Starting phenix.real_space_refine on Wed Mar 27 00:14:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a9z_6396/03_2024/5a9z_6396.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a9z_6396/03_2024/5a9z_6396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a9z_6396/03_2024/5a9z_6396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a9z_6396/03_2024/5a9z_6396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a9z_6396/03_2024/5a9z_6396.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5a9z_6396/03_2024/5a9z_6396.pdb" } resolution = 4.7 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 ------------------------------------------------------------------------------- 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= 0.009 sd= 0.049 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: 5 Type Number sf(0) Gaussians P 4530 5.49 5 S 146 5.16 5 C 76831 2.51 5 N 28356 2.21 5 O 40684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BF GLU 9": "OE1" <-> "OE2" Residue "BF GLU 49": "OE1" <-> "OE2" Residue "BF GLU 52": "OE1" <-> "OE2" Residue "BF PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF ASP 60": "OD1" <-> "OD2" Residue "BF GLU 84": "OE1" <-> "OE2" Residue "BF TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF GLU 116": "OE1" <-> "OE2" Residue "BF ASP 160": "OD1" <-> "OD2" Residue "BF PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF ASP 166": "OD1" <-> "OD2" Residue "BF TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG ASP 36": "OD1" <-> "OD2" Residue "BG GLU 44": "OE1" <-> "OE2" Residue "BG TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG GLU 90": "OE1" <-> "OE2" Residue "BG GLU 161": "OE1" <-> "OE2" Residue "BG ASP 183": "OD1" <-> "OD2" Residue "BG TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG GLU 206": "OE1" <-> "OE2" Residue "BH TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BH GLU 81": "OE1" <-> "OE2" Residue "BH PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BH ASP 102": "OD1" <-> "OD2" Residue "BH ARG 118": "NH1" <-> "NH2" Residue "BH TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BH GLU 145": "OE1" <-> "OE2" Residue "BH GLU 150": "OE1" <-> "OE2" Residue "BH GLU 163": "OE1" <-> "OE2" Residue "BH GLU 179": "OE1" <-> "OE2" Residue "BH PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BH GLU 205": "OE1" <-> "OE2" Residue "BI PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI GLU 79": "OE1" <-> "OE2" Residue "BI GLU 83": "OE1" <-> "OE2" Residue "BI TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI GLU 137": "OE1" <-> "OE2" Residue "BI GLU 149": "OE1" <-> "OE2" Residue "BJ TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ GLU 24": "OE1" <-> "OE2" Residue "BJ GLU 42": "OE1" <-> "OE2" Residue "BJ TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ GLU 95": "OE1" <-> "OE2" Residue "BK GLU 8": "OE1" <-> "OE2" Residue "BK ASP 15": "OD1" <-> "OD2" Residue "BK ASP 20": "OD1" <-> "OD2" Residue "BK TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BK GLU 67": "OE1" <-> "OE2" Residue "BK TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BK GLU 90": "OE1" <-> "OE2" Residue "BK GLU 123": "OE1" <-> "OE2" Residue "BK GLU 142": "OE1" <-> "OE2" Residue "BK TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BK TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BL ASP 8": "OD1" <-> "OD2" Residue "BL ASP 52": "OD1" <-> "OD2" Residue "BL GLU 77": "OE1" <-> "OE2" Residue "BM TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM GLU 12": "OE1" <-> "OE2" Residue "BM PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM GLU 35": "OE1" <-> "OE2" Residue "BM PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM ASP 91": "OD1" <-> "OD2" Residue "BM TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BN PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BN GLU 64": "OE1" <-> "OE2" Residue "BO TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BO ASP 110": "OD1" <-> "OD2" Residue "BP TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP ASP 106": "OD1" <-> "OD2" Residue "BP ASP 112": "OD1" <-> "OD2" Residue "BP GLU 127": "OE1" <-> "OE2" Residue "BQ ASP 16": "OD1" <-> "OD2" Residue "BQ TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ GLU 32": "OE1" <-> "OE2" Residue "BQ GLU 50": "OE1" <-> "OE2" Residue "BQ GLU 58": "OE1" <-> "OE2" Residue "BQ GLU 69": "OE1" <-> "OE2" Residue "BQ GLU 73": "OE1" <-> "OE2" Residue "BQ TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ ARG 93": "NH1" <-> "NH2" Residue "BR PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BS GLU 6": "OE1" <-> "OE2" Residue "BS GLU 14": "OE1" <-> "OE2" Residue "BS PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BS ASP 21": "OD1" <-> "OD2" Residue "BS GLU 26": "OE1" <-> "OE2" Residue "BS GLU 41": "OE1" <-> "OE2" Residue "BS TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BT ASP 29": "OD1" <-> "OD2" Residue "BT ASP 52": "OD1" <-> "OD2" Residue "BT PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BU PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BU TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BU ASP 46": "OD1" <-> "OD2" Residue "BV GLU 46": "OE1" <-> "OE2" Residue "BW ARG 3": "NH1" <-> "NH2" Residue "BW TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BX GLU 60": "OE1" <-> "OE2" Residue "BY TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA GLU 37": "OE1" <-> "OE2" Residue "CA ARG 69": "NH1" <-> "NH2" Residue "CA GLU 84": "OE1" <-> "OE2" Residue "CA GLU 86": "OE1" <-> "OE2" Residue "CA ARG 136": "NH1" <-> "NH2" Residue "CA GLU 156": "OE1" <-> "OE2" Residue "CA GLU 181": "OE1" <-> "OE2" Residue "CA GLU 243": "OE1" <-> "OE2" Residue "CA GLU 264": "OE1" <-> "OE2" Residue "CA GLU 269": "OE1" <-> "OE2" Residue "CA GLU 281": "OE1" <-> "OE2" Residue "CA GLU 304": "OE1" <-> "OE2" Residue "CA GLU 363": "OE1" <-> "OE2" Residue "CA GLU 379": "OE1" <-> "OE2" Residue "CA ASP 425": not complete - not flipped Residue "CA ARG 438": "NH1" <-> "NH2" Residue "CA ASP 474": not complete - not flipped Residue "CA PHE 499": "CD1" <-> "CD2" Residue "CA ASP 506": not complete - not flipped Residue "CA ARG 507": "NH1" <-> "NH2" Residue "CA GLU 517": "OE1" <-> "OE2" Residue "CA ARG 602": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150547 Number of models: 1 Model: "" Number of chains: 58 Chain: "AA" Number of atoms: 62218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2889, 62218 Classifications: {'RNA': 2889} Modifications used: {'p5*END': 1, 'rna2p_pur': 100, 'rna2p_pyr': 46, 'rna3p_pur': 1590, 'rna3p_pyr': 1153} Link IDs: {'rna2p': 146, 'rna3p': 2742} Chain breaks: 4 Chain: "AB" Number of atoms: 2641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2641 Classifications: {'RNA': 123} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 67, 'rna3p_pyr': 54} Link IDs: {'rna2p': 1, 'rna3p': 121} Chain: "AC" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1742 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 214} Chain: "AD" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2124 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 250} Chain: "AE" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1578 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 189} Chain: "AF" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1625 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "AG" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1482 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 172} Chain: "AH" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1328 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 157} Chain: "AI" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 752 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 143} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 419 Unresolved non-hydrogen angles: 533 Unresolved non-hydrogen dihedrals: 331 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 197 Chain: "AJ" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'CIS': 7, 'PTRANS': 10, 'TRANS': 116} Chain: "AK" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1113 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 126} Chain: "AL" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 932 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "AM" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1106 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 134} Chain: "AN" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "AO" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 960 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "AP" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 877 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain: "AQ" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 976 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "AR" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 964 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain: "AS" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "AT" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "AU" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 742 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "AV" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "AW" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1435 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 15, 'TRANS': 164} Chain: "AX" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "AY" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 567 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "AZ" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 469 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain: "Aa" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 581 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "Ab" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 445 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 47} Chain: "Ac" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 426 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "Ad" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 430 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "Ae" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 515 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "Af" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 307 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "Ag" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 620 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'CIS': 1, 'TRANS': 126} Unresolved chain links: 5 Chain breaks: 3 Unresolved chain link angles: 17 Unresolved chain link dihedrals: 19 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 404 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'UNK:plan-1': 128} Unresolved non-hydrogen planarities: 143 Chain: "BA" Number of atoms: 32554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1515, 32554 Classifications: {'RNA': 1515} Modifications used: {'rna2p_pur': 51, 'rna2p_pyr': 28, 'rna3p_pur': 804, 'rna3p_pyr': 632} Link IDs: {'rna2p': 79, 'rna3p': 1435} Chain breaks: 1 Chain: "BF" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1900 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 11, 'TRANS': 222} Chain: "BG" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "BH" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "BI" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1146 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "BJ" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "BK" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1257 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "BL" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "BM" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "BN" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 794 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "BO" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 885 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "BP" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 970 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "BQ" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 107} Chain: "BR" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "BS" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "BT" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 700 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "BU" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 857 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "BV" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 597 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "BW" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 647 Classifications: {'peptide': 80} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 74} Chain: "BX" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 763 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "BY" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 208 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "CA" Number of atoms: 4532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4532 Classifications: {'peptide': 593} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 4} Link IDs: {'CIS': 51, 'PTRANS': 23, 'TRANS': 518} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 72 Chain: "AA" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'NMY': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'NMY': 1} Classifications: {'undetermined': 1} Chain: "CA" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GCP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 NMYAA3001 " occ=0.40 ... (40 atoms not shown) pdb=" O5 NMYAA3001 " occ=0.40 residue: pdb=" C1 NMYBA1601 " occ=0.90 ... (40 atoms not shown) pdb=" O5 NMYBA1601 " occ=0.90 Time building chain proxies: 54.16, per 1000 atoms: 0.36 Number of scatterers: 150547 At special positions: 0 Unit cell: (261.64, 280.24, 282.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 146 16.00 P 4530 15.00 O 40684 8.00 N 28356 7.00 C 76831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYSAV 76 " - pdb=" SG CYSAV 99 " distance=2.03 Simple disulfide: pdb=" SG CYSAb 33 " - pdb=" SG CYSAb 49 " distance=2.04 Simple disulfide: pdb=" SG CYSAb 36 " - pdb=" SG CYSAb 49 " distance=2.03 Simple disulfide: pdb=" SG CYSAf 11 " - pdb=" SG CYSAf 14 " distance=2.08 Simple disulfide: pdb=" SG CYSAf 11 " - pdb=" SG CYSAf 27 " distance=2.05 Simple disulfide: pdb=" SG CYSAf 14 " - pdb=" SG CYSAf 27 " distance=1.95 Simple disulfide: pdb=" SG CYSBH 9 " - pdb=" SG CYSBH 12 " distance=1.99 Simple disulfide: pdb=" SG CYSBH 9 " - pdb=" SG CYSBH 26 " distance=2.03 Simple disulfide: pdb=" SG CYSBH 9 " - pdb=" SG CYSBH 31 " distance=2.01 Simple disulfide: pdb=" SG CYSBH 12 " - pdb=" SG CYSBH 26 " distance=2.04 Simple disulfide: pdb=" SG CYSBH 12 " - pdb=" SG CYSBH 31 " distance=2.06 Simple disulfide: pdb=" SG CYSBH 26 " - pdb=" SG CYSBH 31 " distance=2.02 Simple disulfide: pdb=" SG CYSBR 24 " - pdb=" SG CYSBR 40 " distance=2.06 Simple disulfide: pdb=" SG CYSBR 24 " - pdb=" SG CYSBR 43 " distance=2.02 Simple disulfide: pdb=" SG CYSBR 27 " - pdb=" SG CYSBR 40 " distance=1.98 Simple disulfide: pdb=" SG CYSBR 27 " - pdb=" SG CYSBR 43 " distance=2.06 Simple disulfide: pdb=" SG CYSBR 40 " - pdb=" SG CYSBR 43 " distance=2.04 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 Atom "ATOM A0FDK O4' GBA1220 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0FE7 O4' GBA1221 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23022 O5' GAA1044 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23783 O4' CAA1079 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23025 O4' GAA1044 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23783 O4' CAA1079 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0FE7 O4' GBA1221 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0J7P O5' GBA1454 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0FDK O4' GBA1220 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0H17 O4' CBA1320 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0H0L O4' ABA1319 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23022 O5' GAA1044 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0H6V O5' UBA1330 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23355 O4' GAA1059 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0H17 O4' CBA1320 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0FDK O4' GBA1220 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0BFO O4' ABA 986 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0H17 O4' CBA1320 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23025 O4' GAA1044 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23803 O4' CAA1080 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0FHA O4' CBA1226 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0FE7 O4' GBA1221 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0FHA O4' CBA1226 .