optimal weight: 8.9990 chunk 1039 optimal weight: 5.9990 chunk 357 optimal weight: 10.0000 chunk 840 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 GLN A 724 GLN B 418 GLN C 247 ASN ** LB 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 245 GLN LE 250 GLN LF 39 GLN LG 38 ASN LG 43 GLN LG 225 ASN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 112 ASN LU 27 HIS LU 55 ASN ** LX 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lc 40 GLN Ld 93 ASN Lg 3 GLN Lh 107 GLN Lo 102 GLN Lr 83 ASN Lz 84 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 155454 Z= 0.363 Angle : 0.597 11.682 227929 Z= 0.308 Chirality : 0.039 0.246 28277 Planarity : 0.005 0.063 14917 Dihedral : 22.517 178.519 68286 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.74 % Rotamer: Outliers : 2.84 % Allowed : 14.93 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.09), residues: 7890 helix: 1.78 (0.09), residues: 3237 sheet: 0.24 (0.16), residues: 1011 loop : 0.18 (0.10), residues: 3642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPLN 120 HIS 0.008 0.001 HISLE 128 PHE 0.023 0.002 PHELU 42 TYR 0.021 0.002 TYRLc 74 ARG 0.008 0.001 ARGLI 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 680 time to evaluate : 8.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.4974 (OUTLIER) cc_final: 0.4497 (mtp180) REVERT: A 661 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: LA 44 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8875 (tp) REVERT: LB 356 LYS cc_start: 0.8583 (mttt) cc_final: 0.8251 (mttp) REVERT: LB 378 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8021 (mtt180) REVERT: LC 1 MET cc_start: 0.3622 (ppp) cc_final: 0.3355 (ttp) REVERT: LD 214 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: LG 130 THR cc_start: 0.4947 (OUTLIER) cc_final: 0.4466 (t) REVERT: LG 257 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7484 (ptpt) REVERT: LI 187 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8373 (tptp) REVERT: LJ 65 ASN cc_start: 0.8161 (t0) cc_final: 0.7563 (t0) REVERT: LN 161 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8458 (mtt) REVERT: LN 193 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7625 (ttm110) REVERT: LO 174 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8688 (mt) REVERT: LO 180 GLN cc_start: 0.8658 (tp-100) cc_final: 0.8270 (tp40) REVERT: LV 48 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7816 (ttp80) REVERT: LV 138 SER cc_start: 0.7796 (t) cc_final: 0.7525 (p) REVERT: LZ 112 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8564 (tpt170) REVERT: La 92 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8259 (tmmt) REVERT: Lb 30 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: Ld 118 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7895 (mt0) REVERT: Le 83 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8330 (tmmt) REVERT: Lh 20 GLN cc_start: 0.8989 (tt0) cc_final: 0.8474 (tp40) REVERT: Li 58 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8851 (mtm) REVERT: Ll 21 ARG cc_start: 0.7842 (ttp-170) cc_final: 0.7586 (ttp-170) REVERT: Lr 52 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8212 (pt0) REVERT: Lr 56 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6296 (p0) REVERT: Lz 144 MET cc_start: 0.7479 (pmm) cc_final: 0.6734 (ttp) outliers start: 196 outliers final: 74 residues processed: 813 average time/residue: 2.1688 time to fit residues: 2559.4601 Evaluate side-chains 737 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 643 time to evaluate : 7.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 711 GLN Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain LA residue 44 ILE Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 378 ARG Chi-restraints excluded: chain LC residue 189 MET Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LD residue 109 LEU Chi-restraints excluded: chain LD residue 136 ASP Chi-restraints excluded: chain LD residue 214 GLU Chi-restraints excluded: chain LD residue 262 LYS Chi-restraints excluded: chain LD residue 267 ASN Chi-restraints excluded: chain LE residue 93 THR Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LG residue 130 THR Chi-restraints excluded: chain LG residue 257 LYS Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LI residue 187 LYS Chi-restraints excluded: chain LJ residue 57 VAL Chi-restraints excluded: chain LN residue 161 MET Chi-restraints excluded: chain LN residue 182 HIS Chi-restraints excluded: chain LN residue 188 ARG Chi-restraints excluded: chain LN residue 193 ARG Chi-restraints excluded: chain LO residue 174 LEU Chi-restraints excluded: chain LQ residue 14 ARG Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LQ residue 126 LEU Chi-restraints excluded: chain LR residue 30 ASN Chi-restraints excluded: chain LR residue 114 LYS Chi-restraints excluded: chain LS residue 48 VAL Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 52 MET Chi-restraints excluded: chain LT residue 99 SER Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LT residue 143 THR Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 73 THR Chi-restraints excluded: chain LU residue 98 ASP Chi-restraints excluded: chain LV residue 48 ARG Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LW residue 41 LEU Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LY residue 105 VAL Chi-restraints excluded: chain LY residue 125 SER Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 112 ARG Chi-restraints excluded: chain La residue 92 LYS Chi-restraints excluded: chain Lb residue 30 GLU Chi-restraints excluded: chain Lb residue 54 LEU Chi-restraints excluded: chain Lc residue 21 VAL Chi-restraints excluded: chain Lc residue 97 ILE Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Ld residue 106 VAL Chi-restraints excluded: chain Ld residue 111 VAL Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 83 LYS Chi-restraints excluded: chain Le residue 123 THR Chi-restraints excluded: chain Lf residue 2 SER Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Lh residue 116 LEU Chi-restraints excluded: chain Li residue 18 THR Chi-restraints excluded: chain Li residue 58 MET Chi-restraints excluded: chain Li residue 63 VAL Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Lm residue 84 GLN Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 52 GLU Chi-restraints excluded: chain Lr residue 56 ASP Chi-restraints excluded: chain Lz residue 11 TYR Chi-restraints excluded: chain Lz residue 24 LYS Chi-restraints excluded: chain Lz residue 28 PHE Chi-restraints excluded: chain Lz residue 58 THR Chi-restraints excluded: chain Lz residue 117 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 1035 optimal weight: 9.9990 chunk 787 optimal weight: 6.9990 chunk 543 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 500 optimal weight: 3.9990 chunk 703 optimal weight: 8.9990 chunk 1051 optimal weight: 6.9990 chunk 1113 optimal weight: 7.9990 chunk 549 optimal weight: 10.0000 chunk 996 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 HIS A 711 GLN ** LB 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 245 GLN LE 250 GLN ** LF 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 38 ASN LG 100 HIS LG 225 ASN LM 33 GLN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 91 HIS LT 112 ASN LT 127 GLN LT 131 GLN LU 27 HIS LU 41 GLN LU 50 ASN LU 55 ASN LV 77 HIS LX 73 HIS LY 14 ASN ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lc 40 GLN Ld 93 ASN Lg 3 GLN Lh 107 GLN Lo 102 GLN Lz 84 HIS ** Lz 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lz 182 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 155454 Z= 0.286 Angle : 0.556 10.750 227929 Z= 0.289 Chirality : 0.037 0.235 28277 Planarity : 0.004 0.052 14917 Dihedral : 22.526 178.296 68286 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.41 % Favored : 97.58 % Rotamer: Outliers : 2.56 % Allowed : 16.38 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 7890 helix: 1.80 (0.09), residues: 3237 sheet: 0.12 (0.16), residues: 1003 loop : 0.13 (0.10), residues: 3650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPLN 120 HIS 0.006 0.001 HISLE 128 PHE 0.023 0.001 PHELk 11 TYR 0.018 0.002 TYRLO 54 ARG 0.007 0.000 ARGLI 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 677 time to evaluate : 8.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.4820 (OUTLIER) cc_final: 0.4367 (mtp180) REVERT: A 652 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6520 (ppp) REVERT: LA 44 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8851 (tp) REVERT: LB 378 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8008 (mtt180) REVERT: LC 1 MET cc_start: 0.3479 (ppp) cc_final: 0.3168 (ttp) REVERT: LC 138 MET cc_start: 0.9093 (mmm) cc_final: 0.8683 (mmt) REVERT: LD 109 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8806 (tp) REVERT: LD 214 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: LE 205 ASN cc_start: 0.8454 (p0) cc_final: 0.8044 (p0) REVERT: LG 130 THR cc_start: 0.4969 (OUTLIER) cc_final: 0.4492 (t) REVERT: LG 257 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7523 (ptpt) REVERT: LH 51 LYS cc_start: 0.6102 (OUTLIER) cc_final: 0.5447 (ptmm) REVERT: LI 187 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8377 (tptp) REVERT: LJ 65 ASN cc_start: 0.8138 (t0) cc_final: 0.7522 (t0) REVERT: LN 193 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7623 (ttm110) REVERT: LO 174 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8682 (mt) REVERT: LO 175 MET cc_start: 0.8833 (tpp) cc_final: 0.8592 (tpp) REVERT: LO 180 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8245 (tp40) REVERT: LQ 14 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8697 (ptt90) REVERT: LQ 147 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: LV 48 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7921 (ttp80) REVERT: LV 138 SER cc_start: 0.7794 (t) cc_final: 0.7541 (p) REVERT: LZ 112 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8528 (tpt170) REVERT: La 92 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8159 (tmmt) REVERT: Lb 30 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: Lc 44 LYS cc_start: 0.8856 (mmtm) cc_final: 0.8560 (mmtm) REVERT: Lc 102 SER cc_start: 0.8718 (t) cc_final: 0.8387 (p) REVERT: Ld 118 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: Lf 103 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8915 (t) REVERT: Lg 102 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8289 (tp) REVERT: Lh 20 GLN cc_start: 0.8966 (tt0) cc_final: 0.8678 (tp40) REVERT: Li 12 ASN cc_start: 0.7904 (m-40) cc_final: 0.7670 (t0) REVERT: Lr 52 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8263 (pt0) REVERT: Lr 56 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6901 (p0) REVERT: Lz 42 ASP cc_start: 0.7703 (t0) cc_final: 0.7273 (t0) outliers start: 177 outliers final: 79 residues processed: 802 average time/residue: 2.1571 time to fit residues: 2512.7608 Evaluate side-chains 733 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 631 time to evaluate : 8.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain LA residue 44 ILE Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 378 ARG Chi-restraints excluded: chain LC residue 69 THR Chi-restraints excluded: chain LC residue 189 MET Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LD residue 64 ILE Chi-restraints excluded: chain LD residue 109 LEU Chi-restraints excluded: chain LD residue 136 ASP Chi-restraints excluded: chain LD residue 214 GLU Chi-restraints excluded: chain LD residue 234 ASP Chi-restraints excluded: chain LD residue 262 LYS Chi-restraints excluded: chain LD residue 267 ASN Chi-restraints excluded: chain LE residue 93 THR Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LG residue 130 THR Chi-restraints excluded: chain LG residue 257 LYS Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 51 LYS Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LI residue 187 LYS Chi-restraints excluded: chain LJ residue 26 VAL Chi-restraints excluded: chain LJ residue 57 VAL Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 182 HIS Chi-restraints excluded: chain LN residue 188 ARG Chi-restraints excluded: chain LN residue 193 ARG Chi-restraints excluded: chain LO residue 174 LEU Chi-restraints excluded: chain LQ residue 14 ARG Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LQ residue 126 LEU Chi-restraints excluded: chain LQ residue 147 GLU Chi-restraints excluded: chain LR residue 30 ASN Chi-restraints excluded: chain LR residue 114 LYS Chi-restraints excluded: chain LS residue 48 VAL Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 52 MET Chi-restraints excluded: chain LT residue 99 SER Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LT residue 127 GLN Chi-restraints excluded: chain LT residue 143 THR Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 49 VAL Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 73 THR Chi-restraints excluded: chain LU residue 98 ASP Chi-restraints excluded: chain LV residue 48 ARG Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LW residue 41 LEU Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LY residue 105 VAL Chi-restraints excluded: chain LY residue 125 SER Chi-restraints excluded: chain LY residue 127 GLN Chi-restraints excluded: chain LZ residue 89 ILE Chi-restraints excluded: chain LZ residue 112 ARG Chi-restraints excluded: chain La residue 92 LYS Chi-restraints excluded: chain Lb residue 30 GLU Chi-restraints excluded: chain Lc residue 21 VAL Chi-restraints excluded: chain Lc residue 97 ILE Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 106 VAL Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Ld residue 122 VAL Chi-restraints excluded: chain Le residue 123 THR Chi-restraints excluded: chain Lf residue 2 SER Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 57 THR Chi-restraints excluded: chain Lf residue 103 VAL Chi-restraints excluded: chain Lg residue 102 ILE Chi-restraints excluded: chain Lh residue 37 THR Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Lh residue 116 LEU Chi-restraints excluded: chain Li residue 18 THR Chi-restraints excluded: chain Lk residue 13 LEU Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 52 GLU Chi-restraints excluded: chain Lr residue 56 ASP Chi-restraints excluded: chain Lr residue 122 LYS Chi-restraints excluded: chain Lr residue 125 MET Chi-restraints excluded: chain Lz residue 11 TYR Chi-restraints excluded: chain Lz residue 24 LYS Chi-restraints excluded: chain Lz residue 28 PHE Chi-restraints excluded: chain Lz residue 87 ILE Chi-restraints excluded: chain Lz residue 117 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 927 optimal weight: 9.9990 chunk 632 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 829 optimal weight: 10.0000 chunk 459 optimal weight: 50.0000 chunk 950 optimal weight: 4.9990 chunk 769 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 568 optimal weight: 9.9990 chunk 999 optimal weight: 40.0000 chunk 280 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 352 GLN C 296 GLN ** LB 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 245 GLN LE 250 GLN ** LF 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 100 HIS LG 225 ASN LH 188 GLN LL 188 ASN LN 8 GLN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 112 ASN LT 127 GLN LU 27 HIS LU 41 GLN LU 50 ASN LU 55 ASN LX 73 HIS LY 14 ASN ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lc 40 GLN Ld 93 ASN Lg 3 GLN Lh 107 GLN Ll 25 GLN Lo 102 GLN Lr 83 ASN Lz 21 ASN Lz 84 HIS ** Lz 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 155454 Z= 0.353 Angle : 0.594 11.642 227929 Z= 0.308 Chirality : 0.039 0.244 28277 Planarity : 0.005 0.054 14917 Dihedral : 22.540 178.535 68285 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.53 % Favored : 97.43 % Rotamer: Outliers : 3.10 % Allowed : 16.64 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.09), residues: 7890 helix: 1.68 (0.09), residues: 3230 sheet: -0.04 (0.16), residues: 1026 loop : 0.02 (0.10), residues: 3634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPLp 55 HIS 0.008 0.001 HISLE 128 PHE 0.024 0.002 PHELk 11 TYR 0.020 0.002 TYRLc 74 ARG 0.008 0.000 ARGLI 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 661 time to evaluate : 8.