*. O " rejected from bonding due to valence issues. Atom "ATOM 57289 O5' AAA2670 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23025 O4' GAA1044 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0FE7 O4' GBA1221 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0H17 O4' CBA1320 .*. O " rejected from bonding due to valence issues. Atom "ATOM 23721 O4' CAA1076 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0DTB O5' UBA1125 .*. O " rejected from bonding due to valence issues. Atom "ATOM A0FDH O5' GBA1220 .*. O " rejected from bonding due to valence issues. Atom "ATOM 24374 O5' GAA1107 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 87.24 Conformation dependent library (CDL) restraints added in 8.4 seconds 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12432 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 50 sheets defined 30.2% alpha, 8.8% beta 1290 base pairs and 1336 stacking pairs defined. Time for finding SS restraints: 52.05 Creating SS restraints... Processing helix chain 'AC' and resid 7 through 14 Processing helix chain 'AC' and resid 21 through 33 Processing helix chain 'AC' and resid 79 through 91 Processing helix chain 'AC' and resid 97 through 106 Processing helix chain 'AC' and resid 119 through 127 Processing helix chain 'AC' and resid 127 through 132 Processing helix chain 'AC' and resid 133 through 135 No H-bonds generated for 'chain 'AC' and resid 133 through 135' Processing helix chain 'AC' and resid 148 through 159 Processing helix chain 'AC' and resid 181 through 200 Processing helix chain 'AD' and resid 134 through 136 No H-bonds generated for 'chain 'AD' and resid 134 through 136' Processing helix chain 'AD' and resid 199 through 204 Processing helix chain 'AD' and resid 208 through 217 Processing helix chain 'AE' and resid 59 through 68 Processing helix chain 'AF' and resid 30 through 45 Processing helix chain 'AF' and resid 102 through 121 Processing helix chain 'AF' and resid 135 through 147 Processing helix chain 'AF' and resid 160 through 167 Processing helix chain 'AF' and resid 182 through 189 Processing helix chain 'AF' and resid 196 through 210 Processing helix chain 'AG' and resid 2 through 24 Proline residue: AG 17 - end of helix Processing helix chain 'AG' and resid 43 through 47 Processing helix chain 'AG' and resid 49 through 65 Processing helix chain 'AG' and resid 96 through 111 Processing helix chain 'AG' and resid 165 through 178 Processing helix chain 'AH' and resid 12 through 15 Processing helix chain 'AH' and resid 58 through 81 Processing helix chain 'AH' and resid 137 through 151 Processing helix chain 'AI' and resid 10 through 15 removed outlier: 4.113A pdb=" N GLUAI 15 " --> pdb=" O ALAAI 11 " (cutoff:3.500A) Processing helix chain 'AI' and resid 33 through 41 removed outlier: 3.783A pdb=" N LEUAI 40 " --> pdb=" O GLUAI 36 " (cutoff:3.500A) Processing helix chain 'AI' and resid 43 through 48 removed outlier: 3.559A pdb=" N ASNAI 47 " --> pdb=" O ALAAI 43 " (cutoff:3.500A) Processing helix chain 'AI' and resid 61 through 66 removed outlier: 3.690A pdb=" N LEUAI 66 " --> pdb=" O ALAAI 62 " (cutoff:3.500A) Processing helix chain 'AI' and resid 95 through 100 Processing helix chain 'AJ' and resid 26 through 31 Processing helix chain 'AJ' and resid 36 through 46 removed outlier: 4.420A pdb=" N ALAAJ 40 " --> pdb=" O GLUAJ 36 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALAAJ 43 " --> pdb=" O LYSAJ 39 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALAAJ 44 " --> pdb=" O ALAAJ 40 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 73 through 79 Processing helix chain 'AJ' and resid 102 through 107 Processing helix chain 'AJ' and resid 124 through 135 removed outlier: 3.681A pdb=" N ALAAJ 128 " --> pdb=" O ALAAJ 124 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLYAJ 129 " --> pdb=" O ARGAJ 125 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARGAJ 132 " --> pdb=" O ALAAJ 128 " (cutoff:3.500A) Processing helix chain 'AK' and resid 22 through 34 Processing helix chain 'AK' and resid 87 through 94 Processing helix chain 'AK' and resid 94 through 107 Processing helix chain 'AK' and resid 110 through 119 Processing helix chain 'AK' and resid 127 through 133 Processing helix chain 'AL' and resid 103 through 109 Processing helix chain 'AL' and resid 111 through 118 Processing helix chain 'AM' and resid 33 through 37 Processing helix chain 'AM' and resid 46 through 55 removed outlier: 3.598A pdb=" N ARGAM 50 " --> pdb=" O LYSAM 46 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHEAM 51 " --> pdb=" O ASPAM 47 " (cutoff:3.500A) Processing helix chain 'AM' and resid 77 through 85 Processing helix chain 'AM' and resid 91 through 96 Processing helix chain 'AM' and resid 131 through 142 Processing helix chain 'AN' and resid 44 through 58 Processing helix chain 'AN' and resid 111 through 125 Processing helix chain 'AO' and resid 13 through 32 Processing helix chain 'AO' and resid 38 through 58 Processing helix chain 'AO' and resid 59 through 71 Processing helix chain 'AO' and resid 72 through 83 Processing helix chain 'AO' and resid 83 through 88 Processing helix chain 'AP' and resid 4 through 20 Processing helix chain 'AP' and resid 62 through 81 Processing helix chain 'AP' and resid 96 through 111 Processing helix chain 'AQ' and resid 2 through 16 Processing helix chain 'AQ' and resid 103 through 109 Processing helix chain 'AQ' and resid 110 through 117 Processing helix chain 'AR' and resid 6 through 21 Processing helix chain 'AR' and resid 31 through 73 removed outlier: 4.749A pdb=" N LYSAR 54 " --> pdb=" O ARGAR 50 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ARGAR 55 " --> pdb=" O LYSAR 51 " (cutoff:3.500A) Processing helix chain 'AR' and resid 75 through 86 Processing helix chain 'AR' and resid 94 through 102 Processing helix chain 'AR' and resid 102 through 118 Processing helix chain 'AS' and resid 50 through 56 Processing helix chain 'AT' and resid 13 through 25 Processing helix chain 'AT' and resid 28 through 39 Processing helix chain 'AT' and resid 43 through 62 Processing helix chain 'AT' and resid 65 through 67 No H-bonds generated for 'chain 'AT' and resid 65 through 67' Processing helix chain 'AU' and resid 17 through 24 removed outlier: 3.527A pdb=" N PHEAU 21 " --> pdb=" O ALAAU 17 " (cutoff:3.500A) Processing helix chain 'AU' and resid 35 through 48 Processing helix chain 'AU' and resid 89 through 96 Processing helix chain 'AW' and resid 12 through 22 Processing helix chain 'AW' and resid 41 through 51 removed outlier: 3.937A pdb=" N ALAAW 51 " --> pdb=" O VALAW 47 " (cutoff:3.500A) Processing helix chain 'AW' and resid 51 through 56 Processing helix chain 'AX' and resid 73 through 75 No H-bonds generated for 'chain 'AX' and resid 73 through 75' Processing helix chain 'AY' and resid 2 through 11 Processing helix chain 'AY' and resid 12 through 34 Processing helix chain 'AY' and resid 42 through 67 Processing helix chain 'AZ' and resid 16 through 27 Processing helix chain 'AZ' and resid 40 through 51 Processing helix chain 'Aa' and resid 57 through 71 Processing helix chain 'Ab' and resid 11 through 24 Processing helix chain 'Ad' and resid 8 through 16 Processing helix chain 'Ad' and resid 17 through 24 Processing helix chain 'Ad' and resid 24 through 39 Processing helix chain 'Ad' and resid 42 through 47 Processing helix chain 'Ae' and resid 6 through 12 Processing helix chain 'Ae' and resid 38 through 43 Processing helix chain 'Ae' and resid 54 through 61 Processing helix chain 'Af' and resid 29 through 33 Processing helix chain 'Ag' and resid 294 through 301 removed outlier: 3.595A pdb=" N UNKAg 299 " --> pdb=" O UNKAg 295 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 313 through 317 removed outlier: 3.703A pdb=" N UNKAg 317 " --> pdb=" O UNKAg 314 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 330 through 339 removed outlier: 3.586A pdb=" N UNKAg 334 " --> pdb=" O UNKAg 330 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N UNKAg 336 " --> pdb=" O UNKAg 332 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N UNKAg 337 " --> pdb=" O UNKAg 333 " (cutoff:3.500A) Processing helix chain 'BF' and resid 26 through 31 removed outlier: 5.952A pdb=" N ARGBF 30 " --> pdb=" O PROBF 26 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYRBF 31 " --> pdb=" O LYSBF 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'BF' and resid 26 through 31' Processing helix chain 'BF' and resid 44 through 64 Processing helix chain 'BF' and resid 78 through 88 Processing helix chain 'BF' and resid 101 through 103 No H-bonds generated for 'chain 'BF' and resid 101 through 103' Processing helix chain 'BF' and resid 105 through 120 removed outlier: 3.949A pdb=" N GLNBF 110 " --> pdb=" O LYSBF 106 " (cutoff:3.500A) Processing helix chain 'BF' and resid 132 through 153 removed outlier: 3.568A pdb=" N SERBF 150 " --> pdb=" O GLNBF 146 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLYBF 151 " --> pdb=" O LYSBF 147 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHEBF 152 " --> pdb=" O TYRBF 148 " (cutoff:3.500A) Processing helix chain 'BF' and resid 167 through 180 removed outlier: 8.465A pdb=" N ILEBF 172 " --> pdb=" O THRBF 168 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALABF 173 " --> pdb=" O LYSBF 169 " (cutoff:3.500A) Processing helix chain 'BF' and resid 194 through 196 No H-bonds generated for 'chain 'BF' and resid 194 through 196' Processing helix chain 'BF' and resid 208 through 226 Processing helix chain 'BF' and resid 236 through 238 No H-bonds generated for 'chain 'BF' and resid 236 through 238' Processing helix chain 'BG' and resid 29 through 46 Processing helix chain 'BG' and resid 74 through 77 No H-bonds generated for 'chain 'BG' and resid 74 through 77' Processing helix chain 'BG' and resid 83 through 94 removed outlier: 4.318A pdb=" N ALABG 92 " --> pdb=" O ARGBG 88 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYSBG 93 " --> pdb=" O GLUBG 89 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEUBG 94 " --> pdb=" O GLUBG 90 " (cutoff:3.500A) Processing helix chain 'BG' and resid 113 through 126 Processing helix chain 'BG' and resid 130 through 143 Processing helix chain 'BH' and resid 9 through 15 Processing helix chain 'BH' and resid 20 through 22 No H-bonds generated for 'chain 'BH' and resid 20 through 22' Processing helix chain 'BH' and resid 53 through 68 removed outlier: 4.002A pdb=" N TYRBH 68 " --> pdb=" O LEUBH 64 " (cutoff:3.500A) Processing helix chain 'BH' and resid 72 through 84 Processing helix chain 'BH' and resid 89 through 99 Processing helix chain 'BH' and resid 101 through 107 Processing helix chain 'BH' and resid 114 through 123 Processing helix chain 'BH' and resid 150 through 152 No H-bonds generated for 'chain 'BH' and resid 150 through 152' Processing helix chain 'BH' and resid 156 through 165 Processing helix chain 'BH' and resid 191 through 193 No H-bonds generated for 'chain 'BH' and resid 191 through 193' Processing helix chain 'BH' and resid 201 through 207 Processing helix chain 'BI' and resid 51 through 64 Processing helix chain 'BI' and resid 104 through 114 Processing helix chain 'BI' and resid 128 through 140 Processing helix chain 'BI' and resid 144 through 152 Processing helix chain 'BJ' and resid 16 through 33 Processing helix chain 'BJ' and resid 69 through 81 removed outlier: 5.143A pdb=" N ASNBJ 73 " --> pdb=" O GLUBJ 69 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASPBJ 74 " --> pdb=" O ASPBJ 70 " (cutoff:3.500A) Processing helix chain 'BK' and resid 21 through 30 Processing helix chain 'BK' and resid 36 through 53 Processing helix chain 'BK' and resid 58 through 69 Processing helix chain 'BK' and resid 93 through 110 Processing helix chain 'BK' and resid 116 through 129 Processing helix chain 'BK' and resid 133 through 144 Processing helix chain 'BK' and resid 149 through 154 removed outlier: 4.193A pdb=" N HISBK 153 " --> pdb=" O ARGBK 149 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TYRBK 154 " --> pdb=" O ALABK 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'BK' and resid 149 through 154' Processing helix chain 'BL' and resid 5 through 19 removed outlier: 4.415A pdb=" N VALBL 19 " --> pdb=" O ASNBL 15 " (cutoff:3.500A) Processing helix chain 'BL' and resid 30 through 42 Processing helix chain 'BL' and resid 104 through 106 No H-bonds generated for 'chain 'BL' and resid 104 through 106' Processing helix chain 'BL' and resid 121 through 127 Processing helix chain 'BM' and resid 33 through 36 No H-bonds generated for 'chain 'BM' and resid 33 through 36' Processing helix chain 'BM' and resid 43 through 46 No H-bonds generated for 'chain 'BM' and resid 43 through 46' Processing helix chain 'BM' and resid 48 through 53 removed outlier: 5.029A pdb=" N VALBM 53 " --> pdb=" O PROBM 49 " (cutoff:3.500A) Processing helix chain 'BM' and resid 70 through 88 Processing helix chain 'BM' and resid 93 through 96 No H-bonds generated for 'chain 'BM' and resid 93 through 96' Processing helix chain 'BN' and resid 15 through 26 Processing helix chain 'BN' and resid 79 through 83 removed outlier: 4.905A pdb=" N GLUBN 83 " --> pdb=" O ARGBN 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'BN' and resid 79 through 83' Processing helix chain 'BO' and resid 58 through 74 Processing helix chain 'BO' and resid 91 through 100 Processing helix chain 'BO' and resid 123 through 125 No H-bonds generated for 'chain 'BO' and resid 123 through 125' Processing helix chain 'BP' and resid 7 through 13 Processing helix chain 'BQ' and resid 15 through 21 removed outlier: 4.325A pdb=" N TYRBQ 21 " --> pdb=" O VALBQ 17 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 29 through 37 Processing helix chain 'BQ' and resid 45 through 47 No H-bonds generated for 'chain 'BQ' and resid 45 through 47' Processing helix chain 'BQ' and resid 50 through 62 removed outlier: 4.514A pdb=" N ARGBQ 55 " --> pdb=" O ALABQ 51 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEUBQ 56 " --> pdb=" O GLUBQ 52 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLUBQ 61 " --> pdb=" O ARGBQ 57 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASNBQ 62 " --> pdb=" O GLUBQ 58 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 67 through 83 removed outlier: 4.631A pdb=" N ARGBQ 71 " --> pdb=" O GLUBQ 67 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALABQ 72 " --> pdb=" O GLYBQ 68 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLUBQ 73 " --> pdb=" O GLUBQ 69 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILEBQ 78 " --> pdb=" O VALBQ 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARGBQ 80 " --> pdb=" O ALABQ 76 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEUBQ 81 " --> pdb=" O ASNBQ 77 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N METBQ 82 " --> pdb=" O ILEBQ 78 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 87 through 94 removed outlier: 3.649A pdb=" N ARGBQ 91 " --> pdb=" O TYRBQ 87 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N