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.4861 (OUTLIER) cc_final: 0.4361 (mtp180) REVERT: A 652 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6637 (ppp) REVERT: LA 44 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8887 (tp) REVERT: LB 289 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: LB 378 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8027 (mtt180) REVERT: LC 1 MET cc_start: 0.3467 (ppp) cc_final: 0.3068 (ttp) REVERT: LD 214 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: LE 110 ARG cc_start: 0.5968 (mmm160) cc_final: 0.4171 (ttm110) REVERT: LE 205 ASN cc_start: 0.8496 (p0) cc_final: 0.8108 (p0) REVERT: LG 130 THR cc_start: 0.4991 (OUTLIER) cc_final: 0.4499 (t) REVERT: LG 257 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7518 (ptpt) REVERT: LH 51 LYS cc_start: 0.6061 (OUTLIER) cc_final: 0.5435 (ptmm) REVERT: LJ 65 ASN cc_start: 0.8123 (t0) cc_final: 0.7472 (t0) REVERT: LM 125 ASN cc_start: 0.8718 (m110) cc_final: 0.8143 (m110) REVERT: LN 193 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7664 (ttm110) REVERT: LO 174 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8686 (mt) REVERT: LO 175 MET cc_start: 0.8859 (tpp) cc_final: 0.8603 (tpp) REVERT: LO 180 GLN cc_start: 0.8657 (tp-100) cc_final: 0.8294 (tp40) REVERT: LQ 14 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8635 (ptt90) REVERT: LQ 147 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: LU 40 GLU cc_start: 0.8251 (tt0) cc_final: 0.7931 (tm-30) REVERT: LV 48 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7857 (ttp80) REVERT: LV 138 SER cc_start: 0.7830 (t) cc_final: 0.7589 (p) REVERT: LW 48 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8534 (mt0) REVERT: LZ 112 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8590 (tpt170) REVERT: La 92 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8308 (tmmt) REVERT: Lb 30 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: Lc 42 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8567 (ptpp) REVERT: Lc 44 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8578 (mmtm) REVERT: Lc 102 SER cc_start: 0.8771 (t) cc_final: 0.8416 (p) REVERT: Ld 118 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7871 (mt0) REVERT: Lh 4 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8303 (mm) REVERT: Lh 20 GLN cc_start: 0.8975 (tt0) cc_final: 0.8445 (tp40) REVERT: Li 12 ASN cc_start: 0.7894 (m-40) cc_final: 0.7672 (t0) REVERT: Lr 52 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8236 (pt0) REVERT: Lr 56 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.6977 (p0) REVERT: Lz 87 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7605 (mt) REVERT: Lz 144 MET cc_start: 0.7747 (pmm) cc_final: 0.7344 (ttp) outliers start: 214 outliers final: 98 residues processed: 810 average time/residue: 2.1331 time to fit residues: 2529.3995 Evaluate side-chains 751 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 630 time to evaluate : 7.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain C residue 156 TRP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain LA residue 44 ILE Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 119 LYS Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 289 GLN Chi-restraints excluded: chain LB residue 378 ARG Chi-restraints excluded: chain LC residue 69 THR Chi-restraints excluded: chain LC residue 189 MET Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LD residue 136 ASP Chi-restraints excluded: chain LD residue 214 GLU Chi-restraints excluded: chain LD residue 262 LYS Chi-restraints excluded: chain LD residue 267 ASN Chi-restraints excluded: chain LE residue 93 THR Chi-restraints excluded: chain LE residue 281 ILE Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LG residue 70 LEU Chi-restraints excluded: chain LG residue 130 THR Chi-restraints excluded: chain LG residue 257 LYS Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 51 LYS Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 189 GLN Chi-restraints excluded: chain LJ residue 26 VAL Chi-restraints excluded: chain LJ residue 57 VAL Chi-restraints excluded: chain LN residue 34 SER Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 182 HIS Chi-restraints excluded: chain LN residue 188 ARG Chi-restraints excluded: chain LN residue 193 ARG Chi-restraints excluded: chain LO residue 174 LEU Chi-restraints excluded: chain LQ residue 14 ARG Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LQ residue 126 LEU Chi-restraints excluded: chain LQ residue 147 GLU Chi-restraints excluded: chain LR residue 30 ASN Chi-restraints excluded: chain LR residue 114 LYS Chi-restraints excluded: chain LS residue 12 VAL Chi-restraints excluded: chain LS residue 48 VAL Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 4 THR Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 99 SER Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LT residue 143 THR Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 49 VAL Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 63 ILE Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 73 THR Chi-restraints excluded: chain LU residue 98 ASP Chi-restraints excluded: chain LV residue 48 ARG Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LW residue 41 LEU Chi-restraints excluded: chain LW residue 48 GLN Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LY residue 105 VAL Chi-restraints excluded: chain LY residue 125 SER Chi-restraints excluded: chain LY residue 127 GLN Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 89 ILE Chi-restraints excluded: chain LZ residue 112 ARG Chi-restraints excluded: chain La residue 92 LYS Chi-restraints excluded: chain Lb residue 30 GLU Chi-restraints excluded: chain Lb residue 54 LEU Chi-restraints excluded: chain Lc residue 21 VAL Chi-restraints excluded: chain Lc residue 46 VAL Chi-restraints excluded: chain Lc residue 97 ILE Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 106 VAL Chi-restraints excluded: chain Ld residue 111 VAL Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 123 THR Chi-restraints excluded: chain Lf residue 2 SER Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 57 THR Chi-restraints excluded: chain Lg residue 87 VAL Chi-restraints excluded: chain Lg residue 103 VAL Chi-restraints excluded: chain Lh residue 4 ILE Chi-restraints excluded: chain Lh residue 37 THR Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Lh residue 116 LEU Chi-restraints excluded: chain Lh residue 121 VAL Chi-restraints excluded: chain Li residue 18 THR Chi-restraints excluded: chain Lj residue 2 THR Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Lo residue 2 VAL Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 52 GLU Chi-restraints excluded: chain Lr residue 56 ASP Chi-restraints excluded: chain Lr residue 122 LYS Chi-restraints excluded: chain Lz residue 11 TYR Chi-restraints excluded: chain Lz residue 24 LYS Chi-restraints excluded: chain Lz residue 28 PHE Chi-restraints excluded: chain Lz residue 87 ILE Chi-restraints excluded: chain Lz residue 117 ILE Chi-restraints excluded: chain Lz residue 139 THR Chi-restraints excluded: chain Lz residue 210 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 374 optimal weight: 0.9990 chunk 1002 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 653 optimal weight: 9.9990 chunk 274 optimal weight: 10.0000 chunk 1114 optimal weight: 7.9990 chunk 925 optimal weight: 10.0000 chunk 516 optimal weight: 5.9990 chunk 92 optimal weight: 40.0000 chunk 368 optimal weight: 10.0000 chunk 585 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN ** LB 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 245 GLN LE 250 GLN LF 39 GLN LG 100 HIS LG 225 ASN LH 188 GLN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 112 ASN LT 127 GLN LU 27 HIS LU 41 GLN LU 50 ASN LU 55 ASN LX 73 HIS ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lb 60 ASN Lc 40 GLN Ld 93 ASN Lg 3 GLN Lh 107 GLN Ll 25 GLN Lo 102 GLN Lz 44 GLN ** Lz 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 155454 Z= 0.302 Angle : 0.565 10.788 227929 Z= 0.293 Chirality : 0.037 0.235 28277 Planarity : 0.004 0.052 14917 Dihedral : 22.549 178.423 68283 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 2.71 % Allowed : 17.55 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.09), residues: 7890 helix: 1.73 (0.09), residues: 3234 sheet: -0.08 (0.16), residues: 1010 loop : 0.00 (0.10), residues: 3646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPLN 120 HIS 0.008 0.001 HIS D 70 PHE 0.021 0.001 PHELk 11 TYR 0.019 0.002 TYRLc 74 ARG 0.009 0.000 ARGLI 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 652 time to evaluate : 8.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.4898 (OUTLIER) cc_final: 0.4416 (mtp180) REVERT: A 652 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6739 (ppp) REVERT: B 358 MET cc_start: 0.4539 (ptp) cc_final: 0.4191 (mtm) REVERT: LA 44 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8876 (tp) REVERT: LB 248 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8807 (pp) REVERT: LB 289 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: LB 378 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8011 (mtt180) REVERT: LC 1 MET cc_start: 0.3477 (ppp) cc_final: 0.3113 (ttp) REVERT: LD 214 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: LE 110 ARG cc_start: 0.5739 (mmm160) cc_final: 0.4349 (ttm110) REVERT: LE 205 ASN cc_start: 0.8476 (p0) cc_final: 0.8120 (p0) REVERT: LF 29 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7702 (ttmm) REVERT: LG 130 THR cc_start: 0.4992 (OUTLIER) cc_final: 0.4459 (t) REVERT: LG 257 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7534 (ptpt) REVERT: LH 138 GLN cc_start: 0.8402 (mm-40) cc_final: 0.8052 (mm110) REVERT: LM 125 ASN cc_start: 0.8719 (m110) cc_final: 0.8123 (m110) REVERT: LN 193 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7623 (ttm110) REVERT: LO 174 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8681 (mt) REVERT: LO 175 MET cc_start: 0.8855 (tpp) cc_final: 0.8591 (tpp) REVERT: LQ 14 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8645 (ptt90) REVERT: LQ 147 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: LU 40 GLU cc_start: 0.8246 (tt0) cc_final: 0.7869 (tm-30) REVERT: LV 48 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7905 (ttp80) REVERT: LV 138 SER cc_start: 0.7771 (t) cc_final: 0.7550 (p) REVERT: LZ 39 SER cc_start: 0.9397 (m) cc_final: 0.9192 (m) REVERT: LZ 112 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8553 (tpt170) REVERT: La 92 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8275 (tmmt) REVERT: Lb 30 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: Lc 42 LYS cc_start: 0.8763 (mtpt) cc_final: 0.8562 (ptpp) REVERT: Lc 44 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8565 (mmtm) REVERT: Lc 65 MET cc_start: 0.9014 (tmm) cc_final: 0.8708 (tmm) REVERT: Lc 102 SER cc_start: 0.8757 (t) cc_final: 0.8404 (p) REVERT: Ld 118 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7868 (mt0) REVERT: Le 83 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8363 (tmmt) REVERT: Lh 20 GLN cc_start: 0.8952 (tt0) cc_final: 0.8673 (tp40) REVERT: Lr 56 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7039 (p0) REVERT: Lr 125 MET cc_start: 0.7252 (ptp) cc_final: 0.6924 (ppp) REVERT: Lz 87 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7688 (mt) REVERT: Lz 144 MET cc_start: 0.7781 (pmm) cc_final: 0.7538 (ttp) outliers start: 187 outliers final: 99 residues processed: 786 average time/residue: 2.1401 time to fit residues: 2439.1024 Evaluate side-chains 753 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 632 time to evaluate : 7.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain C residue 156 TRP Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain LA residue 44 ILE Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 106 THR Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 248 LEU Chi-restraints excluded: chain LB residue 289 GLN Chi-restraints excluded: chain LB residue 378 ARG Chi-restraints excluded: chain LC residue 69 THR Chi-restraints excluded: chain LC residue 189 MET Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LD residue 136 ASP Chi-restraints excluded: chain LD residue 214 GLU Chi-restraints excluded: chain LD residue 234 ASP Chi-restraints excluded: chain LD residue 262 LYS Chi-restraints excluded: chain LD residue 267 ASN Chi-restraints excluded: chain LE residue 93 THR Chi-restraints excluded: chain LF residue 29 LYS Chi-restraints excluded: chain LF residue 39 GLN Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LG residue 130 THR Chi-restraints excluded: chain LG residue 257 LYS Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 24 THR Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 189 GLN Chi-restraints excluded: chain LJ residue 26 VAL Chi-restraints excluded: chain LJ residue 57 VAL Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 182 HIS Chi-restraints excluded: chain LN residue 188 ARG Chi-restraints excluded: chain LN residue 193 ARG Chi-restraints excluded: chain LO residue 174 LEU Chi-restraints excluded: chain LP residue 100 SER Chi-restraints excluded: chain LQ residue 14 ARG Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LQ residue 126 LEU Chi-restraints excluded: chain LQ residue 147 GLU Chi-restraints excluded: chain LR residue 114 LYS Chi-restraints excluded: chain LS residue 12 VAL Chi-restraints excluded: chain LS residue 48 VAL Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 4 THR Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 99 SER Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LT residue 143 THR Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 49 VAL Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 73 THR Chi-restraints excluded: chain LU residue 98 ASP Chi-restraints excluded: chain LV residue 48 ARG Chi-restraints excluded: chain LV residue 73 ARG Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 2 LYS Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LW residue 41 LEU Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LY residue 105 VAL Chi-restraints excluded: chain LY residue 125 SER Chi-restraints excluded: chain LY residue 127 GLN Chi-restraints excluded: chain LZ residue 89 ILE Chi-restraints excluded: chain LZ residue 112 ARG Chi-restraints excluded: chain La residue 92 LYS Chi-restraints excluded: chain Lb residue 30 GLU Chi-restraints excluded: chain Lc residue 21 VAL Chi-restraints excluded: chain Lc residue 46 VAL Chi-restraints excluded: chain Lc residue 97 ILE Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 106 VAL Chi-restraints excluded: chain Ld residue 111 VAL Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 83 LYS Chi-restraints excluded: chain Le residue 123 THR Chi-restraints excluded: chain Lf residue 2 SER Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 57 THR Chi-restraints excluded: chain Lg residue 87 VAL Chi-restraints excluded: chain Lg residue 103 VAL Chi-restraints excluded: chain Lh residue 37 THR Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Lh residue 116 LEU Chi-restraints excluded: chain Lj residue 2 THR Chi-restraints excluded: chain Lk residue 13 LEU Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Lo residue 2 VAL Chi-restraints excluded: chain Lo residue 103 VAL Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 52 GLU Chi-restraints excluded: chain Lr residue 56 ASP Chi-restraints excluded: chain Lr residue 122 LYS Chi-restraints excluded: chain Lz residue 11 TYR Chi-restraints excluded: chain Lz residue 28 PHE Chi-restraints excluded: chain Lz residue 65 VAL Chi-restraints excluded: chain Lz residue 87 ILE Chi-restraints excluded: chain Lz residue 117 ILE Chi-restraints excluded: chain Lz residue 139 THR Chi-restraints excluded: chain Lz residue 200 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 1074 optimal weight: 10.0000 chunk 125 optimal weight: 50.0000 chunk 635 optimal weight: 5.9990 chunk 813 optimal weight: 10.0000 chunk 630 optimal weight: 3.9990 chunk 938 optimal weight: 5.9990 chunk 622 optimal weight: 20.0000 chunk 1110 optimal weight: 1.9990 chunk 694 optimal weight: 0.0270 chunk 676 optimal weight: 3.9990 chunk 512 optimal weight: 4.