HISBQ 92 " --> pdb=" O ARGBQ 88 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARGBQ 94 " --> pdb=" O LEUBQ 90 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 108 through 111 No H-bonds generated for 'chain 'BQ' and resid 108 through 111' Processing helix chain 'BR' and resid 4 through 6 No H-bonds generated for 'chain 'BR' and resid 4 through 6' Processing helix chain 'BR' and resid 41 through 50 Processing helix chain 'BS' and resid 5 through 15 Processing helix chain 'BS' and resid 25 through 44 Processing helix chain 'BS' and resid 50 through 73 Processing helix chain 'BS' and resid 76 through 85 Processing helix chain 'BT' and resid 53 through 60 Processing helix chain 'BT' and resid 68 through 79 removed outlier: 3.618A pdb=" N VALBT 79 " --> pdb=" O ARGBT 75 " (cutoff:3.500A) Processing helix chain 'BU' and resid 82 through 96 removed outlier: 3.778A pdb=" N GLNBU 96 " --> pdb=" O ARGBU 92 " (cutoff:3.500A) Processing helix chain 'BV' and resid 37 through 41 Processing helix chain 'BV' and resid 53 through 56 No H-bonds generated for 'chain 'BV' and resid 53 through 56' Processing helix chain 'BV' and resid 60 through 76 Processing helix chain 'BW' and resid 13 through 23 removed outlier: 5.081A pdb=" N LYSBW 18 " --> pdb=" O HISBW 14 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLUBW 21 " --> pdb=" O GLUBW 17 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEUBW 22 " --> pdb=" O LYSBW 18 " (cutoff:3.500A) Processing helix chain 'BW' and resid 42 through 44 No H-bonds generated for 'chain 'BW' and resid 42 through 44' Processing helix chain 'BW' and resid 64 through 66 No H-bonds generated for 'chain 'BW' and resid 64 through 66' Processing helix chain 'BW' and resid 71 through 74 No H-bonds generated for 'chain 'BW' and resid 71 through 74' Processing helix chain 'BX' and resid 14 through 46 Processing helix chain 'BX' and resid 49 through 68 Processing helix chain 'BX' and resid 76 through 91 Processing helix chain 'BY' and resid 9 through 15 Processing helix chain 'CA' and resid 2 through 4 No H-bonds generated for 'chain 'CA' and resid 2 through 4' Processing helix chain 'CA' and resid 18 through 26 removed outlier: 4.662A pdb=" N VALCA 22 " --> pdb=" O LYSCA 18 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASPCA 23 " --> pdb=" O THRCA 19 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYSCA 24 " --> pdb=" O THRCA 20 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEUCA 25 " --> pdb=" O LEUCA 21 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEUCA 26 " --> pdb=" O VALCA 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'CA' and resid 18 through 26' Processing helix chain 'CA' and resid 85 through 89 removed outlier: 3.543A pdb=" N METCA 89 " --> pdb=" O VALCA 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'CA' and resid 85 through 89' Processing helix chain 'CA' and resid 107 through 118 removed outlier: 3.517A pdb=" N PHECA 111 " --> pdb=" O PROCA 107 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VALCA 112 " --> pdb=" O GLNCA 108 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALACA 118 " --> pdb=" O LYSCA 114 " (cutoff:3.500A) Processing helix chain 'CA' and resid 137 through 147 removed outlier: 3.521A pdb=" N VALCA 141 " --> pdb=" O PROCA 137 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASPCA 142 " --> pdb=" O ASPCA 138 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASPCA 146 " --> pdb=" O ASPCA 142 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEUCA 147 " --> pdb=" O GLNCA 143 " (cutoff:3.500A) Processing helix chain 'CA' and resid 184 through 193 removed outlier: 4.217A pdb=" N GLNCA 188 " --> pdb=" O THRCA 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'AC' and resid 170 through 173 Processing sheet with id=AA2, first strand: chain 'AC' and resid 93 through 96 removed outlier: 5.434A pdb=" N LEUAC 75 " --> pdb=" O VALAC 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AD' and resid 9 through 12 Processing sheet with id=AA4, first strand: chain 'AD' and resid 45 through 46 Processing sheet with id=AA5, first strand: chain 'AD' and resid 102 through 105 removed outlier: 5.400A pdb=" N HISAD 96 " --> pdb=" O VALAD 79 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VALAD 79 " --> pdb=" O HISAD 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AD' and resid 130 through 132 removed outlier: 6.750A pdb=" N TYRAD 190 " --> pdb=" O VALAD 145 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VALAD 145 " --> pdb=" O TYRAD 190 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ILEAD 165 " --> pdb=" O ARGAD 176 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ARGAD 176 " --> pdb=" O ILEAD 165 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLYAD 167 " --> pdb=" O ILEAD 174 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLUAD 181 " --> pdb=" O LEUAD 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AE' and resid 163 through 171 removed outlier: 3.920A pdb=" N GLUAE 163 " --> pdb=" O SERAE 108 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASNAE 169 " --> pdb=" O VALAE 102 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VALAE 102 " --> pdb=" O ASNAE 169 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEUAE 195 " --> pdb=" O THRAE 107 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VALAE 7 " --> pdb=" O ILEAE 26 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILEAE 26 " --> pdb=" O VALAE 7 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VALAE 9 " --> pdb=" O THRAE 24 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'AE' and resid 13 through 15 Processing sheet with id=AA9, first strand: chain 'AE' and resid 34 through 36 Processing sheet with id=AB1, first strand: chain 'AE' and resid 142 through 143 Processing sheet with id=AB2, first strand: chain 'AF' and resid 7 through 11 Processing sheet with id=AB3, first strand: chain 'AF' and resid 122 through 124 removed outlier: 6.965A pdb=" N LEUAF 123 " --> pdb=" O METAF 194 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEUAF 155 " --> pdb=" O VALAF 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'AG' and resid 91 through 92 removed outlier: 4.453A pdb=" N LYSAG 36 " --> pdb=" O VALAG 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'AH' and resid 8 through 10 Processing sheet with id=AB6, first strand: chain 'AH' and resid 16 through 19 Processing sheet with id=AB7, first strand: chain 'AH' and resid 84 through 85 Processing sheet with id=AB8, first strand: chain 'AH' and resid 88 through 90 Processing sheet with id=AB9, first strand: chain 'AI' and resid 25 through 27 removed outlier: 5.918A pdb=" N LEUAI 26 " --> pdb=" O GLYAI 114 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'AK' and resid 120 through 122 removed outlier: 5.823A pdb=" N VALAK 52 " --> pdb=" O LYSAK 121 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VALAK 14 " --> pdb=" O VALAK 53 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VALAK 140 " --> pdb=" O TRPAK 13 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEUAK 15 " --> pdb=" O VALAK 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'AK' and resid 70 through 72 Processing sheet with id=AC3, first strand: chain 'AL' and resid 6 through 9 removed outlier: 6.557A pdb=" N VALAL 40 " --> pdb=" O ILEAL 22 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VALAL 24 " --> pdb=" O VALAL 38 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VALAL 38 " --> pdb=" O VALAL 24 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N TYRAL 7 " --> pdb=" O ASPAL 81 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N ALAAL 83 " --> pdb=" O TYRAL 7 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLUAL 9 " --> pdb=" O ALAAL 83 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VALAL 85 " --> pdb=" O GLUAL 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'AL' and resid 68 through 69 removed outlier: 5.135A pdb=" N LEUAQ 78 " --> pdb=" O ARGAQ 64 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARGAQ 64 " --> pdb=" O LEUAQ 78 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'AL' and resid 68 through 69 removed outlier: 5.135A pdb=" N LEUAQ 78 " --> pdb=" O ARGAQ 64 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARGAQ 64 " --> pdb=" O LEUAQ 78 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLYAQ 69 " --> pdb=" O VALAQ 49 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N VALAQ 49 " --> pdb=" O GLYAQ 69 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'AM' and resid 74 through 76 removed outlier: 7.118A pdb=" N GLUAM 74 " --> pdb=" O LYSAM 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'AN' and resid 102 through 104 Processing sheet with id=AC8, first strand: chain 'AN' and resid 40 through 43 Processing sheet with id=AC9, first strand: chain 'AO' and resid 33 through 37 removed outlier: 6.257A pdb=" N ALAAO 109 " --> pdb=" O GLUAO 102 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLUAO 102 " --> pdb=" O ALAAO 109 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEUAO 111 " --> pdb=" O LEUAO 100 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'AP' and resid 38 through 40 Processing sheet with id=AD2, first strand: chain 'AQ' and resid 37 through 38 Processing sheet with id=AD3, first strand: chain 'AS' and resid 33 through 38 Processing sheet with id=AD4, first strand: chain 'AS' and resid 43 through 44 Processing sheet with id=AD5, first strand: chain 'AS' and resid 68 through 79 removed outlier: 4.922A pdb=" N LEUAS 71 " --> pdb=" O TYRAS 91 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N TYRAS 91 " --> pdb=" O LEUAS 71 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SERAS 73 " --> pdb=" O GLNAS 89 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'AT' and resid 3 through 10 removed outlier: 4.036A pdb=" N TYRAT 9 " --> pdb=" O SERAT 101 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N SERAT 101 " --> pdb=" O TYRAT 9 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASPAT 94 " --> pdb=" O LEUAT 86 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N HISAT 102 " --> pdb=" O GLUAT 78 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLUAT 78 " --> pdb=" O HISAT 102 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N THRAT 104 " --> pdb=" O VALAT 76 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VALAT 76 " --> pdb=" O THRAT 104 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILEAT 106 " --> pdb=" O ALAAT 74 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALAAT 74 " --> pdb=" O ILEAT 106 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLYAT 108 " --> pdb=" O LYSAT 72 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYSAT 72 " --> pdb=" O GLYAT 108 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'AU' and resid 9 through 11 removed outlier: 4.315A pdb=" N LYSAU 77 " --> pdb=" O VALAU 30 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARGAU 76 " --> pdb=" O HISAU 58 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N HISAU 58 " --> pdb=" O ARGAU 76 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LYSAU 78 " --> pdb=" O THRAU 56 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THRAU 56 " --> pdb=" O LYSAU 78 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILEAU 80 " --> pdb=" O VALAU 54 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VALAU 54 " --> pdb=" O ILEAU 80 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'AU' and resid 64 through 66 Processing sheet with id=AD9, first strand: chain 'AV' and resid 23 through 24 removed outlier: 3.925A pdb=" N THRAV 12 " --> pdb=" O ARGAV 23 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VALAV 13 " --> pdb=" O SERAV 70 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'AV' and resid 27 through 28 removed outlier: 3.922A pdb=" N VALAV 27 " --> pdb=" O ALAAV 36 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'AV' and resid 96 through 97 Processing sheet with id=AE3, first strand: chain 'AW' and resid 2 through 3 removed outlier: 6.382A pdb=" N THRAW 69 " --> pdb=" O VALAW 90 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VALAW 90 " --> pdb=" O THRAW 69 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VALAW 71 " --> pdb=" O PHEAW 88 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHEAW 88 " --> pdb=" O VALAW 71 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLNAW 73 " --> pdb=" O VALAW 86 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VALAW 86 " --> pdb=" O GLNAW 73 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASNAW 75 " --> pdb=" O GLUAW 84 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N LYSAW 23 " --> pdb=" O GLUAW 84 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N VALAW 86 " --> pdb=" O LYSAW 23 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N PHEAW 88 " --> pdb=" O PROAW 25 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VALAW 27 " --> pdb=" O PHEAW 88 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VALAW 90 " --> pdb=" O VALAW 27 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYRAW 29 " --> pdb=" O VALAW 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'AW' and resid 124 through 127 removed outlier: 8.589A pdb=" N ILEAW 137 " --> pdb=" O TYRAW 99 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VALAW 139 " --> pdb=" O PROAW 101 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARGAW 103 " --> pdb=" O VALAW 139 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N VALAW 141 " --> pdb=" O ARGAW 103 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VALAW 105 " --> pdb=" O VALAW 141 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'AW' and resid 117 through 120 Processing sheet with id=AE6, first strand: chain 'AX' and resid 22 through 23 removed outlier: 6.885A pdb=" N LEUAX 59 " --> pdb=" O LEUAX 37 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'AX' and resid 28 through 31 removed outlier: 5.106A pdb=" N GLNAX 29 " --> pdb=" O VALAX 67 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLYAX 76 " --> pdb=" O ARGAX 72 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'AZ' and resid 34 through 38 Processing sheet with id=AE9, first strand: chain 'Aa' and resid 15 through 16 Processing sheet with id=AF1, first strand: chain 'Aa' and resid 44 through 46 Processing sheet with id=AF2, first strand: chain 'Ab' and resid 31 through 32 Processing sheet with id=AF3, first strand: chain 'Ac' and resid 21 through 28 removed outlier: 5.358A pdb=" N TYRAc 21 " --> pdb=" O CYSAc 16 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N CYSAc 16 " --> pdb=" O TYRAc 21 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Ae' and resid 15 through 17 Processing sheet with id=AF5, first strand: chain 'Af' and resid 15 through 19 1564 hydrogen bonds defined for protein. 4452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3459 hydrogen bonds 6030 hydrogen bond angles 0 basepair planarities 1290 basepair parallelities 1336 stacking parallelities Total time for adding SS restraints: 181.47 Time building geometry restraints manager: 92.