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 245 GLN LE 250 GLN LG 100 HIS LG 225 ASN LH 188 GLN LL 188 ASN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 112 ASN LT 127 GLN LU 27 HIS LU 41 GLN LU 50 ASN LU 55 ASN LX 73 HIS LY 14 ASN ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lc 40 GLN Ld 93 ASN Lg 3 GLN Lh 107 GLN Ll 25 GLN Lo 102 GLN Lz 84 HIS ** Lz 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 155454 Z= 0.161 Angle : 0.515 13.183 227929 Z= 0.271 Chirality : 0.034 0.217 28277 Planarity : 0.004 0.055 14917 Dihedral : 22.588 178.679 68283 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.32 % Favored : 97.66 % Rotamer: Outliers : 2.38 % Allowed : 18.22 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.09), residues: 7890 helix: 1.85 (0.09), residues: 3236 sheet: 0.01 (0.16), residues: 1009 loop : 0.05 (0.10), residues: 3645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPLj 49 HIS 0.007 0.001 HISLG 100 PHE 0.030 0.001 PHE B 363 TYR 0.018 0.001 TYRLO 54 ARG 0.011 0.000 ARGLI 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 657 time to evaluate : 8.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.4902 (OUTLIER) cc_final: 0.4433 (mtp180) REVERT: A 652 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6709 (ppp) REVERT: B 358 MET cc_start: 0.4485 (ptp) cc_final: 0.4164 (mtm) REVERT: LB 248 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8765 (pp) REVERT: LB 289 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: LB 378 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8007 (mtt180) REVERT: LC 1 MET cc_start: 0.3439 (ppp) cc_final: 0.3154 (ttp) REVERT: LC 138 MET cc_start: 0.9144 (mmm) cc_final: 0.8739 (mmt) REVERT: LD 214 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: LE 110 ARG cc_start: 0.5748 (mmm160) cc_final: 0.4373 (ttm110) REVERT: LE 205 ASN cc_start: 0.8455 (p0) cc_final: 0.8093 (p0) REVERT: LF 29 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7787 (ttmm) REVERT: LG 130 THR cc_start: 0.4951 (OUTLIER) cc_final: 0.4432 (t) REVERT: LG 257 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7545 (ptpt) REVERT: LH 51 LYS cc_start: 0.5996 (OUTLIER) cc_final: 0.5401 (ptmm) REVERT: LN 193 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7562 (ttm110) REVERT: LO 174 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8669 (mt) REVERT: LO 175 MET cc_start: 0.8825 (tpp) cc_final: 0.8552 (tpp) REVERT: LQ 14 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8668 (ptt90) REVERT: LQ 147 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: LT 121 GLU cc_start: 0.8647 (pp20) cc_final: 0.8386 (pp20) REVERT: LU 40 GLU cc_start: 0.8233 (tt0) cc_final: 0.7868 (tm-30) REVERT: LV 48 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7917 (ttp80) REVERT: LV 138 SER cc_start: 0.7764 (t) cc_final: 0.7550 (p) REVERT: LZ 112 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8573 (tpt170) REVERT: La 92 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8221 (tmmt) REVERT: Lb 30 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: Lc 102 SER cc_start: 0.8764 (t) cc_final: 0.8415 (p) REVERT: Ld 118 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: Le 83 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8327 (tmmt) REVERT: Lh 20 GLN cc_start: 0.8920 (tt0) cc_final: 0.8488 (tp40) REVERT: Lr 56 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7021 (p0) REVERT: Lr 125 MET cc_start: 0.7251 (ptp) cc_final: 0.6923 (ppp) REVERT: Lz 87 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7746 (mt) REVERT: Lz 144 MET cc_start: 0.7790 (pmm) cc_final: 0.7571 (ttp) outliers start: 164 outliers final: 86 residues processed: 777 average time/residue: 2.1852 time to fit residues: 2474.8842 Evaluate side-chains 739 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 631 time to evaluate : 8.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain C residue 156 TRP Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 106 THR Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 248 LEU Chi-restraints excluded: chain LB residue 289 GLN Chi-restraints excluded: chain LB residue 378 ARG Chi-restraints excluded: chain LC residue 189 MET Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LD residue 136 ASP Chi-restraints excluded: chain LD residue 214 GLU Chi-restraints excluded: chain LD residue 234 ASP Chi-restraints excluded: chain LD residue 262 LYS Chi-restraints excluded: chain LD residue 267 ASN Chi-restraints excluded: chain LE residue 93 THR Chi-restraints excluded: chain LF residue 29 LYS Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LG residue 130 THR Chi-restraints excluded: chain LG residue 257 LYS Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 51 LYS Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LJ residue 26 VAL Chi-restraints excluded: chain LJ residue 57 VAL Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 34 SER Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 182 HIS Chi-restraints excluded: chain LN residue 193 ARG Chi-restraints excluded: chain LO residue 174 LEU Chi-restraints excluded: chain LQ residue 14 ARG Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LQ residue 126 LEU Chi-restraints excluded: chain LQ residue 147 GLU Chi-restraints excluded: chain LR residue 30 ASN Chi-restraints excluded: chain LR residue 114 LYS Chi-restraints excluded: chain LR residue 117 ARG Chi-restraints excluded: chain LS residue 48 VAL Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 99 SER Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LT residue 143 THR Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 49 VAL Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 73 THR Chi-restraints excluded: chain LU residue 98 ASP Chi-restraints excluded: chain LV residue 48 ARG Chi-restraints excluded: chain LV residue 73 ARG Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 2 LYS Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 41 LEU Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LY residue 105 VAL Chi-restraints excluded: chain LZ residue 112 ARG Chi-restraints excluded: chain La residue 92 LYS Chi-restraints excluded: chain Lb residue 30 GLU Chi-restraints excluded: chain Lc residue 21 VAL Chi-restraints excluded: chain Lc residue 46 VAL Chi-restraints excluded: chain Lc residue 97 ILE Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 106 VAL Chi-restraints excluded: chain Ld residue 111 VAL Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 83 LYS Chi-restraints excluded: chain Le residue 123 THR Chi-restraints excluded: chain Lf residue 2 SER Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 105 LEU Chi-restraints excluded: chain Lg residue 87 VAL Chi-restraints excluded: chain Lk residue 13 LEU Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 2 VAL Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 52 GLU Chi-restraints excluded: chain Lr residue 56 ASP Chi-restraints excluded: chain Lr residue 122 LYS Chi-restraints excluded: chain Lz residue 11 TYR Chi-restraints excluded: chain Lz residue 24 LYS Chi-restraints excluded: chain Lz residue 28 PHE Chi-restraints excluded: chain Lz residue 65 VAL Chi-restraints excluded: chain Lz residue 87 ILE Chi-restraints excluded: chain Lz residue 117 ILE Chi-restraints excluded: chain Lz residue 139 THR Chi-restraints excluded: chain Lz residue 165 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 686 optimal weight: 9.9990 chunk 443 optimal weight: 0.8980 chunk 663 optimal weight: 1.9990 chunk 334 optimal weight: 20.0000 chunk 218 optimal weight: 30.0000 chunk 215 optimal weight: 10.0000 chunk 705 optimal weight: 7.9990 chunk 756 optimal weight: 8.9990 chunk 548 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 872 optimal weight: 4.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 HIS ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 245 GLN LE 250 GLN LG 100 HIS LG 225 ASN LH 188 GLN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 112 ASN LT 127 GLN LU 27 HIS LU 41 GLN LU 50 ASN LU 55 ASN LX 73 HIS LY 14 ASN ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lb 60 ASN ** Lc 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 24 HIS Lg 3 GLN Li 12 ASN Lo 102 GLN ** Lz 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 155454 Z= 0.238 Angle : 0.531 11.649 227929 Z= 0.277 Chirality : 0.035 0.225 28277 Planarity : 0.004 0.076 14917 Dihedral : 22.526 178.302 68283 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.52 % Rotamer: Outliers : 2.14 % Allowed : 18.62 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.09), residues: 7890 helix: 1.86 (0.09), residues: 3230 sheet: -0.05 (0.16), residues: 1005 loop : 0.03 (0.10), residues: 3655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPLN 120 HIS 0.007 0.001 HISLG 100 PHE 0.027 0.001 PHELk 11 TYR 0.018 0.001 TYRLO 54 ARG 0.012 0.000 ARGLI 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 649 time to evaluate : 8.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.4934 (OUTLIER) cc_final: 0.4440 (mtp180) REVERT: A 652 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6890 (ppp) REVERT: LA 44 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8856 (tp) REVERT: LB 248 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8811 (pp) REVERT: LB 289 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8124 (tm-30) REVERT: LB 378 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7995 (mtt180) REVERT: LC 1 MET cc_start: 0.3454 (ppp) cc_final: 0.3113 (ttp) REVERT: LC 138 MET cc_start: 0.9120 (mmm) cc_final: 0.8722 (mmt) REVERT: LD 214 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: LE 110 ARG cc_start: 0.5726 (mmm160) cc_final: 0.4509 (ttm110) REVERT: LE 205 ASN cc_start: 0.8432 (p0) cc_final: 0.8071 (p0) REVERT: LF 29 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7816 (ttmm) REVERT: LF 39 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7942 (mt0) REVERT: LG 130 THR cc_start: 0.4946 (OUTLIER) cc_final: 0.4428 (t) REVERT: LN 193 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7609 (ttm110) REVERT: LO 173 GLN cc_start: 0.8382 (tp40) cc_final: 0.7692 (tp40) REVERT: LO 174 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8656 (mt) REVERT: LO 175 MET cc_start: 0.8841 (tpp) cc_final: 0.8555 (tpp) REVERT: LQ 14 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8704 (ptt90) REVERT: LQ 147 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: LT 121 GLU cc_start: 0.8672 (pp20) cc_final: 0.8455 (pp20) REVERT: LU 40 GLU cc_start: 0.8245 (tt0) cc_final: 0.7886 (tm-30) REVERT: LV 48 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7927 (ttp80) REVERT: LV 138 SER cc_start: 0.7784 (t) cc_final: 0.7566 (p) REVERT: LZ 112 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8586 (tpt170) REVERT: La 92 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8253 (tmmt) REVERT: Lb 30 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: Lb 54 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7691 (pt) REVERT: Lc 102 SER cc_start: 0.8768 (t) cc_final: 0.8418 (p) REVERT: Ld 54 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8157 (mtm) REVERT: Ld 118 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: Le 83 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8363 (tmmt) REVERT: Lh 20 GLN cc_start: 0.8953 (tt0) cc_final: 0.8492 (tp40) REVERT: Lp 61 MET cc_start: 0.8896 (mpp) cc_final: 0.8464 (mpp) REVERT: Lr 56 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.6996 (p0) REVERT: Lr 125 MET cc_start: 0.7315 (ptp) cc_final: 0.6930 (ppp) REVERT: Lz 97 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8349 (ttmt) outliers start: 148 outliers final: 89 residues processed: 758 average time/residue: 2.1475 time to fit residues: 2367.7733 Evaluate side-chains 743 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 630 time to evaluate : 8.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain C residue 156 TRP Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain LA residue 44 ILE Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 106 THR Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 248 LEU Chi-restraints excluded: chain LB residue 289 GLN Chi-restraints excluded: chain LB residue 378 ARG Chi-restraints excluded: chain LC residue 69 THR Chi-restraints excluded: chain LC residue 189 MET Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LD residue 136 ASP Chi-restraints excluded: chain LD residue 214 GLU Chi-restraints excluded: chain LD residue 234 ASP Chi-restraints excluded: chain LD residue 262 LYS Chi-restraints excluded: chain LD residue 267 ASN Chi-restraints excluded: chain LE residue 93 THR Chi-restraints excluded: chain LF residue 29 LYS Chi-restraints excluded: chain LF residue 39 GLN Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LG residue 130 THR Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LJ residue 26 VAL Chi-restraints excluded: chain LJ residue 57 VAL Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 34 SER Chi-restraints excluded: chain LN residue 182 HIS Chi-restraints excluded: chain LN residue 193 ARG Chi-restraints excluded: chain LO residue 174 LEU Chi-restraints excluded: chain LQ residue 14 ARG Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LQ residue 126 LEU Chi-restraints excluded: chain LQ residue 147 GLU Chi-restraints excluded: chain LR residue 30 ASN Chi-restraints excluded: chain LR residue 114 LYS Chi-restraints excluded: chain LS residue 48 VAL Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 52 MET Chi-restraints excluded: chain LT residue 99 SER Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LT residue 143 THR Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 49 VAL Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 73 THR Chi-restraints excluded: chain LU residue 98 ASP Chi-restraints excluded: chain LV residue 48 ARG Chi-restraints excluded: chain LV residue 73 ARG Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 2 LYS Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 41 LEU Chi-restraints excluded: chain LY residue 83 GLU Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LY residue 105 VAL Chi-restraints excluded: chain LZ residue 89 ILE Chi-restraints excluded: chain LZ residue 112 ARG Chi-restraints excluded: chain La residue 92 LYS Chi-restraints excluded: chain Lb residue 30 GLU Chi-restraints excluded: chain Lb residue 54 LEU Chi-restraints excluded: chain Lc residue 21 VAL Chi-restraints excluded: chain Lc residue 35 LEU Chi-restraints excluded: chain Lc residue 46 VAL Chi-restraints excluded: chain Lc residue 97 ILE Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 54 MET Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 106 VAL Chi-restraints excluded: chain Ld residue 111 VAL Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 83 LYS Chi-restraints excluded: chain Le residue 123 THR Chi-restraints excluded: chain Lf residue 2 SER Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 105 LEU Chi-restraints excluded: chain Lg residue 87 VAL Chi-restraints excluded: chain Lh residue 82 ASP Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 2 VAL Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 52 GLU Chi-restraints excluded: chain Lr residue 56 ASP Chi-restraints excluded: chain Lr residue 122 LYS Chi-restraints excluded: chain Lz residue 11 TYR Chi-restraints excluded: chain Lz residue 24 LYS Chi-restraints excluded: chain Lz residue 28 PHE Chi-restraints excluded: chain Lz residue 65 VAL Chi-restraints excluded: chain Lz residue 97 LYS Chi-restraints excluded: chain Lz residue 117 ILE Chi-restraints excluded: chain Lz residue 139 THR Chi-restraints excluded: chain Lz residue 165 LEU Chi-restraints excluded: chain Lz residue 200 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 1010 optimal weight: 0.0670 chunk 1063 optimal weight: 1.9990 chunk 970 optimal weight: 5.9990 chunk 1034 optimal weight: 0.0970 chunk 622 optimal weight: 20.0000 chunk 450 optimal weight: 30.0000 chunk 812 optimal weight: 0.9980 chunk 317 optimal weight: 10.0000 chunk 934 optimal weight: 5.9990 chunk 978 optimal weight: 9.9990 chunk 1031 optimal weight: 9.9990 overall best weight: 1.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 HIS ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 245 GLN LE 250 GLN LG 100 HIS LG 225 ASN LH 188 GLN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 112 ASN LT 127 GLN LU 27 HIS LU 41 GLN LU 50 ASN LU 55 ASN LX 73 HIS LY 14 ASN ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lb 60 ASN ** Lc 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ld 93 ASN Lg 3 GLN Ll 25 GLN Lo 102 GLN ** Lz 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.120 155454 Z= 0.140 Angle : 0.503 14.090 227929 Z= 0.263 Chirality : 0.033 0.247 28277 Planarity : 0.004 0.062 14917 Dihedral : 22.570 178.349 68283 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.74 % Rotamer: Outliers : 1.90 % Allowed : 19.00 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.09), residues: 7890 helix: 1.93 (0.09), residues: 3228 sheet: 0.03 (0.16), residues: 1000 loop : 0.06 (0.10), residues: 3662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPLR 95 HIS 0.013 0.001 HISLz 171 PHE 0.030 0.001 PHE B 363 TYR 0.036 0.001 TYR C 189 ARG 0.013 0.000 ARGLI 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 645 time to evaluate : 8.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ARG cc_start: 0.4931 (OUTLIER) cc_final: 0.4397 (mtp180) REVERT: LB 248 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8760 (pp) REVERT: LB 289 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: LC 1 MET cc_start: 0.3416 (ppp) cc_final: 0.3076 (ttp) REVERT: LC 138 MET cc_start: 0.9088 (mmm) cc_final: 0.8706 (mmt) REVERT: LD 214 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: LE 110 ARG cc_start: 0.5765 (mmm160) cc_final: 0.4540 (ttm110) REVERT: LE 205 ASN cc_start: 0.8427 (p0) cc_final: 0.8054 (p0) REVERT: LF 29 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7820 (ttmm) REVERT: LF 39 GLN cc_start: 0.8185 (tt0) cc_final: 0.7978 (mt0) REVERT: LG 130 THR cc_start: 0.5010 (OUTLIER) cc_final: 0.4494 (t) REVERT: LN 193 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7516 (ttm110) REVERT: LO 173 GLN cc_start: 0.8367 (tp40) cc_final: 0.7687 (tp40) REVERT: LO 174 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8651 (mt) REVERT: LO 175 MET cc_start: 0.8823 (tpp) cc_final: 0.8537 (tpp) REVERT: LQ 14 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8693 (ptt90) REVERT: LT 121 GLU cc_start: 0.8679 (pp20) cc_final: 0.8465 (pp20) REVERT: LU 40 GLU cc_start: 0.8236 (tt0) cc_final: 0.7881 (tm-30) REVERT: LV 48 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8026 (ttp80) REVERT: LV 138 SER cc_start: 0.7716 (t) cc_final: 0.7513 (p) REVERT: LZ 112 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8565 (tpt170) REVERT: La 92 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8223 (tmmt) REVERT: Lb 30 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: Lb 54 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7682 (pt) REVERT: Lc 102 SER cc_start: 0.8769 (t) cc_final: 0.8436 (p) REVERT: Ld 118 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: Le 83 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8301 (tmmt) REVERT: Le 109 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8193 (mmpt) REVERT: Lh 20 GLN cc_start: 0.8897 (tt0) cc_final: 0.8472 (tp40) REVERT: Ll 34 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8236 (mtmt) REVERT: Lr 56 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6977 (p0) REVERT: Lr 125 MET cc_start: 0.7330 (ptp) cc_final: 0.6920 (ppp) REVERT: Lz 184 HIS cc_start: 0.7599 (t-170) cc_final: 0.7367 (t-170) outliers start: 131 outliers final: 78 residues processed: 739 average time/residue: 2.1662 time to fit residues: 2323.9024 Evaluate side-chains 728 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 631 time to evaluate : 8.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 433 ARG Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain C residue 156 TRP Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 106 THR Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 248 LEU Chi-restraints excluded: chain LB residue 289 GLN Chi-restraints excluded: chain LC residue 69 THR Chi-restraints excluded: chain LC residue 189 MET Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LD residue 136 ASP Chi-restraints excluded: chain LD residue 214 GLU Chi-restraints excluded: chain LD residue 234 ASP Chi-restraints excluded: chain LD residue 267 ASN Chi-restraints excluded: chain LE residue 93 THR Chi-restraints excluded: chain LF residue 29 LYS Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LG residue 130 THR Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LJ residue 26 VAL Chi-restraints excluded: chain LJ residue 57 VAL Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 34 SER Chi-restraints excluded: chain LN residue 182 HIS Chi-restraints excluded: chain LN residue 193 ARG Chi-restraints excluded: chain LO residue 174 LEU Chi-restraints excluded: chain LQ residue 14 ARG Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LQ residue 126 LEU Chi-restraints excluded: chain LR residue 30 ASN Chi-restraints excluded: chain LR residue 114 LYS Chi-restraints excluded: chain LS residue 48 VAL Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 99 SER Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 49 VAL Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 73 THR Chi-restraints excluded: chain LU residue 98 ASP Chi-restraints excluded: chain LV residue 48 ARG Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 2 LYS Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LY residue 105 VAL Chi-restraints excluded: chain LZ residue 112 ARG Chi-restraints excluded: chain La residue 92 LYS Chi-restraints excluded: chain Lb residue 30 GLU Chi-restraints excluded: chain Lb residue 54 LEU Chi-restraints excluded: chain Lc residue 21 VAL Chi-restraints excluded: chain Lc residue 46 VAL Chi-restraints excluded: chain Lc residue 97 ILE Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 106 VAL Chi-restraints excluded: chain Ld residue 111 VAL Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 83 LYS Chi-restraints excluded: chain Le residue 109 LYS Chi-restraints excluded: chain Le residue 123 THR Chi-restraints excluded: chain Lf residue 2 SER Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 105 LEU Chi-restraints excluded: chain Lh residue 82 ASP Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain Ll residue 34 LYS Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 52 GLU Chi-restraints excluded: chain Lr residue 56 ASP Chi-restraints excluded: chain Lr residue 122 LYS Chi-restraints excluded: chain Lz residue 11 TYR Chi-restraints excluded: chain Lz residue 24 LYS Chi-restraints excluded: chain Lz residue 28 PHE Chi-restraints excluded: chain Lz residue 65 VAL Chi-restraints excluded: chain Lz residue 117 ILE Chi-restraints excluded: chain Lz residue 139 THR Chi-restraints excluded: chain Lz residue 165 LEU Chi-restraints excluded: chain Lz residue 200 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 679 optimal weight: 8.9990 chunk 1094 optimal weight: 2.9990 chunk 667 optimal weight: 6.9990 chunk 519 optimal weight: 10.0000 chunk 760 optimal weight: 10.0000 chunk 1147 optimal weight: 7.9990 chunk 1056 optimal weight: 7.9990 chunk 913 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 705 optimal weight: 5.9990 chunk 560 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 HIS A 703 HIS ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 245 GLN LE 250 GLN LG 100 HIS LG 225 ASN LH 188 GLN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 112 ASN LT 127 GLN LU 27 HIS LU 41 GLN LU 50 ASN LU 55 ASN LX 73 HIS LY 14 ASN ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lb 60 ASN ** Lc 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lo 102 GLN ** Lz 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 155454 Z= 0.239 Angle : 0.531 12.903 227929 Z= 0.276 Chirality : 0.035 0.237 28277 Planarity : 0.004 0.063 14917 Dihedral : 22.501 178.101 68283 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.53 % Favored : 97.44 % Rotamer: Outliers : 1.74 % Allowed : 19.20 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.09), residues: 7890 helix: 1.89 (0.09), residues: 3229 sheet: -0.04 (0.16), residues: 994 loop : 0.03 (0.10), residues: 3667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPLR 95 HIS 0.013 0.001 HISLz 171 PHE 0.031 0.001 PHELk 11 TYR 0.021 0.001 TYR C 189 ARG 0.013 0.000 ARGLI 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15780 Ramachandran restraints generated. 7890 Oldfield, 0 Emsley, 7890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 636 time to evaluate : 8.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 652 MET cc_start: 0.7467 (pmm) cc_final: 0.7150 (ppp) REVERT: A 701 MET cc_start: 0.5951 (mmm) cc_final: 0.5572 (mmt) REVERT: LB 248 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8801 (pp) REVERT: LC 138 MET cc_start: 0.9101 (mmm) cc_final: 0.8740 (mmt) REVERT: LD 214 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: LE 110 ARG cc_start: 0.5742 (mmm160) cc_final: 0.4589 (ttm110) REVERT: LE 205 ASN cc_start: 0.8427 (p0) cc_final: 0.8055 (p0) REVERT: LF 29 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7852 (ttmm) REVERT: LF 39 GLN cc_start: 0.8216 (tt0) cc_final: 0.7996 (mt0) REVERT: LG 130 THR cc_start: 0.4945 (OUTLIER) cc_final: 0.4406 (t) REVERT: LN 193 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7598 (ttm110) REVERT: LO 174 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8699 (mt) REVERT: LO 175 MET cc_start: 0.8850 (tpp) cc_final: 0.8571 (tpp) REVERT: LU 40 GLU cc_start: 0.8256 (tt0) cc_final: 0.7860 (tm-30) REVERT: LV 48 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7897 (ttp80) REVERT: LV 138 SER cc_start: 0.7776 (t) cc_final: 0.7560 (p) REVERT: LZ 112 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8553 (tpt170) REVERT: La 92 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8261 (tmmt) REVERT: Lb 30 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: Lc 102 SER cc_start: 0.8758 (t) cc_final: 0.8418 (p) REVERT: Ld 118 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7891 (mt0) REVERT: Le 83 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8366 (tmmt) REVERT: Le 109 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8183 (mmpt) REVERT: Lh 20 GLN cc_start: 0.8935 (tt0) cc_final: 0.8461 (tp40) REVERT: Ll 34 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8259 (mtmt) REVERT: Lp 61 MET cc_start: 0.8877 (mpp) cc_final: 0.8412 (mpp) REVERT: Lr 56 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7006 (p0) REVERT: Lr 125 MET cc_start: 0.7295 (ptp) cc_final: 0.6884 (ppp) outliers start: 120 outliers final: 86 residues processed: 725 average time/residue: 2.1678 time to fit residues: 2284.8197 Evaluate side-chains 727 residues out of total 6910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 626 time to evaluate : 8.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain C residue 156 TRP Chi-restraints excluded: chain D residue 52 ASN Chi-restraints excluded: chain LA residue 96 LEU Chi-restraints excluded: chain LA residue 106 THR Chi-restraints excluded: chain LA residue 119 LYS Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 248 LEU Chi-restraints excluded: chain LC residue 69 THR Chi-restraints excluded: chain LC residue 189 MET Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LD residue 136 ASP Chi-restraints excluded: chain LD residue 214 GLU Chi-restraints excluded: chain LD residue 234 ASP Chi-restraints excluded: chain LD residue 262 LYS Chi-restraints excluded: chain LD residue 267 ASN Chi-restraints excluded: chain LE residue 93 THR Chi-restraints excluded: chain LF residue 29 LYS Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LG residue 130 THR Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LJ residue 26 VAL Chi-restraints excluded: chain LJ residue 57 VAL Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 34 SER Chi-restraints excluded: chain LN residue 182 HIS Chi-restraints excluded: chain LN residue 193 ARG Chi-restraints excluded: chain LO residue 174 LEU Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LQ residue 126 LEU Chi-restraints excluded: chain LR residue 30 ASN Chi-restraints excluded: chain LR residue 114 LYS Chi-restraints excluded: chain LS residue 48 VAL Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 99 SER Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 49 VAL Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 73 THR Chi-restraints excluded: chain LU residue 98 ASP Chi-restraints excluded: chain LV residue 48 ARG Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 1 MET Chi-restraints excluded: chain LW residue 2 LYS Chi-restraints excluded: chain LW residue 4 GLU Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LY residue 83 GLU Chi-restraints excluded: chain LY residue 105 VAL Chi-restraints excluded: chain LZ residue 112 ARG Chi-restraints excluded: chain La residue 92 LYS Chi-restraints excluded: chain Lb residue 30 GLU Chi-restraints excluded: chain Lc residue 21 VAL Chi-restraints excluded: chain Lc residue 46 VAL Chi-restraints excluded: chain Lc residue 97 ILE Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 106 VAL Chi-restraints excluded: chain Ld residue 111 VAL Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 83 LYS Chi-restraints excluded: chain Le residue 109 LYS Chi-restraints excluded: chain Le residue 123 THR Chi-restraints excluded: chain Lf residue 2 SER Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 105 LEU Chi-restraints excluded: chain Lg residue 87 VAL Chi-restraints excluded: chain Lh residue 116 LEU Chi-restraints excluded: chain Lk residue 22 SER Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 34 LYS Chi-restraints excluded: chain Lo residue 2 VAL Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 52 GLU Chi-restraints excluded: chain Lr residue 56 ASP Chi-restraints excluded: chain Lr residue 122 LYS Chi-restraints excluded: chain Lz residue 11 TYR Chi-restraints excluded: chain Lz residue 24 LYS Chi-restraints excluded: chain Lz residue 28 PHE Chi-restraints excluded: chain Lz residue 65 VAL Chi-restraints excluded: chain Lz residue 117 ILE Chi-restraints excluded: chain Lz residue 139 THR Chi-restraints excluded: chain Lz residue 165 LEU Chi-restraints excluded: chain Lz residue 200 ASN Chi-restraints excluded: chain Lz residue 210 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1152 random chunks: chunk 725 optimal weight: 10.0000 chunk 973 optimal weight: 1.9990 chunk 279 optimal weight: 10.0000 chunk 842 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 253 optimal weight: 50.0000 chunk 915 optimal weight: 20.0000 chunk 383 optimal weight: 40.0000 chunk 939 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 overall best weight: 7.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 HIS ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 328 ASN LE 245 GLN LE 250 GLN LG 100 HIS LG 225 ASN LH 188 GLN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 112 ASN LT 127 GLN LU 41 GLN LU 50 ASN LU 55 ASN LX 73 HIS ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lb 60 ASN ** Lc 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 24 HIS Lh 107 GLN Ll 25 GLN Lo 102 GLN ** Lz 171 HIS ** 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 = 0.3349 r_free = 0.3349 target = 0.070952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.048782 restraints weight = 368992.875| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 1.18 r_work: 0.2616 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 155454 Z= 0.353 Angle : 0.597 12.396 227929 Z= 0.309 Chirality : 0.039 0.240 28277 Planarity : 0.005 0.080 14917 Dihedral : 22.538 178.601 68279 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.29 % Rotamer: Outliers : 1.84 % Allowed : 19.13 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.09), residues: 7890 helix: 1.73 (0.09), residues: 3223 sheet: -0.13 (0.16), residues: 1009 loop : -0.04 (0.10), residues: 3658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPLp 55 HIS 0.012 0.001 HISLz 171 PHE 0.029 0.002 PHELk 11 TYR 0.023 0.002 TYRLc 74 ARG 0.014 0.000 ARGLI 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37967.13 seconds wall clock time: 664 minutes 14.62 seconds (39854.62 seconds total)