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 1.07: 2 1.07 - 1.50: 116581 1.50 - 1.93: 46488 1.93 - 2.36: 2 2.36 - 2.79: 2 Bond restraints: 163075 Sorted by residual: bond pdb=" O3' AAA1073 " pdb=" P GAA1074 " ideal model delta sigma weight residual 1.607 2.793 -1.186 1.50e-02 4.44e+03 6.25e+03 bond pdb=" O3' GAA 883 " pdb=" P CAA 884 " ideal model delta sigma weight residual 1.607 2.680 -1.073 1.50e-02 4.44e+03 5.12e+03 bond pdb=" O3' UAA1060 " pdb=" P UAA1061 " ideal model delta sigma weight residual 1.607 0.644 0.963 1.50e-02 4.44e+03 4.12e+03 bond pdb=" O3' CBA1317 " pdb=" P ABA1318 " ideal model delta sigma weight residual 1.607 0.766 0.841 1.50e-02 4.44e+03 3.14e+03 bond pdb=" O3' UAA1033 " pdb=" P GAA1034 " ideal model delta sigma weight residual 1.607 2.344 -0.737 1.50e-02 4.44e+03 2.42e+03 ... (remaining 163070 not shown) Histogram of bond angle deviations from ideal: 25.44 - 54.15: 4 54.15 - 82.86: 12 82.86 - 111.57: 106746 111.57 - 140.28: 136090 140.28 - 168.99: 11 Bond angle restraints: 242863 Sorted by residual: angle pdb=" C3' GAA 883 " pdb=" O3' GAA 883 " pdb=" P CAA 884 " ideal model delta sigma weight residual 120.20 49.22 70.98 1.50e+00 4.44e-01 2.24e+03 angle pdb=" C3' CBA1317 " pdb=" O3' CBA1317 " pdb=" P ABA1318 " ideal model delta sigma weight residual 120.20 61.18 59.02 1.50e+00 4.44e-01 1.55e+03 angle pdb=" O3' CBA1317 " pdb=" P ABA1318 " pdb=" O5' ABA1318 " ideal model delta sigma weight residual 104.00 162.12 -58.12 1.50e+00 4.44e-01 1.50e+03 angle pdb=" O3' UAA1060 " pdb=" P UAA1061 " pdb=" O5' UAA1061 " ideal model delta sigma weight residual 104.00 158.46 -54.46 1.50e+00 4.44e-01 1.32e+03 angle pdb=" C3' GAA 882 " pdb=" O3' GAA 882 " pdb=" P GAA 883 " ideal model delta sigma weight residual 120.20 77.53 42.67 1.50e+00 4.44e-01 8.09e+02 ... (remaining 242858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 88570 35.99 - 71.97: 14982 71.97 - 107.96: 1628 107.96 - 143.94: 198 143.94 - 179.93: 116 Dihedral angle restraints: 105494 sinusoidal: 86138 harmonic: 19356 Sorted by residual: dihedral pdb=" CA LEUAI 153 " pdb=" C LEUAI 153 " pdb=" N GLYAI 154 " pdb=" CA GLYAI 154 " ideal model delta harmonic sigma weight residual 180.00 122.06 57.94 0 5.00e+00 4.00e-02 1.34e+02 dihedral pdb=" C4' AAA2503 " pdb=" C3' AAA2503 " pdb=" C2' AAA2503 " pdb=" C1' AAA2503 " ideal model delta sinusoidal sigma weight residual -35.00 44.42 -79.42 1 8.00e+00 1.56e-02 1.22e+02 dihedral pdb=" C5' ABA1004 " pdb=" C4' ABA1004 " pdb=" C3' ABA1004 " pdb=" O3' ABA1004 " ideal model delta sinusoidal sigma weight residual 147.00 68.45 78.55 1 8.00e+00 1.56e-02 1.20e+02 ... (remaining 105491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.253: 28868 0.253 - 0.506: 1699 0.506 - 0.758: 91 0.758 - 1.011: 15 1.011 - 1.264: 2 Chirality restraints: 30675 Sorted by residual: chirality pdb=" C3' UAA2491 " pdb=" C4' UAA2491 " pdb=" O3' UAA2491 " pdb=" C2' UAA2491 " both_signs ideal model delta sigma weight residual False -2.48 -1.21 -1.26 2.00e-01 2.50e+01 3.99e+01 chirality pdb=" C1' AAA1204 " pdb=" O4' AAA1204 " pdb=" C2' AAA1204 " pdb=" N9 AAA1204 " both_signs ideal model delta sigma weight residual False 2.44 1.34 1.10 2.00e-01 2.50e+01 3.01e+01 chirality pdb=" CA GLUAc 24 " pdb=" N GLUAc 24 " pdb=" C GLUAc 24 " pdb=" CB GLUAc 24 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.44e+01 ... (remaining 30672 not shown) Planarity restraints: 13938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CAA 650 " -0.666 2.00e-02 2.50e+03 3.62e-01 2.95e+03 pdb=" N1 CAA 650 " -0.018 2.00e-02 2.50e+03 pdb=" C2 CAA 650 " 0.073 2.00e-02 2.50e+03 pdb=" O2 CAA 650 " 0.354 2.00e-02 2.50e+03 pdb=" N3 CAA 650 " -0.022 2.00e-02 2.50e+03 pdb=" C4 CAA 650 " 0.009 2.00e-02 2.50e+03 pdb=" N4 CAA 650 " -0.528 2.00e-02 2.50e+03 pdb=" C5 CAA 650 " 0.451 2.00e-02 2.50e+03 pdb=" C6 CAA 650 " 0.348 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' UAA1576 " -0.579 2.00e-02 2.50e+03 3.35e-01 2.52e+03 pdb=" N1 UAA1576 " -0.026 2.00e-02 2.50e+03 pdb=" C2 UAA1576 " 0.064 2.00e-02 2.50e+03 pdb=" O2 UAA1576 " 0.299 2.00e-02 2.50e+03 pdb=" N3 UAA1576 " 0.010 2.00e-02 2.50e+03 pdb=" C4 UAA1576 " 0.091 2.00e-02 2.50e+03 pdb=" O4 UAA1576 " -0.562 2.00e-02 2.50e+03 pdb=" C5 UAA1576 " 0.417 2.00e-02 2.50e+03 pdb=" C6 UAA1576 " 0.285 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' UAA1541 " 0.544 2.00e-02 2.50e+03 3.15e-01 2.24e+03 pdb=" N1 UAA1541 " 0.037 2.00e-02 2.50e+03 pdb=" C2 UAA1541 " -0.045 2.00e-02 2.50e+03 pdb=" O2 UAA1541 " -0.347 2.00e-02 2.50e+03 pdb=" N3 UAA1541 " 0.057 2.00e-02 2.50e+03 pdb=" C4 UAA1541 " -0.073 2.00e-02 2.50e+03 pdb=" O4 UAA1541 " 0.488 2.00e-02 2.50e+03 pdb=" C5 UAA1541 " -0.402 2.00e-02 2.50e+03 pdb=" C6 UAA1541 " -0.258 2.00e-02 2.50e+03 ... (remaining 13935 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 168 0.98 - 1.96: 1549 1.96 - 2.94: 106022 2.94 - 3.92: 526740 3.92 - 4.90: 851941 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1486420 Sorted by model distance: nonbonded pdb=" N UNKAg 255 " pdb=" N UNKAg 285 " model vdw 0.000 3.200 nonbonded pdb=" NH1 ARGBQ 29 " pdb=" CD1 LEUBQ 66 " model vdw 0.140 3.540 nonbonded pdb=" P AAA1048 " pdb=" N3 GAA1110 " model vdw 0.186 3.480 nonbonded pdb=" O ASNCA 169 " pdb=" OD2 ASPCA 182 " model vdw 0.220 3.040 nonbonded pdb=" C1' UAA1105 " pdb=" C8 GAA1106 " model vdw 0.221 3.690 ... (remaining 1486415 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 10.950 Check model and map are aligned: 1.500 Set scattering table: 0.970 Process input model: 490.230 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.360 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 511.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.186 163075 Z= 0.800 Angle : 1.890 82.556 242863 Z= 1.168 Chirality : 0.136 1.264 30675 Planarity : 0.027 0.362 13938 Dihedral : 28.047 179.927 93011 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 199.42 Ramachandran Plot: Outliers : 25.22 % Allowed : 25.13 % Favored : 49.64 % Rotamer: Outliers : 29.15 % Allowed : 18.43 % Favored : 52.42 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 1.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.73 (0.06), residues: 6565 helix: -4.94 (0.05), residues: 1855 sheet: -3.51 (0.17), residues: 653 loop : -5.92 (0.06), residues: 4057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.145 0.014 TRPAG 100 HIS 0.006 0.001 HISBS 42 PHE 0.103 0.012 PHEAN 104 TYR 0.238 0.021 TYRAE 151 ARG 0.025 0.002 ARGAD 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3735 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1569 poor density : 2166 time to evaluate : 6.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AC 6 ARG cc_start: 0.4643 (OUTLIER) cc_final: 0.3124 (ttt180) REVERT: AC 13 LYS cc_start: 0.4092 (mttm) cc_final: 0.3759 (tptt) REVERT: AC 59 ARG cc_start: 0.2208 (OUTLIER) cc_final: -0.1549 (ptp90) REVERT: AC 92 ASP cc_start: -0.4268 (OUTLIER) cc_final: -0.4544 (m-30) REVERT: AC 161 ILE cc_start: 0.4392 (OUTLIER) cc_final: 0.4108 (mp) REVERT: AC 164 ARG cc_start: 0.3382 (OUTLIER) cc_final: 0.2838 (ptt180) REVERT: AC 167 LYS cc_start: 0.2729 (pttt) cc_final: 0.1622 (tmtt) REVERT: AC 209 LEU cc_start: -0.0669 (OUTLIER) cc_final: -0.1170 (mt) REVERT: AC 218 MET cc_start: -0.3168 (ttp) cc_final: -0.4202 (ttp) REVERT: AC 222 VAL cc_start: 0.3550 (OUTLIER) cc_final: 0.2871 (p) REVERT: AD 58 HIS cc_start: 0.5889 (m90) cc_final: 0.5651 (m90) REVERT: AD 62 TYR cc_start: 0.7167 (m-10) cc_final: 0.6754 (m-80) REVERT: AD 146 GLU cc_start: 0.5582 (OUTLIER) cc_final: 0.4986 (pp20) REVERT: AD 148 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7445 (mt-10) REVERT: AD 164 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: AD 176 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.6788 (tpp80) REVERT: AD 177 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7089 (pt) REVERT: AD 186 HIS cc_start: 0.7003 (OUTLIER) cc_final: 0.6588 (p90) REVERT: AD 200 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8485 (p0) REVERT: AD 220 HIS cc_start: 0.6939 (OUTLIER) cc_final: 0.6333 (m-70) REVERT: AE 24 THR cc_start: 0.6641 (m) cc_final: 0.5557 (m) REVERT: AE 38 THR cc_start: 0.6706 (OUTLIER) cc_final: 0.6314 (m) REVERT: AE 53 PRO cc_start: 0.7839 (OUTLIER) cc_final: 0.7547 (Cg_endo) REVERT: AE 98 PRO cc_start: 0.6693 (Cg_endo) cc_final: 0.6386 (Cg_exo) REVERT: AE 119 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6668 (tmt-80) REVERT: AE 121 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7724 (t0) REVERT: AE 135 HIS cc_start: -0.0632 (OUTLIER) cc_final: -0.0865 (m-70) REVERT: AF 8 GLN cc_start: 0.6354 (OUTLIER) cc_final: 0.6011 (pm20) REVERT: AF 23 ASP cc_start: 0.5775 (OUTLIER) cc_final: 0.5534 (t70) REVERT: AF 31 HIS cc_start: 0.8016 (p90) cc_final: 0.7809 (p90) REVERT: AF 65 TRP cc_start: 0.6847 (t-100) cc_final: 0.6095 (t-100) REVERT: AF 95 ARG cc_start: 0.4554 (OUTLIER) cc_final: 0.3586 (ttp-110) REVERT: AF 124 LEU cc_start: 0.6391 (OUTLIER) cc_final: 0.6135 (tp) REVERT: AF 145 GLU cc_start: 0.9365 (mm-30) cc_final: 0.8956 (tm-30) REVERT: AF 183 VAL cc_start: 0.5928 (OUTLIER) cc_final: 0.5240 (t) REVERT: AG 32 PRO cc_start: 0.5810 (OUTLIER) cc_final: 0.5497 (Cg_exo) REVERT: AG 33 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.5047 (mmm160) REVERT: AG 94 LEU cc_start: 0.4604 (OUTLIER) cc_final: 0.3186 (mp) REVERT: AG 155 MET cc_start: 0.6807 (mpt) cc_final: 0.6509 (mpt) REVERT: AG 162 THR cc_start: 0.7104 (m) cc_final: 0.6687 (p) REVERT: AH 18 GLU cc_start: 0.4721 (OUTLIER) cc_final: 0.3787 (pm20) REVERT: AH 51 ARG cc_start: 0.7651 (tpp-160) cc_final: 0.6841 (ttp80) REVERT: AH 52 VAL cc_start: 0.1372 (OUTLIER) cc_final: 0.0814 (p) REVERT: AH 103 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7736 (mp) REVERT: AH 171 LEU cc_start: 0.8353 (mt) cc_final: 0.7320 (mt) REVERT: AH 172 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.5831 (pttp) REVERT: AJ 16 LYS cc_start: 0.0960 (OUTLIER) cc_final: 0.0667 (pttt) REVERT: AJ 30 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.7972 (t70) REVERT: AJ 64 SER cc_start: 0.4652 (OUTLIER) cc_final: 0.4425 (p) REVERT: AJ 79 ARG cc_start: -0.1449 (OUTLIER) cc_final: -0.2266 (ptt90) REVERT: AJ 86 LYS cc_start: 0.3884 (OUTLIER) cc_final: 0.3402 (ptmt) REVERT: AJ 137 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: AK 48 MET cc_start: 0.3315 (OUTLIER) cc_final: 0.0870 (tpp) REVERT: AK 52 VAL cc_start: 0.6800 (OUTLIER) cc_final: 0.6135 (m) REVERT: AK 55 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.6908 (p) REVERT: AK 68 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6671 (tt0) REVERT: AK 106 MET cc_start: 0.5705 (mtm) cc_final: 0.5192 (mpp) REVERT: AK 127 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8310 (p0) REVERT: AL 13 ASN cc_start: 0.9166 (t0) cc_final: 0.8951 (p0) REVERT: AM 60 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6537 (mtp) REVERT: AM 74 GLU cc_start: 0.4271 (OUTLIER) cc_final: 0.3949 (tt0) REVERT: AM 85 LEU cc_start: 0.5844 (mp) cc_final: 0.5448 (mp) REVERT: AM 117 GLU cc_start: 0.4499 (OUTLIER) cc_final: 0.2677 (mm-30) REVERT: AM 130 PHE cc_start: 0.1291 (OUTLIER) cc_final: 0.0138 (m-10) REVERT: AM 147 LEU cc_start: 0.5288 (OUTLIER) cc_final: 0.4951 (mp) REVERT: AN 18 LYS cc_start: 0.4210 (OUTLIER) cc_final: 0.3926 (mttt) REVERT: AN 25 ASP cc_start: 0.6138 (m-30) cc_final: 0.5934 (m-30) REVERT: AN 57 HIS cc_start: 0.8270 (t-170) cc_final: 0.7987 (t-90) REVERT: AN 58 PHE cc_start: 0.7775 (m-80) cc_final: 0.7544 (t80) REVERT: AN 60 ARG cc_start: 0.6082 (OUTLIER) cc_final: 0.4950 (tpt-90) REVERT: AN 65 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6238 (m-10) REVERT: AN 66 ILE cc_start: 0.4552 (mp) cc_final: 0.4028 (mp) REVERT: AN 68 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7593 (tp) REVERT: AN 97 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8111 (m) REVERT: AN 104 PHE cc_start: 0.2537 (OUTLIER) cc_final: 0.0003 (m-80) REVERT: AN 133 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6961 (mmt90) REVERT: AO 26 LYS cc_start: 0.8213 (mttt) cc_final: 0.8006 (mttp) REVERT: AO 64 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7968 (tpp80) REVERT: AO 113 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.5168 (tm) REVERT: AQ 62 THR cc_start: 0.6796 (OUTLIER) cc_final: 0.6356 (t) REVERT: AQ 93 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7160 (tpt170) REVERT: AQ 101 PHE cc_start: 0.4844 (OUTLIER) cc_final: 0.4473 (m-10) REVERT: AR 51 LYS cc_start: 0.6706 (mttm) cc_final: 0.6484 (tptt) REVERT: AR 52 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7618 (ptm160) REVERT: AS 29 PRO cc_start: 0.6998 (OUTLIER) cc_final: 0.6678 (Cg_endo) REVERT: AS 84 LYS cc_start: 0.5584 (OUTLIER) cc_final: 0.4898 (pptt) REVERT: AT 30 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8625 (tm-30) REVERT: AT 97 LYS cc_start: 0.8126 (pttt) cc_final: 0.7374 (mtpp) REVERT: AU 8 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.6954 (pt) REVERT: AU 28 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: AU 52 VAL cc_start: 0.7769 (t) cc_final: 0.7550 (t) REVERT: AU 55 ASN cc_start: 0.5074 (OUTLIER) cc_final: 0.4595 (p0) REVERT: AW 59 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7422 (pp) REVERT: AW 62 PRO cc_start: 0.6187 (OUTLIER) cc_final: 0.5399 (Cg_exo) REVERT: AW 132 ASN cc_start: 0.6228 (m-40) cc_final: 0.5930 (m-40) REVERT: AW 155 LEU cc_start: 0.4474 (OUTLIER) cc_final: 0.3693 (mp) REVERT: AW 174 VAL cc_start: 0.4267 (OUTLIER) cc_final: 0.3782 (m) REVERT: AX 45 PHE cc_start: 0.5658 (m-10) cc_final: 0.4584 (m-80) REVERT: AX 75 LEU cc_start: 0.1756 (mp) cc_final: 0.1437 (mp) REVERT: AY 15 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8783 (mp0) REVERT: AY 45 ILE cc_start: 0.7334 (OUTLIER) cc_final: 0.6687 (pp) REVERT: AY 61 GLU cc_start: 0.8608 (tt0) cc_final: 0.8015 (tm-30) REVERT: AY 65 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8583 (mm110) REVERT: AZ 6 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8136 (m) REVERT: Aa 8 LYS cc_start: 0.8706 (tttt) cc_final: 0.8389 (mtmm) REVERT: Aa 11 PRO cc_start: 0.7001 (OUTLIER) cc_final: 0.6092 (Cg_exo) REVERT: Aa 39 CYS cc_start: 0.6187 (t) cc_final: 0.5576 (t) REVERT: Aa 48 ARG cc_start: 0.1557 (mtt180) cc_final: 0.1297 (mtm110) REVERT: Ab 25 LEU cc_start: 0.3758 (OUTLIER) cc_final: 0.3428 (pt) REVERT: Ab 28 PRO cc_start: 0.5942 (Cg_endo) cc_final: 0.5226 (Cg_exo) REVERT: Ab 29 THR cc_start: 0.7237 (m) cc_final: 0.6842 (m) REVERT: Ac 50 ARG cc_start: 0.7784 (ttt180) cc_final: 0.7368 (ttm170) REVERT: Ac 52 VAL cc_start: 0.9186 (t) cc_final: 0.8646 (t) REVERT: Ae 5 LYS cc_start: 0.4638 (OUTLIER) cc_final: 0.3380 (pmtt) REVERT: Ae 6 THR cc_start: 0.4254 (t) cc_final: 0.3835 (t) REVERT: Ae 26 LYS cc_start: 0.6649 (mttt) cc_final: 0.6008 (tmtt) REVERT: Ae 29 LYS cc_start: 0.7866 (mtpt) cc_final: 0.7666 (mtmm) REVERT: Ae 56 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: BF 17 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7604 (m-10) REVERT: BF 95 GLN cc_start: 0.7256 (mm110) cc_final: 0.6917 (tm-30) REVERT: BF 154 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7886 (tp) REVERT: BF 175 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7731 (ptt-90) REVERT: BF 212 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8523 (mm-40) REVERT: BG 17 ASP cc_start: 0.5875 (m-30) cc_final: 0.5312 (m-30) REVERT: BG 44 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8612 (tm-30) REVERT: BG 55 VAL cc_start: 0.7837 (t) cc_final: 0.7168 (t) REVERT: BG 72 LYS cc_start: 0.7243 (mttt) cc_final: 0.7008 (mmmt) REVERT: BG 77 ILE cc_start: 0.8672 (mm) cc_final: 0.8367 (tp) REVERT: BG 107 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.6141 (pp30) REVERT: BG 188 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8419 (tt) REVERT: BG 202 ILE cc_start: 0.8866 (mt) cc_final: 0.8557 (tt) REVERT: BH 13 ARG cc_start: 0.4351 (mtm180) cc_final: 0.3398 (ttm170) REVERT: BH 34 GLU cc_start: 0.8224 (tp30) cc_final: 0.7933 (mp0) REVERT: BH 61 LYS cc_start: 0.6794 (OUTLIER) cc_final: 0.6095 (tmtt) REVERT: BH 68 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.7836 (m-10) REVERT: BH 116 GLN cc_start: 0.5341 (OUTLIER) cc_final: 0.5096 (pt0) REVERT: BH 154 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7340 (p0) REVERT: BH 155 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.3893 (mm) REVERT: BH 158 ILE cc_start: 0.6148 (mm) cc_final: 0.5137 (mm) REVERT: BH 168 ARG cc_start: 0.4669 (OUTLIER) cc_final: 0.1976 (ptm-80) REVERT: BH 201 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8242 (mm-40) REVERT: BI 20 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7572 (mp-120) REVERT: BI 67 VAL cc_start: 0.7737 (OUTLIER) cc_final: 0.7376 (t) REVERT: BI 78 HIS cc_start: 0.8114 (OUTLIER) cc_final: 0.7647 (p90) REVERT: BI 109 ILE cc_start: 0.8585 (tt) cc_final: 0.8320 (tt) REVERT: BJ 67 MET cc_start: 0.2941 (pmm) cc_final: 0.1052 (pmm) REVERT: BK 11 GLN cc_start: 0.7152 (tp40) cc_final: 0.6719 (mm-40) REVERT: BK 18 TYR cc_start: 0.7417 (m-80) cc_final: 0.7103 (m-80) REVERT: BK 36 LYS cc_start: 0.4064 (OUTLIER) cc_final: 0.3269 (tptp) REVERT: BK 67 GLU cc_start: 0.5934 (tp30) cc_final: 0.5676 (mm-30) REVERT: BK 70 LYS cc_start: 0.8031 (mtmt) cc_final: 0.7347 (mtpp) REVERT: BL 9 MET cc_start: 0.8629 (ttt) cc_final: 0.8226 (mpp) REVERT: BL 12 ARG cc_start: 0.8582 (mtp180) cc_final: 0.7651 (tmt170) REVERT: BL 13 ILE cc_start: 0.9067 (mt) cc_final: 0.8777 (mt) REVERT: BL 57 PRO cc_start: 0.7025 (Cg_exo) cc_final: 0.6102 (Cg_endo) REVERT: BL 86 ILE cc_start: 0.8271 (mp) cc_final: 0.7269 (mp) REVERT: BM 36 TYR cc_start: 0.3691 (t80) cc_final: 0.2912 (t80) REVERT: BM 64 THR cc_start: 0.2652 (OUTLIER) cc_final: 0.2326 (m) REVERT: BM 79 LEU cc_start: 0.4650 (OUTLIER) cc_final: 0.4228 (tp) REVERT: BM 117 HIS cc_start: 0.5642 (OUTLIER) cc_final: 0.5132 (m170) REVERT: BN 29 ARG cc_start: 0.8797 (mtt180) cc_final: 0.8352 (mtt180) REVERT: BN 48 THR cc_start: 0.5045 (m) cc_final: 0.4685 (m) REVERT: BN 49 VAL cc_start: 0.6798 (OUTLIER) cc_final: 0.5293 (t) REVERT: BN 95 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6338 (mm-30) REVERT: BO 62 GLN cc_start: 0.5828 (OUTLIER) cc_final: 0.5291 (tt0) REVERT: BO 83 ILE cc_start: 0.5040 (mp) cc_final: 0.4444 (mp) REVERT: BP 9 GLN cc_start: 0.7680 (mt0) cc_final: 0.7405 (mm-40) REVERT: BP 21 LYS cc_start: 0.8043 (mttt) cc_final: 0.7535 (tttt) REVERT: BP 66 VAL cc_start: 0.5442 (OUTLIER) cc_final: 0.4948 (m) REVERT: BP 97 ARG cc_start: 0.7638 (ttm170) cc_final: 0.7291 (mmp80) REVERT: BP 102 ARG cc_start: 0.5455 (mtp180) cc_final: 0.4676 (mmm160) REVERT: BQ 4 ILE cc_start: 0.4606 (mm) cc_final: 0.4224 (mm) REVERT: BQ 27 LYS cc_start: 0.1590 (OUTLIER) cc_final: 0.1132 (mtpt) REVERT: BQ 48 LEU cc_start: 0.5257 (OUTLIER) cc_final: 0.4921 (mp) REVERT: BR 26 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7806 (tpp-160) REVERT: BR 41 ARG cc_start: 0.7028 (ptt-90) cc_final: 0.6443 (mtt180) REVERT: BR 43 CYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6544 (p) REVERT: BR 57 ARG cc_start: 0.7336 (ttt180) cc_final: 0.6737 (ttt-90) REVERT: BS 56 LEU cc_start: 0.9318 (tp) cc_final: 0.8794 (tp) REVERT: BT 75 ARG cc_start: 0.4766 (OUTLIER) cc_final: 0.3020 (ttt180) REVERT: BU 48 GLU cc_start: 0.4614 (OUTLIER) cc_final: 0.3665 (pm20) REVERT: BU 50 LYS cc_start: 0.6175 (ttmt) cc_final: 0.5829 (tttp) REVERT: BU 101 ARG cc_start: 0.4837 (OUTLIER) cc_final: 0.2338 (tpt170) REVERT: BV 49 LYS cc_start: 0.1307 (OUTLIER) cc_final: 0.0524 (mmmm) REVERT: BV 58 LEU cc_start: 0.7990 (mt) cc_final: 0.7134 (mt) REVERT: BW 7 LYS cc_start: 0.6366 (OUTLIER) cc_final: 0.5968 (pttm) REVERT: BW 18 LYS cc_start: -0.0861 (OUTLIER) cc_final: -0.1345 (mttt) REVERT: BW 41 VAL cc_start: 0.4951 (OUTLIER) cc_final: 0.4740 (m) REVERT: BW 74 PHE cc_start: 0.3885 (OUTLIER) cc_final: 0.3416 (m-80) REVERT: BX 18 GLN cc_start: 0.8524 (mt0) cc_final: 0.8060 (mm110) REVERT: BX 51 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5728 (tm-30) REVERT: BY 9 ARG cc_start: 0.2954 (OUTLIER) cc_final: 0.2370 (mpt180) REVERT: CA 41 ARG cc_start: 0.6054 (mmt90) cc_final: 0.3360 (tpt90) REVERT: CA 42 VAL cc_start: 0.6113 (OUTLIER) cc_final: 0.5009 (m) REVERT: CA 68 TYR cc_start: 0.5688 (OUTLIER) cc_final: 0.4707 (p90) REVERT: CA 298 PRO cc_start: 0.7187 (Cg_endo) cc_final: 0.6678 (Cg_exo) REVERT: CA 301 SER cc_start: 0.7849 (OUTLIER) cc_final: 0.7409 (t) REVERT: CA 341 HIS cc_start: 0.6917 (m90) cc_final: 0.6708 (m90) REVERT: CA 369 LEU cc_start: 0.8840 (tp) cc_final: 0.8517 (tp) REVERT: CA 460 SER cc_start: 0.7050 (OUTLIER) cc_final: 0.6627 (p) REVERT: CA 464 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7941 (pp) REVERT: CA 524 ILE cc_start: 0.9403 (pt) cc_final: 0.9101 (mp) REVERT: CA 527 HIS cc_start: 0.8933 (t-170) cc_final: 0.8598 (t-170) REVERT: CA 563 MET cc_start: 0.7541 (mmp) cc_final: 0.6928 (tpp) outliers start: 1569 outliers final: 574 residues processed: 3100 average time/residue: 1.5863 time to fit residues: 8159.2648 Evaluate side-chains 2108 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 688 poor density : 1420 time to evaluate : 6.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 933 optimal weight: 10.0000 chunk 838 optimal weight: 4.9990 chunk 465 optimal weight: 9.9990 chunk 286 optimal weight: 9.9990 chunk 565 optimal weight: 20.0000 chunk 447 optimal weight: 20.0000 chunk 866 optimal weight: 7.9990 chunk 335 optimal weight: 10.0000 chunk 527 optimal weight: 10.0000 chunk 645 optimal weight: 5.9990 chunk 1004 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 27 HIS ** AC 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AD 186 HIS ** AD 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AD 233 HIS ** AE 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 132 HIS ** AE 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 38 HIS ** AK 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AL 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 88 ASN ** AM 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 89 ASN ** AO 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 81 HIS ** AR 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 57 ASN AT 60 ASN AU 82 GLN AU 87 GLN ** AV 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AV 43 ASN ** AV 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AW 32 HIS AX 3 HIS ** AY 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 51 GLN ** Aa 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 31 HIS Ae 33 ASN ** Ae 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 20 HIS ** Af 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BG 104 GLN BG 108 ASN BG 136 GLN ** BG 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 77 ASN ** BH 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 18 GLN BJ 32 ASN ** BJ 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 97 GLN BK 109 ASN BK 110 GLN BL 70 GLN BL 82 HIS BM 38 GLN BN 68 HIS BN 84 GLN ** BO 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 99 HIS ** BQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BR 52 GLN ** BS 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BT 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BT 82 GLN BW 53 ASN ** BW 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BX 18 GLN BX 45 GLN ** CA 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.583 163075 Z= 0.484 Angle : 1.429 44.110 242863 Z= 0.698 Chirality : 0.067 1.732 30675 Planarity : 0.012 0.150 13938 Dihedral : 27.376 179.206 79709 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 49.20 Ramachandran Plot: Outliers : 6.14 % Allowed : 24.07 % Favored : 69.79 % Rotamer: Outliers : 2.19 % Allowed : 12.00 % Favored : 85.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.97 % Twisted Proline : 0.90 % Twisted General : 0.80 % 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: -6.41 (0.07), residues: 6565 helix: -3.61 (0.08), residues: 1838 sheet: -2.73 (0.16), residues: 829 loop : -5.26 (0.07), residues: 3898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.005 TRPAe 34 HIS 0.037 0.004 HISAK 130 PHE 0.045 0.005 PHEAD 135 TYR 0.076 0.005 TYRAJ 76 ARG 0.056 0.002 ARGAJ 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2028 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1910 time to evaluate : 6.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AC 6 ARG cc_start: 0.5295 (ppt170) cc_final: 0.3217 (ttm170) REVERT: AC 99 ILE cc_start: 0.5537 (OUTLIER) cc_final: 0.5255 (pt) REVERT: AC 136 LEU cc_start: 0.1671 (OUTLIER) cc_final: 0.1403 (mm) REVERT: AC 218 MET cc_start: -0.3082 (ttp) cc_final: -0.3837 (ttp) REVERT: AD 26 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7551 (mmmm) REVERT: AD 46 GLN cc_start: 0.8374 (pm20) cc_final: 0.8068 (pm20) REVERT: AD 58 HIS cc_start: 0.7833 (m90) cc_final: 0.7446 (m90) REVERT: AD 63 ARG cc_start: 0.6658 (mmp80) cc_final: 0.5344 (tpp-160) REVERT: AD 83 GLU cc_start: 0.8435 (tp30) cc_final: 0.7401 (tp30) REVERT: AD 115 GLN cc_start: 0.8325 (pp30) cc_final: 0.7921 (pp30) REVERT: AD 133 LEU cc_start: 0.8954 (mt) cc_final: 0.8652 (mp) REVERT: AD 164 GLN cc_start: 0.8681 (tm-30) cc_final: 0.7729 (tm-30) REVERT: AD 169 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7405 (mm-30) REVERT: AD 176 ARG cc_start: 0.7860 (tpp-160) cc_final: 0.7431 (tpp80) REVERT: AD 177 LEU cc_start: 0.8191 (pt) cc_final: 0.7908 (pt) REVERT: AD 263 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8094 (mtm-85) REVERT: AE 38 THR cc_start: 0.6787 (m) cc_final: 0.6319 (m) REVERT: AE 44 TYR cc_start: 0.7362 (t80) cc_final: 0.6905 (t80) REVERT: AE 51 PHE cc_start: 0.7434 (p90) cc_final: 0.6594 (p90) REVERT: AE 57 LYS cc_start: 0.9178 (tmtt) cc_final: 0.8305 (ttpp) REVERT: AE 117 MET cc_start: 0.7519 (mtp) cc_final: 0.6666 (mtp) REVERT: AE 127 ASP cc_start: 0.8350 (t0) cc_final: 0.7843 (t0) REVERT: AE 170 LEU cc_start: 0.8712 (mt) cc_final: 0.8409 (tp) REVERT: AE 180 ASN cc_start: 0.8297 (p0) cc_final: 0.8034 (p0) REVERT: AE 185 LYS cc_start: 0.7434 (pttp) cc_final: 0.6896 (ttmm) REVERT: AE 197 ILE cc_start: 0.9036 (mp) cc_final: 0.8788 (mm) REVERT: AF 34 TRP cc_start: 0.8472 (t-100) cc_final: 0.7774 (t-100) REVERT: AF 112 MET cc_start: 0.8593 (ptm) cc_final: 0.8286 (ppp) REVERT: AF 145 GLU cc_start: 0.9516 (mm-30) cc_final: 0.8935 (tm-30) REVERT: AF 169 ASN cc_start: 0.6983 (p0) cc_final: 0.6729 (p0) REVERT: AF 194 MET cc_start: 0.4899 (ppp) cc_final: 0.4576 (ppp) REVERT: AG 15 VAL cc_start: 0.7343 (p) cc_final: 0.6982 (p) REVERT: AG 155 MET cc_start: 0.8770 (mtt) cc_final: 0.8415 (mpp) REVERT: AG 161 THR cc_start: 0.7811 (p) cc_final: 0.7245 (t) REVERT: AH 41 MET cc_start: 0.6379 (mtm) cc_final: 0.5842 (mtp) REVERT: AH 88 LEU cc_start: 0.6894 (tt) cc_final: 0.6317 (tp) REVERT: AH 171 LEU cc_start: 0.8337 (mt) cc_final: 0.7619 (mt) REVERT: AH 172 LYS cc_start: 0.7882 (mppt) cc_final: 0.7040 (pttm) REVERT: AK 55 VAL cc_start: 0.7736 (p) cc_final: 0.6512 (p) REVERT: AK 61 ARG cc_start: 0.8779 (mmm-85) cc_final: 0.8515 (ttp-170) REVERT: AK 82 LEU cc_start: 0.6659 (mm) cc_final: 0.6010 (tp) REVERT: AK 106 MET cc_start: 0.8483 (mtm) cc_final: 0.7986 (mtt) REVERT: AK 123 TYR cc_start: 0.7462 (m-10) cc_final: 0.7144 (m-10) REVERT: AL 1 MET cc_start: 0.4375 (ppp) cc_final: 0.3203 (ppp) REVERT: AL 20 MET cc_start: 0.8023 (tpt) cc_final: 0.7474 (tmm) REVERT: AL 31 LYS cc_start: 0.8704 (mttt) cc_final: 0.8401 (ttmt) REVERT: AL 37 ASP cc_start: 0.8310 (m-30) cc_final: 0.7926 (m-30) REVERT: AL 77 ILE cc_start: 0.5063 (tt) cc_final: 0.4723 (tt) REVERT: AL 86 ILE cc_start: 0.8272 (mt) cc_final: 0.7775 (mt) REVERT: AM 45 LEU cc_start: 0.7420 (tt) cc_final: 0.6056 (tp) REVERT: AM 59 LEU cc_start: 0.4576 (pp) cc_final: 0.3558 (mt) REVERT: AN 25 ASP cc_start: 0.6777 (m-30) cc_final: 0.4769 (m-30) REVERT: AN 37 LEU cc_start: 0.7568 (mt) cc_final: 0.7197 (mt) REVERT: AN 57 HIS cc_start: 0.7743 (t-170) cc_final: 0.7272 (t70) REVERT: AN 113 GLN cc_start: 0.8516 (tt0) cc_final: 0.7834 (tm-30) REVERT: AN 126 PRO cc_start: 0.8044 (OUTLIER) cc_final: 0.7584 (Cg_exo) REVERT: AN 127 ILE cc_start: 0.8412 (pt) cc_final: 0.8006 (pt) REVERT: AN 133 ARG cc_start: 0.8791 (pmt170) cc_final: 0.8589 (ptp-170) REVERT: AO 20 LEU cc_start: 0.8866 (tp) cc_final: 0.8609 (tp) REVERT: AO 40 LYS cc_start: 0.7475 (mmtm) cc_final: 0.6883 (mtpp) REVERT: AO 54 LEU cc_start: 0.9701 (mp) cc_final: 0.9288 (tp) REVERT: AO 64 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7710 (tpp80) REVERT: AP 18 ILE cc_start: 0.6396 (OUTLIER) cc_final: 0.6129 (mp) REVERT: AQ 9 LEU cc_start: 0.8805 (mt) cc_final: 0.8593 (tp) REVERT: AQ 21 GLU cc_start: 0.8518 (pp20) cc_final: 0.7859 (tm-30) REVERT: AQ 53 ARG cc_start: 0.6539 (tpm170) cc_final: 0.5692 (tpm170) REVERT: AQ 82 LEU cc_start: 0.8564 (tt) cc_final: 0.7917 (tt) REVERT: AQ 111 ARG cc_start: 0.7959 (ptt180) cc_final: 0.7529 (ptt180) REVERT: AR 14 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.7013 (m-70) REVERT: AR 32 PHE cc_start: 0.8170 (m-10) cc_final: 0.7917 (m-10) REVERT: AR 36 ARG cc_start: 0.6360 (mtt90) cc_final: 0.5980 (mtm180) REVERT: AR 64 ARG cc_start: 0.8245 (mmt90) cc_final: 0.7592 (mmt-90) REVERT: AR 109 LEU cc_start: 0.8726 (tt) cc_final: 0.8424 (tt) REVERT: AS 71 LEU cc_start: 0.8008 (tp) cc_final: 0.7536 (tp) REVERT: AT 38 TYR cc_start: 0.8183 (m-10) cc_final: 0.7950 (m-80) REVERT: AT 52 GLU cc_start: 0.8675 (mm-30) cc_final: 0.7803 (tt0) REVERT: AT 69 LEU cc_start: 0.8796 (mp) cc_final: 0.8265 (mp) REVERT: AT 96 ILE cc_start: 0.8881 (pt) cc_final: 0.8605 (mp) REVERT: AT 97 LYS cc_start: 0.7662 (pttt) cc_final: 0.7185 (tttm) REVERT: AU 7 VAL cc_start: 0.8274 (p) cc_final: 0.7453 (p) REVERT: AU 38 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8682 (tm-30) REVERT: AU 51 VAL cc_start: 0.7048 (t) cc_final: 0.6740 (p) REVERT: AU 75 ASP cc_start: 0.7611 (m-30) cc_final: 0.7248 (m-30) REVERT: AU 83 VAL cc_start: 0.7808 (m) cc_final: 0.7566 (t) REVERT: AW 1 MET cc_start: 0.7134 (pmm) cc_final: 0.6355 (ppp) REVERT: AW 132 ASN cc_start: 0.6995 (m-40) cc_final: 0.6542 (m-40) REVERT: AW 139 VAL cc_start: 0.6590 (t) cc_final: 0.5952 (t) REVERT: AW 155 LEU cc_start: 0.5185 (OUTLIER) cc_final: 0.4837 (mt) REVERT: AX 1 MET cc_start: 0.0360 (ptt) cc_final: -0.0651 (mtt) REVERT: AX 57 PHE cc_start: 0.8490 (m-10) cc_final: 0.8009 (m-10) REVERT: AX 62 LEU cc_start: 0.9380 (mt) cc_final: 0.9140 (mt) REVERT: AY 28 MET cc_start: 0.7978 (mtt) cc_final: 0.7343 (mtt) REVERT: AY 31 ARG cc_start: 0.8164 (mpp-170) cc_final: 0.7957 (mtt-85) REVERT: AY 52 ILE cc_start: 0.8647 (pt) cc_final: 0.8244 (pt) REVERT: Aa 6 HIS cc_start: 0.7512 (m90) cc_final: 0.7205 (m90) REVERT: Aa 43 TYR cc_start: 0.7474 (t80) cc_final: 0.7265 (t80) REVERT: Aa 48 ARG cc_start: 0.3835 (mtt-85) cc_final: 0.3597 (mtm-85) REVERT: Aa 52 THR cc_start: 0.6455 (m) cc_final: 0.6205 (m) REVERT: Aa 60 GLN cc_start: 0.8027 (mt0) cc_final: 0.7711 (mp10) REVERT: Ac 9 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5711 (mm) REVERT: Ac 50 ARG cc_start: 0.8307 (ttt180) cc_final: 0.7808 (ttp-110) REVERT: Ae 4 MET cc_start: 0.3475 (mmt) cc_final: 0.2142 (mmt) REVERT: Ae 21 LYS cc_start: 0.8572 (mtmm) cc_final: 0.8363 (mtmm) REVERT: Ae 26 LYS cc_start: 0.6647 (mttt) cc_final: 0.6343 (tmtt) REVERT: Ae 27 THR cc_start: 0.7262 (t) cc_final: 0.6933 (p) REVERT: Ae 54 GLU cc_start: 0.8754 (mp0) cc_final: 0.8284 (pm20) REVERT: Af 7 VAL cc_start: 0.7707 (t) cc_final: 0.7467 (t) REVERT: Af 15 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8587 (tttt) REVERT: BF 28 PHE cc_start: 0.6642 (t80) cc_final: 0.5932 (t80) REVERT: BF 30 ARG cc_start: 0.9064 (ptt180) cc_final: 0.8114 (tmt170) REVERT: BF 63 MET cc_start: 0.8364 (mmp) cc_final: 0.7633 (tmm) REVERT: BF 76 GLN cc_start: 0.9035 (mm110) cc_final: 0.8834 (tt0) REVERT: BF 108 ILE cc_start: 0.9524 (mm) cc_final: 0.9085 (mm) REVERT: BF 193 ASP cc_start: 0.7392 (m-30) cc_final: 0.7128 (m-30) REVERT: BG 12 LEU cc_start: 0.7690 (tp) cc_final: 0.7453 (tp) REVERT: BG 62 ASP cc_start: 0.8662 (t0) cc_final: 0.8412 (p0) REVERT: BG 110 ASN cc_start: 0.8106 (m-40) cc_final: 0.7819 (m-40) REVERT: BG 135 LYS cc_start: 0.9529 (mtmm) cc_final: 0.9313 (mttt) REVERT: BG 136 GLN cc_start: 0.9175 (tm130) cc_final: 0.8897 (tm-30) REVERT: BG 181 ASN cc_start: 0.8771 (t0) cc_final: 0.8450 (t0) REVERT: BG 204 LEU cc_start: 0.8696 (mt) cc_final: 0.7961 (tp) REVERT: BH 28 SER cc_start: 0.9242 (m) cc_final: 0.9029 (p) REVERT: BH 35 ARG cc_start: 0.8319 (mmp-170) cc_final: 0.7773 (ptt180) REVERT: BH 53 ASP cc_start: 0.8962 (p0) cc_final: 0.8570 (t70) REVERT: BH 70 ILE cc_start: 0.7449 (pt) cc_final: 0.7163 (pt) REVERT: BH 110 PHE cc_start: 0.7907 (t80) cc_final: 0.7572 (m-80) REVERT: BH 192 GLU cc_start: 0.6528 (mp0) cc_final: 0.6239 (mp0) REVERT: BH 201 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7762 (tp40) REVERT: BH 204 ILE cc_start: 0.8959 (mp) cc_final: 0.8698 (mp) REVERT: BI 12 LEU cc_start: 0.7806 (tt) cc_final: 0.7420 (tt) REVERT: BI 31 LEU cc_start: 0.8762 (mm) cc_final: 0.8176 (mm) REVERT: BI 33 VAL cc_start: 0.8741 (t) cc_final: 0.8182 (t) REVERT: BI 36 ASP cc_start: 0.8875 (p0) cc_final: 0.7176 (p0) REVERT: BI 38 GLN cc_start: 0.9443 (tm-30) cc_final: 0.9143 (mp10) REVERT: BI 64 ARG cc_start: 0.9087 (mmp80) cc_final: 0.8813 (mmp80) REVERT: BI 72 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7975 (tm-30) REVERT: BI 84 PHE cc_start: 0.6449 (t80) cc_final: 0.6186 (t80) REVERT: BI 92 LYS cc_start: 0.9256 (mmtp) cc_final: 0.8784 (mmmt) REVERT: BI 111 GLU cc_start: 0.9394 (tt0) cc_final: 0.9080 (pt0) REVERT: BI 139 LEU cc_start: 0.9216 (mp) cc_final: 0.9004 (mp) REVERT: BI 147 ASP cc_start: 0.8577 (t0) cc_final: 0.8322 (m-30) REVERT: BJ 3 ARG cc_start: 0.8667 (pmt-80) cc_final: 0.8255 (pmt-80) REVERT: BJ 67 MET cc_start: 0.4885 (pmm) cc_final: 0.4155 (pmm) REVERT: BJ 75 LEU cc_start: 0.8529 (mt) cc_final: 0.7992 (mt) REVERT: BJ 78 GLU cc_start: 0.8880 (tt0) cc_final: 0.8503 (pt0) REVERT: BJ 87 ARG cc_start: 0.4218 (mmt-90) cc_final: 0.2735 (mmm160) REVERT: BK 51 GLN cc_start: 0.7754 (mp-120) cc_final: 0.7419 (mp10) REVERT: BK 73 MET cc_start: 0.7292 (mmm) cc_final: 0.6286 (tmm) REVERT: BK 74 GLU cc_start: 0.7647 (pp20) cc_final: 0.7143 (pp20) REVERT: BK 137 LYS cc_start: 0.8104 (tmmt) cc_final: 0.7705 (tmtt) REVERT: BK 141 VAL cc_start: 0.8890 (t) cc_final: 0.8654 (t) REVERT: BL 3 THR cc_start: 0.4956 (p) cc_final: 0.4555 (p) REVERT: BL 12 ARG cc_start: 0.8779 (mtp180) cc_final: 0.8078 (tmt-80) REVERT: BL 15 ASN cc_start: 0.8024 (m-40) cc_final: 0.7809 (m110) REVERT: BL 26 VAL cc_start: 0.8646 (p) cc_final: 0.8402 (t) REVERT: BL 59 LEU cc_start: 0.8821 (mt) cc_final: 0.8538 (mt) REVERT: BM 7 THR cc_start: 0.2730 (m) cc_final: 0.2509 (m) REVERT: BN 56 HIS cc_start: 0.6787 (m-70) cc_final: 0.5778 (m90) REVERT: BO 18 ARG cc_start: 0.7884 (mtt-85) cc_final: 0.7405 (mmt180) REVERT: BO 32 ILE cc_start: 0.6996 (mp) cc_final: 0.6776 (pt) REVERT: BO 41 THR cc_start: 0.6500 (p) cc_final: 0.6277 (m) REVERT: BP 17 LYS cc_start: 0.9247 (mppt) cc_final: 0.8824 (mmtt) REVERT: BP 18 VAL cc_start: 0.8907 (m) cc_final: 0.8665 (p) REVERT: BP 21 LYS cc_start: 0.8388 (mttt) cc_final: 0.8132 (tmtt) REVERT: BP 22 SER cc_start: 0.8767 (t) cc_final: 0.8506 (t) REVERT: BP 27 LEU cc_start: 0.7469 (tp) cc_final: 0.7255 (tp) REVERT: BP 67 THR cc_start: 0.8490 (p) cc_final: 0.8263 (p) REVERT: BR 58 LYS cc_start: 0.8153 (tmtt) cc_final: 0.7912 (tmtt) REVERT: BS 35 ARG cc_start: 0.8971 (mtp-110) cc_final: 0.8494 (ttt180) REVERT: BS 38 ARG cc_start: 0.8688 (ptt180) cc_final: 0.8158 (ttp80) REVERT: BS 57 LEU cc_start: 0.9275 (mp) cc_final: 0.9065 (mp) REVERT: BT 11 SER cc_start: 0.8310 (p) cc_final: 0.8079 (m) REVERT: BT 72 ARG cc_start: 0.5983 (OUTLIER) cc_final: 0.5085 (ppt170) REVERT: BU 11 VAL cc_start: 0.8473 (t) cc_final: 0.8225 (m) REVERT: BU 29 HIS cc_start: 0.9466 (t-90) cc_final: 0.9009 (t-90) REVERT: BU 70 ARG cc_start: 0.7605 (mmt180) cc_final: 0.7357 (mmt-90) REVERT: BV 22 VAL cc_start: 0.6453 (m) cc_final: 0.5911 (p) REVERT: BV 32 ARG cc_start: 0.7353 (mtt-85) cc_final: 0.6440 (mmp-170) REVERT: BV 56 THR cc_start: 0.7036 (p) cc_final: 0.6125 (p) REVERT: BW 4 SER cc_start: 0.4797 (t) cc_final: 0.4418 (t) REVERT: BW 7 LYS cc_start: 0.7736 (tmtt) cc_final: 0.7501 (pttm) REVERT: BW 66 MET cc_start: 0.3907 (ptp) cc_final: 0.3635 (ptp) REVERT: BX 18 GLN cc_start: 0.8876 (mt0) cc_final: 0.8344 (mm110) REVERT: BX 36 LEU cc_start: 0.7912 (mt) cc_final: 0.7661 (mt) REVERT: CA 22 VAL cc_start: 0.8149 (m) cc_final: 0.7747 (m) REVERT: CA 42 VAL cc_start: 0.6718 (OUTLIER) cc_final: 0.6176 (t) REVERT: CA 72 ILE cc_start: 0.6611 (OUTLIER) cc_final: 0.6330 (mt) REVERT: CA 106 MET cc_start: 0.8112 (tpp) cc_final: 0.7729 (tpt) REVERT: CA 146 ASP cc_start: 0.8979 (p0) cc_final: 0.8568 (m-30) REVERT: CA 147 LEU cc_start: 0.8482 (tp) cc_final: 0.7949 (tp) REVERT: CA 188 GLN cc_start: 0.8080 (tt0) cc_final: 0.7618 (tp-100) REVERT: CA 218 VAL cc_start: 0.9075 (t) cc_final: 0.8832 (t) REVERT: CA 226 ILE cc_start: 0.9301 (mm) cc_final: 0.8706 (mm) REVERT: CA 309 MET cc_start: 0.7051 (mmp) cc_final: 0.6752 (mmp) REVERT: CA 324 LYS cc_start: 0.8707 (ptpt) cc_final: 0.8480 (ptpt) REVERT: CA 374 ARG cc_start: 0.8442 (mtp-110) cc_final: 0.8229 (mtp-110) REVERT: CA 416 MET cc_start: 0.8110 (mtt) cc_final: 0.7875 (mtm) REVERT: CA 507 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7755 (mmm-85) REVERT: CA 563 MET cc_start: 0.7202 (tpp) cc_final: 0.6838 (tpp) REVERT: CA 579 GLU cc_start: 0.8856 (tt0) cc_final: 0.8596 (tt0) outliers start: 118 outliers final: 36 residues processed: 1993 average time/residue: 1.4591 time to fit residues: 4851.3969 Evaluate side-chains 1445 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1396 time to evaluate : 6.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 558 optimal weight: 7.9990 chunk 311 optimal weight: 10.0000 chunk 835 optimal weight: 4.9990 chunk 683 optimal weight: 20.0000 chunk 277 optimal weight: 10.0000 chunk 1006 optimal weight: 5.9990 chunk 1086 optimal weight: 8.9990 chunk 896 optimal weight: 7.9990 chunk 997 optimal weight: 9.9990 chunk 343 optimal weight: 6.9990 chunk 807 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 143 HIS ** AD 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 180 ASN AE 192 ASN ** AG 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 108 ASN ** AG 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 130 ASN AH 143 GLN ** AJ 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 94 HIS AK 101 HIS ** AN 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 57 HIS ** AO 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AO 31 HIS ** AR 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 117 GLN ** AS 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AT 34 ASN ** AT 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AV 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AV 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY 41 GLN ** AY 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 47 GLN ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 26 ASN Ae 7 HIS Ae 33 ASN ** Af 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 25 ASN ** BF 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 69 HIS ** BH 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BI 130 ASN ** BJ 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 50 HIS BW 56 GLN BW 57 HIS BX 18 GLN CA 16 HIS ** CA 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 176 HIS ** CA 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 527 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.7481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.565 163075 Z= 0.409 Angle : 1.128 40.117 242863 Z= 0.559 Chirality : 0.055 2.067 30675 Planarity : 0.010 0.162 13938 Dihedral : 26.959 179.247 79709 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 43.10 Ramachandran Plot: Outliers : 4.30 % Allowed : 23.82 % Favored : 71.88 % Rotamer: Outliers : 1.30 % Allowed : 9.60 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.92 % Twisted Proline : 0.90 % Twisted General : 0.68 % 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: -5.37 (0.08), residues: 6565 helix: -2.37 (0.10), residues: 1863 sheet: -2.46 (0.16), residues: 909 loop : -4.77 (0.08), residues: 3793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRPBQ 64 HIS 0.018 0.003 HISCA 16 PHE 0.063 0.004 PHECA 148 TYR 0.066 0.004 TYRAS 91 ARG 0.027 0.002 ARGAL 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1838 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1768 time to evaluate : 6.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AC 6 ARG cc_start: 0.5372 (ppt170) cc_final: 0.2985 (ttm170) REVERT: AC 218 MET cc_start: -0.3324 (ttp) cc_final: -0.3532 (ttp) REVERT: AD 46 GLN cc_start: 0.8187 (pm20) cc_final: 0.7248 (pm20) REVERT: AD 58 HIS cc_start: 0.8066 (m90) cc_final: 0.7474 (m90) REVERT: AD 71 ASP cc_start: 0.9400 (t70) cc_final: 0.8831 (t0) REVERT: AD 87 ASN cc_start: 0.9544 (m-40) cc_final: 0.9324 (m110) REVERT: AD 115 GLN cc_start: 0.8466 (pp30) cc_final: 0.8027 (pp30) REVERT: AD 164 GLN cc_start: 0.8612 (tm-30) cc_final: 0.7855 (tm-30) REVERT: AD 176 ARG cc_start: 0.7668 (tpp-160) cc_final: 0.7442 (tpp80) REVERT: AD 177 LEU cc_start: 0.8395 (pt) cc_final: 0.7997 (pt) REVERT: AD 190 TYR cc_start: 0.8195 (m-80) cc_final: 0.7935 (m-80) REVERT: AD 200 ASP cc_start: 0.8798 (m-30) cc_final: 0.8565 (p0) REVERT: AD 217 ARG cc_start: 0.8440 (ptp-170) cc_final: 0.8113 (ptp-170) REVERT: AD 242 ARG cc_start: 0.7723 (ptt180) cc_final: 0.7429 (ptt180) REVERT: AE 22 PRO cc_start: 0.8586 (OUTLIER) cc_final: 0.8173 (Cg_endo) REVERT: AE 27 LEU cc_start: 0.8553 (tp) cc_final: 0.8240 (tp) REVERT: AE 51 PHE cc_start: 0.7023 (p90) cc_final: 0.5948 (p90) REVERT: AE 127 ASP cc_start: 0.8407 (t0) cc_final: 0.7837 (t0) REVERT: AE 156 MET cc_start: 0.7616 (tpt) cc_final: 0.6649 (tpt) REVERT: AE 160 TYR cc_start: 0.7690 (m-80) cc_final: 0.6788 (m-80) REVERT: AE 170 LEU cc_start: 0.8678 (mt) cc_final: 0.8428 (tp) REVERT: AF 74 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7439 (mtt-85) REVERT: AF 112 MET cc_start: 0.8643 (ptm) cc_final: 0.8340 (ptm) REVERT: AF 124 LEU cc_start: 0.7121 (tp) cc_final: 0.6846 (tp) REVERT: AF 145 GLU cc_start: 0.9567 (mm-30) cc_final: 0.9000 (tm-30) REVERT: AF 160 ASN cc_start: 0.9123 (t0) cc_final: 0.8809 (t0) REVERT: AG 14 GLU cc_start: 0.9413 (tm-30) cc_final: 0.8593 (tm-30) REVERT: AG 18 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8221 (pt0) REVERT: AG 155 MET cc_start: 0.8830 (mtt) cc_final: 0.8527 (mpp) REVERT: AH 35 VAL cc_start: 0.2853 (OUTLIER) cc_final: 0.2646 (m) REVERT: AH 38 SER cc_start: 0.7599 (t) cc_final: 0.7065 (p) REVERT: AH 41 MET cc_start: 0.6936 (mtm) cc_final: 0.6296 (mtm) REVERT: AH 67 LEU cc_start: 0.6514 (mt) cc_final: 0.6264 (mt) REVERT: AH 83 TYR cc_start: 0.8201 (t80) cc_final: 0.7876 (t80) REVERT: AH 97 ARG cc_start: 0.8514 (ptp90) cc_final: 0.8229 (mpp80) REVERT: AJ 10 LEU cc_start: 0.7828 (pt) cc_final: 0.6724 (tp) REVERT: AJ 109 LYS cc_start: 0.8135 (tttt) cc_final: 0.7706 (mmtm) REVERT: AJ 136 VAL cc_start: 0.5337 (t) cc_final: 0.4876 (m) REVERT: AK 28 THR cc_start: 0.8436 (p) cc_final: 0.7883 (p) REVERT: AK 58 ASP cc_start: 0.9236 (p0) cc_final: 0.9003 (p0) REVERT: AK 82 LEU cc_start: 0.6879 (mm) cc_final: 0.6416 (tp) REVERT: AK 106 MET cc_start: 0.8470 (mtm) cc_final: 0.8158 (mtt) REVERT: AK 123 TYR cc_start: 0.7511 (m-80) cc_final: 0.7261 (m-80) REVERT: AL 5 GLN cc_start: 0.8005 (tp40) cc_final: 0.7400 (tp-100) REVERT: AL 6 THR cc_start: 0.8536 (t) cc_final: 0.7935 (t) REVERT: AL 20 MET cc_start: 0.8208 (tpt) cc_final: 0.7938 (tmm) REVERT: AL 31 LYS cc_start: 0.9006 (mttt) cc_final: 0.8647 (ttmt) REVERT: AL 39 ILE cc_start: 0.8148 (mp) cc_final: 0.7943 (mp) REVERT: AL 86 ILE cc_start: 0.8871 (mt) cc_final: 0.8584 (mt) REVERT: AM 45 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7095 (tt) REVERT: AM 70 GLN cc_start: 0.6569 (pt0) cc_final: 0.6203 (mm-40) REVERT: AN 7 MET cc_start: 0.7536 (mtt) cc_final: 0.7329 (mtp) REVERT: AN 37 LEU cc_start: 0.8187 (mt) cc_final: 0.7918 (mt) REVERT: AN 74 TYR cc_start: 0.6117 (m-10) cc_final: 0.5091 (m-10) REVERT: AN 83 MET cc_start: 0.7598 (pmm) cc_final: 0.7347 (pmm) REVERT: AN 113 GLN cc_start: 0.8428 (tt0) cc_final: 0.8032 (tm-30) REVERT: AN 133 ARG cc_start: 0.8894 (pmt170) cc_final: 0.8209 (mtt-85) REVERT: AO 17 ARG cc_start: 0.8463 (mtt90) cc_final: 0.7824 (mtt-85) REVERT: AO 64 ARG cc_start: 0.8733 (pmt-80) cc_final: 0.8163 (tpp80) REVERT: AO 70 LEU cc_start: 0.9016 (mt) cc_final: 0.8364 (pp) REVERT: AO 78 LYS cc_start: 0.9076 (tmtt) cc_final: 0.8860 (tptp) REVERT: AO 117 VAL cc_start: 0.8702 (p) cc_final: 0.8462 (m) REVERT: AP 20 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.5975 (mmt-90) REVERT: AP 92 TYR cc_start: 0.7694 (t80) cc_final: 0.7207 (t80) REVERT: AQ 21 GLU cc_start: 0.8859 (pp20) cc_final: 0.8442 (pm20) REVERT: AQ 53 ARG cc_start: 0.6970 (tpm170) cc_final: 0.6083 (tpm170) REVERT: AQ 70 VAL cc_start: 0.7786 (t) cc_final: 0.7475 (t) REVERT: AQ 75 ILE cc_start: 0.7344 (mt) cc_final: 0.6933 (mt) REVERT: AQ 82 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8236 (mt) REVERT: AR 20 LEU cc_start: 0.8656 (mt) cc_final: 0.8282 (mt) REVERT: AR 64 ARG cc_start: 0.8642 (mmt90) cc_final: 0.8141 (mmm-85) REVERT: AS 71 LEU cc_start: 0.8311 (tp) cc_final: 0.7655 (tp) REVERT: AT 27 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7545 (ptpp) REVERT: AT 34 ASN cc_start: 0.8624 (m-40) cc_final: 0.8289 (m110) REVERT: AT 37 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7662 (ptm160) REVERT: AT 52 GLU cc_start: 0.8654 (mm-30) cc_final: 0.7840 (tt0) REVERT: AT 97 LYS cc_start: 0.7391 (ptpp) cc_final: 0.7124 (ttmt) REVERT: AU 8 ILE cc_start: 0.8687 (pt) cc_final: 0.8321 (pt) REVERT: AU 9 LEU cc_start: 0.8420 (pp) cc_final: 0.7901 (pp) REVERT: AU 38 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8748 (tm-30) REVERT: AU 57 LEU cc_start: 0.8254 (tp) cc_final: 0.8006 (tt) REVERT: AW 28 MET cc_start: 0.7406 (ppp) cc_final: 0.7172 (ppp) REVERT: AW 89 PHE cc_start: 0.6343 (m-80) cc_final: 0.5801 (m-10) REVERT: AW 138 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8174 (tm-30) REVERT: AX 1 MET cc_start: 0.1105 (ptt) cc_final: 0.0627 (mmt) REVERT: AX 17 GLN cc_start: 0.7748 (tp40) cc_final: 0.7373 (tp40) REVERT: AX 36 ILE cc_start: 0.8594 (mt) cc_final: 0.8304 (mt) REVERT: AX 49 LYS cc_start: 0.9226 (mttt) cc_final: 0.8985 (mtmm) REVERT: AX 62 LEU cc_start: 0.9416 (mt) cc_final: 0.9177 (mt) REVERT: AY 28 MET cc_start: 0.7673 (mtt) cc_final: 0.7009 (mtt) REVERT: AY 39 LEU cc_start: 0.8772 (mt) cc_final: 0.8564 (mt) REVERT: AY 48 LEU cc_start: 0.7927 (mp) cc_final: 0.7445 (mp) REVERT: AY 65 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8946 (pt0) REVERT: AZ 4 LEU cc_start: 0.8944 (tt) cc_final: 0.8612 (mm) REVERT: AZ 6 VAL cc_start: 0.8905 (m) cc_final: 0.8676 (m) REVERT: Aa 6 HIS cc_start: 0.8182 (m90) cc_final: 0.7665 (m90) REVERT: Aa 32 TYR cc_start: 0.6579 (p90) cc_final: 0.5867 (p90) REVERT: Aa 47 GLN cc_start: 0.7522 (tt0) cc_final: 0.7194 (mm-40) REVERT: Aa 55 ARG cc_start: 0.7314 (tpt170) cc_final: 0.6786 (tpt170) REVERT: Aa 57 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7496 (mm-30) REVERT: Ac 14 THR cc_start: 0.6173 (p) cc_final: 0.5852 (p) REVERT: Ac 18 ARG cc_start: 0.8130 (mmp80) cc_final: 0.7890 (mmp80) REVERT: Ac 37 ARG cc_start: 0.7863 (mtt180) cc_final: 0.6469 (mmt90) REVERT: Ac 50 ARG cc_start: 0.8388 (ttt180) cc_final: 0.7661 (ttp80) REVERT: Ac 51 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7742 (tm-30) REVERT: Ad 6 GLN cc_start: 0.7125 (pm20) cc_final: 0.6884 (pm20) REVERT: Ae 27 THR cc_start: 0.7862 (t) cc_final: 0.7377 (m) REVERT: Ae 54 GLU cc_start: 0.7993 (mp0) cc_final: 0.7739 (pm20) REVERT: Af 15 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8398 (tttt) REVERT: Af 17 ILE cc_start: 0.8717 (mt) cc_final: 0.8066 (mt) REVERT: Af 18 ARG cc_start: 0.8284 (tpp80) cc_final: 0.7842 (tpp80) REVERT: Af 19 ARG cc_start: 0.7837 (ttm170) cc_final: 0.7497 (mtt-85) REVERT: Af 22 ARG cc_start: 0.6389 (mtt180) cc_final: 0.6044 (mtm-85) REVERT: BF 17 PHE cc_start: 0.7554 (m-80) cc_final: 0.7121 (m-10) REVERT: BF 28 PHE cc_start: 0.7305 (t80) cc_final: 0.6275 (t80) REVERT: BF 69 LEU cc_start: 0.9319 (tp) cc_final: 0.9064 (mm) REVERT: BF 76 GLN cc_start: 0.8705 (mm110) cc_final: 0.8436 (tt0) REVERT: BF 96 ARG cc_start: 0.8051 (mpt180) cc_final: 0.6605 (tpm170) REVERT: BF 106 LYS cc_start: 0.8531 (pptt) cc_final: 0.8048 (pptt) REVERT: BF 182 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8971 (mp) REVERT: BF 191 ASP cc_start: 0.8315 (p0) cc_final: 0.8080 (p0) REVERT: BF 199 TYR cc_start: 0.8609 (m-10) cc_final: 0.8305 (m-10) REVERT: BF 212 GLN cc_start: 0.7759 (tp40) cc_final: 0.7554 (tp40) REVERT: BG 36 ASP cc_start: 0.8590 (t70) cc_final: 0.8184 (m-30) REVERT: BG 123 GLN cc_start: 0.8808 (mt0) cc_final: 0.8601 (mt0) REVERT: BG 131 ARG cc_start: 0.9446 (mtm-85) cc_final: 0.9044 (mtp-110) REVERT: BG 142 MET cc_start: 0.8578 (tmm) cc_final: 0.8073 (tpt) REVERT: BG 143 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8876 (pt0) REVERT: BG 190 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7199 (tpm170) REVERT: BG 191 THR cc_start: 0.8975 (p) cc_final: 0.8751 (p) REVERT: BG 201 TYR cc_start: 0.7833 (m-10) cc_final: 0.7487 (m-80) REVERT: BG 204 LEU cc_start: 0.8718 (mt) cc_final: 0.8258 (mp) REVERT: BH 33 MET cc_start: 0.8117 (mpp) cc_final: 0.7880 (mmt) REVERT: BH 35 ARG cc_start: 0.8889 (mmp-170) cc_final: 0.7491 (ptt180) REVERT: BH 53 ASP cc_start: 0.9168 (p0) cc_final: 0.8587 (t0) REVERT: BH 61 LYS cc_start: 0.8766 (tmtt) cc_final: 0.8162 (tmtt) REVERT: BH 106 TYR cc_start: 0.8813 (t80) cc_final: 0.8296 (t80) REVERT: BH 192 GLU cc_start: 0.6910 (mp0) cc_final: 0.6701 (mp0) REVERT: BH 205 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8316 (mt-10) REVERT: BI 7 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6971 (mt-10) REVERT: BI 9 LYS cc_start: 0.9036 (tppt) cc_final: 0.8815 (tppt) REVERT: BI 36 ASP cc_start: 0.8987 (p0) cc_final: 0.8599 (p0) REVERT: BI 56 GLN cc_start: 0.9160 (mp10) cc_final: 0.8931 (mp10) REVERT: BI 64 ARG cc_start: 0.9094 (mmp80) cc_final: 0.8794 (mmp80) REVERT: BI 80 ILE cc_start: 0.8560 (tp) cc_final: 0.8058 (tp) REVERT: BI 84 PHE cc_start: 0.6697 (t80) cc_final: 0.6348 (t80) REVERT: BI 92 LYS cc_start: 0.9100 (mmtp) cc_final: 0.8778 (mmmt) REVERT: BI 100 VAL cc_start: 0.8717 (t) cc_final: 0.8516 (p) REVERT: BI 111 GLU cc_start: 0.9225 (tt0) cc_final: 0.8872 (pt0) REVERT: BI 129 ILE cc_start: 0.9093 (pt) cc_final: 0.8700 (pt) REVERT: BI 133 TYR cc_start: 0.8795 (m-80) cc_final: 0.8427 (m-80) REVERT: BJ 4 TYR cc_start: 0.5462 (m-10) cc_final: 0.5146 (m-10) REVERT: BJ 45 LEU cc_start: 0.9228 (tt) cc_final: 0.8949 (tt) REVERT: BJ 52 ILE cc_start: 0.3926 (mt) cc_final: 0.3297 (mt) REVERT: BJ 67 MET cc_start: 0.5674 (pmm) cc_final: 0.5006 (pmm) REVERT: BJ 73 ASN cc_start: 0.9068 (t0) cc_final: 0.8434 (p0) REVERT: BJ 75 LEU cc_start: 0.8636 (mt) cc_final: 0.8436 (mt) REVERT: BJ 87 ARG cc_start: 0.4165 (mmt-90) cc_final: 0.3565 (mmm160) REVERT: BK 73 MET cc_start: 0.6733 (mmm) cc_final: 0.6130 (tmm) REVERT: BK 74 GLU cc_start: 0.8157 (pp20) cc_final: 0.7827 (pp20) REVERT: BK 89 MET cc_start: 0.7556 (ppp) cc_final: 0.6779 (ppp) REVERT: BK 142 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8002 (mm-30) REVERT: BL 54 ASP cc_start: 0.8213 (m-30) cc_final: 0.7772 (t0) REVERT: BL 67 PRO cc_start: 0.7368 (Cg_exo) cc_final: 0.7143 (Cg_endo) REVERT: BL 82 HIS cc_start: 0.8912 (t-90) cc_final: 0.8196 (t-170) REVERT: BL 86 ILE cc_start: 0.9144 (mp) cc_final: 0.8302 (mp) REVERT: BO 124 LYS cc_start: 0.8566 (mmmm) cc_final: 0.8327 (mttp) REVERT: BP 9 GLN cc_start: 0.9189 (pt0) cc_final: 0.8976 (pt0) REVERT: BP 17 LYS cc_start: 0.9385 (mppt) cc_final: 0.8868 (mmtt) REVERT: BP 21 LYS cc_start: 0.8718 (mttt) cc_final: 0.8371 (tmtt) REVERT: BP 22 SER cc_start: 0.8789 (t) cc_final: 0.8493 (t) REVERT: BP 70 ILE cc_start: 0.9490 (mm) cc_final: 0.9232 (mm) REVERT: BP 100 ILE cc_start: 0.8737 (mp) cc_final: 0.8505 (mp) REVERT: BQ 82 MET cc_start: 0.8162 (ppp) cc_final: 0.7859 (ppp) REVERT: BS 28 GLN cc_start: 0.8520 (mm-40) cc_final: 0.7844 (mm-40) REVERT: BS 29 VAL cc_start: 0.9195 (t) cc_final: 0.8837 (p) REVERT: BS 42 HIS cc_start: 0.6977 (OUTLIER) cc_final: 0.5701 (p90) REVERT: BT 27 LYS cc_start: 0.8848 (tmtt) cc_final: 0.8480 (pttt) REVERT: BT 31 LYS cc_start: 0.7995 (tmtt) cc_final: 0.7479 (tttt) REVERT: BT 35 LYS cc_start: 0.8958 (tmtt) cc_final: 0.8756 (tptp) REVERT: BT 54 GLU cc_start: 0.9218 (pt0) cc_final: 0.8896 (pp20) REVERT: BU 11 VAL cc_start: 0.8487 (t) cc_final: 0.8188 (m) REVERT: BU 26 GLN cc_start: 0.8425 (tp-100) cc_final: 0.8197 (tp-100) REVERT: BU 29 HIS cc_start: 0.9453 (t-90) cc_final: 0.8942 (t-90) REVERT: BU 32 TYR cc_start: 0.9204 (m-10) cc_final: 0.8989 (m-10) REVERT: BU 34 LYS cc_start: 0.9438 (tmmt) cc_final: 0.8925 (tttt) REVERT: BU 63 ARG cc_start: 0.7081 (ttp-170) cc_final: 0.6659 (ttp-170) REVERT: BV 32 ARG cc_start: 0.7275 (mtt-85) cc_final: 0.6768 (mmp80) REVERT: BW 4 SER cc_start: 0.5666 (t) cc_final: 0.5334 (m) REVERT: BW 7 LYS cc_start: 0.7998 (tmtt) cc_final: 0.7721 (ptpp) REVERT: BW 28 LYS cc_start: 0.8112 (tmmt) cc_final: 0.7658 (mmtt) REVERT: BW 37 ARG cc_start: 0.3042 (mmp80) cc_final: 0.2819 (mmt-90) REVERT: BW 73 GLU cc_start: 0.7233 (pt0) cc_final: 0.6773 (pt0) REVERT: CA 70 ILE cc_start: 0.7560 (mt) cc_final: 0.7181 (mm) REVERT: CA 89 MET cc_start: 0.8577 (mtm) cc_final: 0.8302 (mtm) REVERT: CA 106 MET cc_start: 0.8493 (tpp) cc_final: 0.8195 (tpp) REVERT: CA 146 ASP cc_start: 0.9048 (p0) cc_final: 0.8542 (m-30) REVERT: CA 147 LEU cc_start: 0.8475 (tp) cc_final: 0.7961 (tp) REVERT: CA 156 GLU cc_start: 0.7898 (tt0) cc_final: 0.7638 (tt0) REVERT: CA 223 ILE cc_start: 0.8855 (mm) cc_final: 0.8385 (mm) REVERT: CA 248 ASN cc_start: 0.8179 (t0) cc_final: 0.7792 (t0) REVERT: CA 253 LYS cc_start: 0.7659 (pttt) cc_final: 0.7230 (ptmt) REVERT: CA 266 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.6579 (p0) REVERT: CA 324 LYS cc_start: 0.8698 (ptpt) cc_final: 0.8196 (ptpt) REVERT: CA 373 MET cc_start: 0.8499 (mmp) cc_final: 0.8215 (mmm) REVERT: CA 488 LEU cc_start: 0.8438 (mt) cc_final: 0.8227 (mt) REVERT: CA 493 GLN cc_start: 0.9020 (pm20) cc_final: 0.8799 (pp30) REVERT: CA 505 GLN cc_start: 0.8387 (pt0) cc_final: 0.7844 (pt0) REVERT: CA 507 ARG cc_start: 0.8161 (mmm-85) cc_final: 0.7762 (mmm-85) REVERT: CA 519 TYR cc_start: 0.8305 (p90) cc_final: 0.7844 (p90) REVERT: CA 563 MET cc_start: 0.7452 (tpp) cc_final: 0.7190 (tpp) REVERT: CA 579 GLU cc_start: 0.8612 (tt0) cc_final: 0.7984 (tt0) outliers start: 70 outliers final: 26 residues processed: 1820 average time/residue: 1.4290 time to fit residues: 4356.6825 Evaluate side-chains 1391 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1357 time to evaluate : 6.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 994 optimal weight: 30.0000 chunk 756 optimal weight: 20.0000 chunk 522 optimal weight: 5.9990 chunk 111 optimal weight: 30.0000 chunk 480 optimal weight: 9.9990 chunk 675 optimal weight: 30.0000 chunk 1009 optimal weight: 0.0070 chunk 1069 optimal weight: 7.9990 chunk 527 optimal weight: 8.9990 chunk 957 optimal weight: 20.0000 chunk 288 optimal weight: 30.0000 overall best weight: 6.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AD 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 11 GLN AK 94 HIS AK 101 HIS AM 81 GLN ** AN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 91 GLN AP 38 GLN ** AQ 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 104 ASN AR 14 HIS AR 44 ASN ** AR 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AT 60 ASN ** AT 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AV 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BG 102 ASN BG 110 ASN BG 118 GLN BG 136 GLN ** BG 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 78 HIS ** BJ 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 15 ASN ** BL 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 13 HIS BO 116 HIS ** BP 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 92 HIS ** BR 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 46 HIS ** BS 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 18 GLN ** CA 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.8916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.571 163075 Z= 0.393 Angle : 1.046 41.186 242863 Z= 0.516 Chirality : 0.052 2.394 30675 Planarity : 0.009 0.164 13938 Dihedral : 26.893 179.772 79709 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 39.67 Ramachandran Plot: Outliers : 3.64 % Allowed : 21.14 % Favored : 75.22 % Rotamer: Outliers : 0.48 % Allowed : 7.23 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.92 % Twisted Proline : 0.90 % Twisted General : 0.62 % 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: -4.97 (0.09), residues: 6565 helix: -1.90 (0.10), residues: 1889 sheet: -2.23 (0.16), residues: 889 loop : -4.59 (0.08), residues: 3787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRPAe 34 HIS 0.022 0.003 HISAK 130 PHE 0.047 0.004 PHEAW 48 TYR 0.095 0.004 TYRAD 84 ARG 0.027 0.001 ARGAc 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1760 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1734 time to evaluate : 7.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AC 6 ARG cc_start: 0.5245 (ppt170) cc_final: 0.2907 (ttt180) REVERT: AC 217 THR cc_start: 0.6459 (m) cc_final: 0.6124 (m) REVERT: AC 218 MET cc_start: -0.3025 (ttp) cc_final: -0.3241 (ttp) REVERT: AD 46 GLN cc_start: 0.7813 (pm20) cc_final: 0.6885 (pm20) REVERT: AD 58 HIS cc_start: 0.7895 (m90) cc_final: 0.7494 (m90) REVERT: AD 66 ASP cc_start: 0.8220 (t0) cc_final: 0.7590 (t0) REVERT: AD 106 ILE cc_start: 0.8984 (mp) cc_final: 0.8770 (mm) REVERT: AD 115 GLN cc_start: 0.8356 (pp30) cc_final: 0.7751 (pp30) REVERT: AD 164 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8022 (tm-30) REVERT: AD 174 ILE cc_start: 0.8638 (mp) cc_final: 0.8016 (mp) REVERT: AD 176 ARG cc_start: 0.7813 (tpp-160) cc_final: 0.7504 (tpp80) REVERT: AD 177 LEU cc_start: 0.8538 (pt) cc_final: 0.8251 (pt) REVERT: AD 186 HIS cc_start: 0.7345 (m90) cc_final: 0.6726 (m90) REVERT: AD 190 TYR cc_start: 0.7958 (m-80) cc_final: 0.7638 (m-10) REVERT: AD 200 ASP cc_start: 0.8937 (m-30) cc_final: 0.8624 (p0) REVERT: AD 230 ASP cc_start: 0.8970 (m-30) cc_final: 0.8110 (p0) REVERT: AD 233 HIS cc_start: 0.8472 (p-80) cc_final: 0.8186 (p-80) REVERT: AD 242 ARG cc_start: 0.8187 (ptt180) cc_final: 0.7971 (ptt180) REVERT: AD 250 TRP cc_start: 0.7977 (t-100) cc_final: 0.7716 (t-100) REVERT: AE 11 MET cc_start: 0.8723 (mmp) cc_final: 0.8521 (mmp) REVERT: AE 51 PHE cc_start: 0.7279 (p90) cc_final: 0.6417 (p90) REVERT: AE 79 ARG cc_start: 0.4182 (ttt180) cc_final: 0.3908 (ttt180) REVERT: AE 127 ASP cc_start: 0.8572 (t0) cc_final: 0.8081 (t0) REVERT: AE 156 MET cc_start: 0.7985 (tpt) cc_final: 0.7546 (tpt) REVERT: AE 160 TYR cc_start: 0.7658 (m-80) cc_final: 0.7064 (m-80) REVERT: AE 168 MET cc_start: 0.8922 (mmp) cc_final: 0.7216 (mtp) REVERT: AE 185 LYS cc_start: 0.8251 (pttp) cc_final: 0.7677 (ptmm) REVERT: AF 88 VAL cc_start: 0.8638 (t) cc_final: 0.8297 (m) REVERT: AF 112 MET cc_start: 0.8952 (ptm) cc_final: 0.8652 (ptm) REVERT: AF 124 LEU cc_start: 0.7484 (tp) cc_final: 0.7133 (tp) REVERT: AF 145 GLU cc_start: 0.9587 (mm-30) cc_final: 0.9005 (tm-30) REVERT: AF 157 VAL cc_start: 0.8919 (m) cc_final: 0.8654 (p) REVERT: AF 160 ASN cc_start: 0.9047 (t0) cc_final: 0.8740 (t0) REVERT: AF 162 LEU cc_start: 0.9000 (mt) cc_final: 0.8555 (mt) REVERT: AF 169 ASN cc_start: 0.7795 (t0) cc_final: 0.7369 (t0) REVERT: AG 155 MET cc_start: 0.8827 (mtt) cc_final: 0.8560 (mpp) REVERT: AH 30 LYS cc_start: 0.8522 (tmtt) cc_final: 0.7815 (pttm) REVERT: AH 38 SER cc_start: 0.7533 (t) cc_final: 0.7049 (p) REVERT: AH 41 MET cc_start: 0.7820 (mtm) cc_final: 0.7213 (mtm) REVERT: AJ 10 LEU cc_start: 0.7553 (pt) cc_final: 0.6636 (tp) REVERT: AJ 35 MET cc_start: 0.5389 (tpt) cc_final: 0.5056 (tpp) REVERT: AJ 126 MET cc_start: 0.0457 (mmm) cc_final: 0.0249 (mmm) REVERT: AJ 136 VAL cc_start: 0.5529 (t) cc_final: 0.5140 (m) REVERT: AK 84 LYS cc_start: 0.9009 (mtmm) cc_final: 0.8457 (mmmt) REVERT: AK 106 MET cc_start: 0.8773 (mtt) cc_final: 0.8529 (mtt) REVERT: AK 107 LEU cc_start: 0.8758 (tt) cc_final: 0.8549 (tt) REVERT: AK 123 TYR cc_start: 0.8089 (m-80) cc_final: 0.7860 (m-80) REVERT: AL 7 TYR cc_start: 0.9206 (m-80) cc_final: 0.8998 (m-10) REVERT: AL 9 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7771 (mp0) REVERT: AL 20 MET cc_start: 0.8344 (tpt) cc_final: 0.7720 (tmm) REVERT: AL 31 LYS cc_start: 0.9174 (mttt) cc_final: 0.8716 (ttmt) REVERT: AL 32 TYR cc_start: 0.8276 (m-80) cc_final: 0.7126 (m-80) REVERT: AL 115 VAL cc_start: 0.8336 (t) cc_final: 0.8062 (m) REVERT: AM 70 GLN cc_start: 0.6735 (pt0) cc_final: 0.6308 (mm-40) REVERT: AM 136 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8894 (pp20) REVERT: AN 25 ASP cc_start: 0.4722 (m-30) cc_final: 0.3774 (p0) REVERT: AN 37 LEU cc_start: 0.8291 (mt) cc_final: 0.7887 (mt) REVERT: AN 77 LYS cc_start: 0.8692 (tmmt) cc_final: 0.8463 (tttt) REVERT: AN 80 GLU cc_start: 0.9093 (pm20) cc_final: 0.8513 (mp0) REVERT: AN 83 MET cc_start: 0.7796 (pmm) cc_final: 0.7566 (pmm) REVERT: AN 103 MET cc_start: 0.3958 (mpp) cc_final: 0.3697 (mpp) REVERT: AN 113 GLN cc_start: 0.8359 (tt0) cc_final: 0.7599 (tm-30) REVERT: AN 128 LYS cc_start: 0.7073 (mmmt) cc_final: 0.6643 (mmmt) REVERT: AN 133 ARG cc_start: 0.8921 (pmt170) cc_final: 0.8278 (mtt-85) REVERT: AO 26 LYS cc_start: 0.8814 (mttm) cc_final: 0.8493 (mmtt) REVERT: AO 40 LYS cc_start: 0.8633 (mptt) cc_final: 0.8430 (mmtm) REVERT: AO 54 LEU cc_start: 0.9745 (mp) cc_final: 0.9419 (tt) REVERT: AO 69 ASP cc_start: 0.9063 (t70) cc_final: 0.8756 (t70) REVERT: AO 74 LYS cc_start: 0.9328 (mmtm) cc_final: 0.9036 (tptp) REVERT: AP 18 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6573 (mp) REVERT: AQ 1 MET cc_start: 0.7971 (ppp) cc_final: 0.7444 (ppp) REVERT: AQ 41 ARG cc_start: 0.8163 (mmp80) cc_final: 0.7842 (mmp80) REVERT: AQ 70 VAL cc_start: 0.7951 (t) cc_final: 0.7576 (t) REVERT: AQ 75 ILE cc_start: 0.7269 (mt) cc_final: 0.6739 (mt) REVERT: AQ 96 ARG cc_start: 0.7367 (mtm-85) cc_final: 0.7025 (mtm-85) REVERT: AQ 111 ARG cc_start: 0.8402 (ptt180) cc_final: 0.8128 (ptt90) REVERT: AR 40 PHE cc_start: 0.8772 (m-80) cc_final: 0.8567 (m-80) REVERT: AR 91 ASP cc_start: 0.8035 (m-30) cc_final: 0.7265 (m-30) REVERT: AS 40 LEU cc_start: 0.8117 (tp) cc_final: 0.7533 (tp) REVERT: AS 51 VAL cc_start: 0.5956 (t) cc_final: 0.4880 (t) REVERT: AS 82 ARG cc_start: 0.5411 (mtm-85) cc_final: 0.5099 (mpp80) REVERT: AS 98 GLU cc_start: 0.7814 (mp0) cc_final: 0.7224 (mp0) REVERT: AT 37 ARG cc_start: 0.8143 (ttm170) cc_final: 0.7783 (ptm160) REVERT: AT 52 GLU cc_start: 0.8742 (mm-30) cc_final: 0.7946 (tt0) REVERT: AT 64 MET cc_start: 0.8608 (pmm) cc_final: 0.8167 (pmm) REVERT: AT 71 VAL cc_start: 0.8631 (p) cc_final: 0.8403 (p) REVERT: AT 88 ARG cc_start: 0.7414 (mmp80) cc_final: 0.7000 (mmp80) REVERT: AU 75 ASP cc_start: 0.7802 (m-30) cc_final: 0.7357 (m-30) REVERT: AV 5 MET cc_start: 0.8155 (mmm) cc_final: 0.7832 (mmm) REVERT: AV 11 ASP cc_start: 0.8480 (m-30) cc_final: 0.8223 (m-30) REVERT: AV 13 VAL cc_start: 0.7940 (t) cc_final: 0.7640 (t) REVERT: AV 91 GLU cc_start: 0.6839 (tp30) cc_final: 0.6133 (tm-30) REVERT: AW 28 MET cc_start: 0.7695 (ppp) cc_final: 0.7423 (ppp) REVERT: AW 38 TYR cc_start: 0.6912 (m-10) cc_final: 0.6611 (m-10) REVERT: AW 75 ASN cc_start: 0.7987 (m-40) cc_final: 0.7605 (m110) REVERT: AW 98 MET cc_start: 0.7652 (mmp) cc_final: 0.7070 (tmm) REVERT: AW 138 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8560 (tm-30) REVERT: AX 1 MET cc_start: 0.0979 (ptt) cc_final: 0.0600 (mmt) REVERT: AX 17 GLN cc_start: 0.8268 (tp40) cc_final: 0.7593 (tp40) REVERT: AX 36 ILE cc_start: 0.8687 (mt) cc_final: 0.8419 (mt) REVERT: AX 62 LEU cc_start: 0.9445 (mt) cc_final: 0.9202 (mt) REVERT: AY 6 GLU cc_start: 0.8595 (mp0) cc_final: 0.8313 (mp0) REVERT: AY 39 LEU cc_start: 0.9075 (mt) cc_final: 0.8857 (mt) REVERT: AY 48 LEU cc_start: 0.8126 (mp) cc_final: 0.7605 (mt) REVERT: AZ 9 VAL cc_start: 0.9032 (p) cc_final: 0.8781 (m) REVERT: Aa 6 HIS cc_start: 0.8256 (m90) cc_final: 0.7832 (m90) REVERT: Aa 8 LYS cc_start: 0.8122 (tttm) cc_final: 0.7616 (mtmm) REVERT: Aa 32 TYR cc_start: 0.7083 (p90) cc_final: 0.6414 (p90) REVERT: Aa 33 VAL cc_start: 0.5838 (t) cc_final: 0.5615 (t) REVERT: Aa 42 PHE cc_start: 0.8650 (t80) cc_final: 0.8374 (t80) REVERT: Aa 47 GLN cc_start: 0.7751 (tt0) cc_final: 0.7424 (mm-40) REVERT: Aa 53 GLU cc_start: 0.8246 (mp0) cc_final: 0.8021 (pm20) REVERT: Aa 57 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7255 (mm-30) REVERT: Ab 16 ARG cc_start: 0.8309 (ttp-110) cc_final: 0.8070 (ttp80) REVERT: Ab 23 HIS cc_start: 0.9421 (t70) cc_final: 0.9203 (t70) REVERT: Ab 51 TYR cc_start: 0.8754 (p90) cc_final: 0.8322 (p90) REVERT: Ab 55 ARG cc_start: 0.8810 (mmt-90) cc_final: 0.8445 (mmm160) REVERT: Ac 37 ARG cc_start: 0.8347 (mtt180) cc_final: 0.6289 (mmt90) REVERT: Ac 50 ARG cc_start: 0.8312 (ttt180) cc_final: 0.7572 (ttm170) REVERT: Ad 11 LYS cc_start: 0.9193 (tptt) cc_final: 0.8355 (tptp) REVERT: Ad 15 THR cc_start: 0.9214 (p) cc_final: 0.8631 (p) REVERT: Ad 42 LEU cc_start: 0.6822 (mt) cc_final: 0.6526 (mt) REVERT: Ae 17 THR cc_start: 0.9488 (p) cc_final: 0.9288 (t) REVERT: Ae 22 VAL cc_start: 0.9020 (t) cc_final: 0.8746 (t) REVERT: Ae 27 THR cc_start: 0.7840 (t) cc_final: 0.7355 (m) REVERT: Ae 32 LEU cc_start: 0.8571 (mt) cc_final: 0.7932 (mt) REVERT: Af 15 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8295 (tttt) REVERT: Af 18 ARG cc_start: 0.8383 (tpp80) cc_final: 0.8164 (tpp80) REVERT: BF 28 PHE cc_start: 0.7211 (t80) cc_final: 0.6689 (t80) REVERT: BF 30 ARG cc_start: 0.9287 (ptt180) cc_final: 0.8505 (tmt170) REVERT: BF 52 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8438 (tm-30) REVERT: BF 96 ARG cc_start: 0.7704 (mpt180) cc_final: 0.6711 (ttm-80) REVERT: BF 102 LEU cc_start: 0.9381 (mp) cc_final: 0.9159 (mp) REVERT: BF 139 LYS cc_start: 0.8584 (tttt) cc_final: 0.8249 (mmtt) REVERT: BF 176 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8127 (tt0) REVERT: BF 193 ASP cc_start: 0.8342 (m-30) cc_final: 0.8070 (m-30) REVERT: BG 8 ILE cc_start: 0.9144 (mm) cc_final: 0.8795 (mm) REVERT: BG 11 ARG cc_start: 0.6967 (mmp80) cc_final: 0.6605 (mmp80) REVERT: BG 29 TYR cc_start: 0.6371 (t80) cc_final: 0.5789 (t80) REVERT: BG 123 GLN cc_start: 0.8666 (mt0) cc_final: 0.8335 (mt0) REVERT: BG 142 MET cc_start: 0.8965 (tmm) cc_final: 0.8620 (tpt) REVERT: BG 190 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7034 (tpm170) REVERT: BG 204 LEU cc_start: 0.8907 (mt) cc_final: 0.8507 (mp) REVERT: BH 27 TYR cc_start: 0.8912 (t80) cc_final: 0.8670 (t80) REVERT: BH 33 MET cc_start: 0.8139 (mpp) cc_final: 0.7880 (mmt) REVERT: BH 53 ASP cc_start: 0.9332 (p0) cc_final: 0.8717 (t0) REVERT: BH 54 TYR cc_start: 0.8800 (t80) cc_final: 0.8416 (t80) REVERT: BH 75 PHE cc_start: 0.9320 (t80) cc_final: 0.9079 (t80) REVERT: BH 76 ARG cc_start: 0.8980 (ppt170) cc_final: 0.8766 (ptp-110) REVERT: BH 106 TYR cc_start: 0.8946 (t80) cc_final: 0.8418 (t80) REVERT: BH 165 MET cc_start: 0.7672 (mmp) cc_final: 0.7308 (tpp) REVERT: BH 199 ASN cc_start: 0.8361 (t0) cc_final: 0.8053 (t0) REVERT: BH 200 GLU cc_start: 0.7840 (mp0) cc_final: 0.7602 (mp0) REVERT: BH 205 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8214 (mt-10) REVERT: BI 7 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6621 (pm20) REVERT: BI 10 MET cc_start: 0.9466 (ppp) cc_final: 0.9217 (ppp) REVERT: BI 50 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8867 (mm-30) REVERT: BI 64 ARG cc_start: 0.9166 (mmp80) cc_final: 0.8841 (mmp80) REVERT: BI 92 LYS cc_start: 0.8992 (mmtp) cc_final: 0.8695 (mmmt) REVERT: BI 111 GLU cc_start: 0.9191 (tt0) cc_final: 0.8729 (tt0) REVERT: BI 129 ILE cc_start: 0.9164 (pt) cc_final: 0.8284 (tp) REVERT: BI 133 TYR cc_start: 0.8637 (m-80) cc_final: 0.7873 (m-80) REVERT: BI 137 GLU cc_start: 0.9669 (tp30) cc_final: 0.9141 (tm-30) REVERT: BJ 43 LEU cc_start: 0.6918 (pt) cc_final: 0.6558 (tp) REVERT: BJ 52 ILE cc_start: 0.4302 (mt) cc_final: 0.3689 (mt) REVERT: BJ 67 MET cc_start: 0.6307 (pmm) cc_final: 0.5515 (pmm) REVERT: BJ 73 ASN cc_start: 0.9307 (t0) cc_final: 0.8583 (p0) REVERT: BJ 75 LEU cc_start: 0.8915 (mt) cc_final: 0.8425 (mt) REVERT: BJ 78 GLU cc_start: 0.8969 (tt0) cc_final: 0.8729 (pt0) REVERT: BK 73 MET cc_start: 0.6764 (mmm) cc_final: 0.6207 (ppp) REVERT: BK 89 MET cc_start: 0.7724 (ppp) cc_final: 0.7195 (ppp) REVERT: BK 149 ARG cc_start: 0.7343 (mmm160) cc_final: 0.7000 (tpt170) REVERT: BL 50 ARG cc_start: 0.8045 (tpt170) cc_final: 0.7752 (tpt170) REVERT: BL 54 ASP cc_start: 0.8600 (m-30) cc_final: 0.8345 (t0) REVERT: BL 59 LEU cc_start: 0.9082 (mt) cc_final: 0.8874 (mt) REVERT: BL 98 LYS cc_start: 0.8718 (ptpt) cc_final: 0.8495 (pttm) REVERT: BN 22 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7688 (mmmt) REVERT: BO 120 ARG cc_start: 0.8821 (ttp-170) cc_final: 0.8459 (ttm-80) REVERT: BP 16 GLU cc_start: 0.7848 (mp0) cc_final: 0.7452 (mp0) REVERT: BP 55 VAL cc_start: 0.8165 (t) cc_final: 0.7826 (m) REVERT: BP 70 ILE cc_start: 0.9606 (mm) cc_final: 0.9364 (mm) REVERT: BQ 36 LYS cc_start: 0.6439 (tptp) cc_final: 0.6229 (mtmm) REVERT: BQ 59 TYR cc_start: 0.6480 (t80) cc_final: 0.6250 (t80) REVERT: BQ 87 TYR cc_start: 0.5984 (m-10) cc_final: 0.5192 (m-80) REVERT: BQ 90 LEU cc_start: 0.8075 (mt) cc_final: 0.7873 (mt) REVERT: BR 37 PHE cc_start: 0.8062 (m-80) cc_final: 0.7730 (m-80) REVERT: BS 43 LEU cc_start: 0.7911 (tp) cc_final: 0.7543 (mt) REVERT: BS 44 LYS cc_start: 0.8919 (tptp) cc_final: 0.8463 (mtpp) REVERT: BS 53 HIS cc_start: 0.8739 (t-170) cc_final: 0.8519 (t-90) REVERT: BT 1 MET cc_start: 0.6965 (mmp) cc_final: 0.6364 (mmp) REVERT: BT 31 LYS cc_start: 0.8017 (tmtt) cc_final: 0.7368 (tptt) REVERT: BT 33 ILE cc_start: 0.8235 (mt) cc_final: 0.7879 (mt) REVERT: BT 38 TYR cc_start: 0.6518 (p90) cc_final: 0.6077 (p90) REVERT: BU 29 HIS cc_start: 0.9459 (t-90) cc_final: 0.9032 (t-90) REVERT: BU 34 LYS cc_start: 0.9427 (tmmt) cc_final: 0.8900 (tttt) REVERT: BU 89 LEU cc_start: 0.8643 (mt) cc_final: 0.8298 (mt) REVERT: BV 32 ARG cc_start: 0.7336 (mtt-85) cc_final: 0.6962 (mmp80) REVERT: BV 56 THR cc_start: 0.7802 (p) cc_final: 0.7379 (p) REVERT: BW 28 LYS cc_start: 0.7979 (tmmt) cc_final: 0.7590 (mmtt) REVERT: BW 66 MET cc_start: 0.5418 (ptt) cc_final: 0.5183 (ptp) REVERT: BW 70 LYS cc_start: 0.5124 (pttt) cc_final: 0.4222 (tttm) REVERT: BW 79 THR cc_start: 0.7309 (m) cc_final: 0.7036 (p) REVERT: BX 21 LYS cc_start: 0.8747 (tptp) cc_final: 0.8531 (tptt) REVERT: BX 36 LEU cc_start: 0.8654 (mp) cc_final: 0.8433 (mt) REVERT: BX 81 LYS cc_start: 0.7833 (mttt) cc_final: 0.6818 (mmtm) REVERT: CA 1 MET cc_start: 0.5922 (mpp) cc_final: 0.5318 (mpp) REVERT: CA 13 HIS cc_start: 0.6330 (p-80) cc_final: 0.5974 (p-80) REVERT: CA 14 VAL cc_start: 0.6878 (p) cc_final: 0.6627 (m) REVERT: CA 57 LEU cc_start: 0.7220 (tt) cc_final: 0.6471 (tt) REVERT: CA 70 ILE cc_start: 0.7585 (mt) cc_final: 0.7296 (mm) REVERT: CA 91 MET cc_start: 0.7575 (pmm) cc_final: 0.7169 (pmm) REVERT: CA 106 MET cc_start: 0.8437 (tpp) cc_final: 0.8219 (tpp) REVERT: CA 117 PHE cc_start: 0.6782 (m-10) cc_final: 0.6554 (m-10) REVERT: CA 156 GLU cc_start: 0.8244 (tt0) cc_final: 0.8043 (tt0) REVERT: CA 207 MET cc_start: 0.7559 (tpp) cc_final: 0.7109 (tpp) REVERT: CA 214 TYR cc_start: 0.8407 (t80) cc_final: 0.8150 (t80) REVERT: CA 218 VAL cc_start: 0.9013 (t) cc_final: 0.8763 (t) REVERT: CA 248 ASN cc_start: 0.8319 (t0) cc_final: 0.7993 (t0) REVERT: CA 309 MET cc_start: 0.8335 (mmt) cc_final: 0.8123 (mmp) REVERT: CA 341 HIS cc_start: 0.8336 (m-70) cc_final: 0.8131 (m170) REVERT: CA 429 MET cc_start: 0.8582 (ppp) cc_final: 0.8361 (ppp) REVERT: CA 487 VAL cc_start: 0.9091 (m) cc_final: 0.8668 (p) REVERT: CA 488 LEU cc_start: 0.8468 (mt) cc_final: 0.8186 (mt) REVERT: CA 495 LYS cc_start: 0.8764 (tptp) cc_final: 0.8550 (tmmt) REVERT: CA 505 GLN cc_start: 0.8651 (pt0) cc_final: 0.8263 (pt0) REVERT: CA 517 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8324 (mm-30) REVERT: CA 519 TYR cc_start: 0.8602 (p90) cc_final: 0.8335 (p90) REVERT: CA 563 MET cc_start: 0.7266 (tpp) cc_final: 0.7006 (tpp) REVERT: CA 579 GLU cc_start: 0.8481 (tt0) cc_final: 0.7833 (tp30) outliers start: 26 outliers final: 16 residues processed: 1752 average time/residue: 1.4283 time to fit residues: 4208.8707 Evaluate side-chains 1413 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1395 time to evaluate : 6.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 890 optimal weight: 30.0000 chunk 606 optimal weight: 6.9990 chunk 15 optimal weight: 30.0000 chunk 795 optimal weight: 6.9990 chunk 441 optimal weight: 10.0000 chunk 912 optimal weight: 7.9990 chunk 738 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 545 optimal weight: 9.9990 chunk 959 optimal weight: 20.0000 chunk 269 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 71 GLN AC 172 HIS ** AD 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 87 ASN ** AD 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 57 HIS ** AO 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AS 87 HIS ** AS 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 34 ASN ** AV 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AV 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 121 HIS ** AW 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AX 12 ASN ** AY 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Af 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 34 GLN ** BF 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 139 GLN ** BG 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 161 ASN ** BH 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 73 ASN BI 141 GLN ** BJ 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 153 HIS BN 68 HIS ** BO 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 101 GLN ** BR 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 62 GLN ** CA 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.9898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.551 163075 Z= 0.418 Angle : 1.032 39.885 242863 Z= 0.510 Chirality : 0.050 0.709 30675 Planarity : 0.009 0.228 13938 Dihedral : 26.878 179.673 79709 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 43.71 Ramachandran Plot: Outliers : 3.32 % Allowed : 21.80 % Favored : 74.88 % Rotamer: Outliers : 0.32 % Allowed : 6.45 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.92 % Twisted Proline : 1.20 % Twisted General : 0.59 % 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: -4.77 (0.09), residues: 6565 helix: -1.71 (0.10), residues: 1923 sheet: -2.20 (0.16), residues: 922 loop : -4.49 (0.08), residues: 3720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRPAe 34 HIS 0.020 0.003 HISAW 151 PHE 0.067 0.004 PHEAd 18 TYR 0.046 0.003 TYRAW 99 ARG 0.025 0.001 ARGAE 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1677 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1660 time to evaluate : 7.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AC 6 ARG cc_start: 0.4721 (ppt170) cc_final: 0.1997 (ttp-170) REVERT: AC 103 ILE cc_start: 0.0980 (mt) cc_final: 0.0544 (mt) REVERT: AC 120 MET cc_start: 0.3309 (tpt) cc_final: 0.2895 (tpt) REVERT: AC 167 LYS cc_start: 0.2382 (pttt) cc_final: 0.0679 (mptt) REVERT: AC 217 THR cc_start: 0.6796 (m) cc_final: 0.6492 (m) REVERT: AC 218 MET cc_start: -0.2724 (ttp) cc_final: -0.3333 (ttp) REVERT: AD 58 HIS cc_start: 0.7941 (m90) cc_final: 0.7340 (m90) REVERT: AD 99 ASP cc_start: 0.8896 (p0) cc_final: 0.8636 (p0) REVERT: AD 106 ILE cc_start: 0.8921 (mp) cc_final: 0.8710 (mm) REVERT: AD 164 GLN cc_start: 0.8610 (tm-30) cc_final: 0.7987 (tm-30) REVERT: AD 190 TYR cc_start: 0.8127 (m-80) cc_final: 0.7857 (m-80) REVERT: AD 220 HIS cc_start: 0.5493 (m-70) cc_final: 0.5058 (m90) REVERT: AD 268 ARG cc_start: 0.7970 (tmt170) cc_final: 0.7133 (tmt170) REVERT: AE 63 LEU cc_start: 0.9416 (mt) cc_final: 0.8784 (mt) REVERT: AE 127 ASP cc_start: 0.8611 (t0) cc_final: 0.8136 (t0) REVERT: AE 156 MET cc_start: 0.8259 (tpt) cc_final: 0.7989 (tpt) REVERT: AE 160 TYR cc_start: 0.7849 (m-80) cc_final: 0.7156 (m-80) REVERT: AE 168 MET cc_start: 0.9023 (mmp) cc_final: 0.7572 (mtp) REVERT: AE 185 LYS cc_start: 0.8194 (pttp) cc_final: 0.7688 (ptmm) REVERT: AF 43 LYS cc_start: 0.8399 (tttt) cc_final: 0.8112 (ptmm) REVERT: AF 53 THR cc_start: 0.6986 (m) cc_final: 0.6783 (m) REVERT: AF 88 VAL cc_start: 0.8862 (t) cc_final: 0.8455 (m) REVERT: AF 112 MET cc_start: 0.9067 (ptm) cc_final: 0.8759 (ptm) REVERT: AF 145 GLU cc_start: 0.9558 (mm-30) cc_final: 0.9049 (tm-30) REVERT: AF 160 ASN cc_start: 0.9295 (t0) cc_final: 0.9044 (t0) REVERT: AF 169 ASN cc_start: 0.7921 (t0) cc_final: 0.7596 (t0) REVERT: AG 148 MET cc_start: 0.0528 (ptt) cc_final: 0.0043 (ptt) REVERT: AG 155 MET cc_start: 0.8875 (mtt) cc_final: 0.8503 (mpp) REVERT: AH 30 LYS cc_start: 0.8549 (tmtt) cc_final: 0.7942 (pttm) REVERT: AH 41 MET cc_start: 0.8023 (mtm) cc_final: 0.7108 (mmt) REVERT: AH 68 THR cc_start: 0.7356 (p) cc_final: 0.7144 (p) REVERT: AJ 10 LEU cc_start: 0.7228 (pt) cc_final: 0.6499 (tp) REVERT: AK 48 MET cc_start: 0.3148 (ttt) cc_final: 0.2549 (ttt) REVERT: AK 56 ASN cc_start: 0.8377 (m-40) cc_final: 0.6997 (p0) REVERT: AK 84 LYS cc_start: 0.8908 (mtmm) cc_final: 0.8446 (mmmt) REVERT: AK 106 MET cc_start: 0.8767 (mtt) cc_final: 0.8384 (mtt) REVERT: AL 20 MET cc_start: 0.8319 (tpt) cc_final: 0.7997 (tmm) REVERT: AL 31 LYS cc_start: 0.9219 (mttt) cc_final: 0.8491 (ttmt) REVERT: AL 32 TYR cc_start: 0.8211 (m-80) cc_final: 0.6574 (m-80) REVERT: AL 114 ILE cc_start: 0.8982 (mt) cc_final: 0.8722 (mt) REVERT: AM 70 GLN cc_start: 0.6490 (pt0) cc_final: 0.6115 (mm-40) REVERT: AM 90 ARG cc_start: 0.8955 (tmm160) cc_final: 0.8673 (tpp80) REVERT: AM 136 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8970 (pp20) REVERT: AN 29 PHE cc_start: 0.7501 (t80) cc_final: 0.7190 (t80) REVERT: AN 37 LEU cc_start: 0.8416 (mt) cc_final: 0.7883 (mt) REVERT: AN 45 GLN cc_start: 0.9128 (mp10) cc_final: 0.8904 (mp10) REVERT: AN 74 TYR cc_start: 0.5488 (m-10) cc_final: 0.4927 (m-10) REVERT: AN 83 MET cc_start: 0.8039 (pmm) cc_final: 0.7119 (ptt) REVERT: AN 89 ASN cc_start: 0.8732 (m-40) cc_final: 0.8434 (m-40) REVERT: AN 113 GLN cc_start: 0.8376 (tt0) cc_final: 0.7721 (tm-30) REVERT: AN 115 MET cc_start: 0.9275 (mmm) cc_final: 0.9014 (mmt) REVERT: AN 128 LYS cc_start: 0.6926 (mmmt) cc_final: 0.6546 (mmtm) REVERT: AO 23 ASN cc_start: 0.9265 (m-40) cc_final: 0.8478 (m-40) REVERT: AO 26 LYS cc_start: 0.9038 (mttm) cc_final: 0.8622 (mtmm) REVERT: AO 40 LYS cc_start: 0.8704 (mptt) cc_final: 0.8477 (mmtm) REVERT: AO 42 LYS cc_start: 0.8881 (mtmm) cc_final: 0.8459 (ptmt) REVERT: AO 54 LEU cc_start: 0.9754 (mp) cc_final: 0.9434 (tt) REVERT: AP 18 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6897 (mp) REVERT: AP 19 LYS cc_start: 0.8413 (tptp) cc_final: 0.8110 (ttpt) REVERT: AQ 1 MET cc_start: 0.7806 (ppp) cc_final: 0.7388 (ppp) REVERT: AQ 70 VAL cc_start: 0.7487 (OUTLIER) cc_final: 0.6657 (t) REVERT: AQ 75 ILE cc_start: 0.7744 (mt) cc_final: 0.7323 (mt) REVERT: AR 20 LEU cc_start: 0.9192 (mm) cc_final: 0.8960 (mm) REVERT: AR 25 TRP cc_start: 0.7127 (t-100) cc_final: 0.6911 (t-100) REVERT: AR 91 ASP cc_start: 0.8033 (m-30) cc_final: 0.7697 (m-30) REVERT: AT 34 ASN cc_start: 0.8679 (m-40) cc_final: 0.8356 (m110) REVERT: AT 37 ARG cc_start: 0.8448 (ttm170) cc_final: 0.8045 (ptm160) REVERT: AT 52 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8155 (tt0) REVERT: AT 97 LYS cc_start: 0.6756 (mtpt) cc_final: 0.6425 (ttmt) REVERT: AU 9 LEU cc_start: 0.8292 (mt) cc_final: 0.7343 (pp) REVERT: AU 21 PHE cc_start: 0.7244 (m-10) cc_final: 0.6821 (m-10) REVERT: AU 44 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8215 (mm-30) REVERT: AU 64 LYS cc_start: 0.7416 (tttt) cc_final: 0.7122 (mttt) REVERT: AU 75 ASP cc_start: 0.8127 (m-30) cc_final: 0.7649 (m-30) REVERT: AV 11 ASP cc_start: 0.8499 (m-30) cc_final: 0.8247 (m-30) REVERT: AV 39 VAL cc_start: 0.8031 (t) cc_final: 0.7782 (t) REVERT: AV 91 GLU cc_start: 0.7240 (tp30) cc_final: 0.6733 (tm-30) REVERT: AW 28 MET cc_start: 0.7830 (ppp) cc_final: 0.7565 (ppp) REVERT: AW 75 ASN cc_start: 0.8259 (m-40) cc_final: 0.7960 (m-40) REVERT: AX 1 MET cc_start: 0.0940 (ptt) cc_final: 0.0646 (mmm) REVERT: AX 17 GLN cc_start: 0.8084 (tp40) cc_final: 0.7784 (tp40) REVERT: AX 36 ILE cc_start: 0.8804 (mt) cc_final: 0.8515 (mt) REVERT: AX 60 PHE cc_start: 0.8517 (p90) cc_final: 0.8282 (p90) REVERT: AY 28 MET cc_start: 0.6582 (mtt) cc_final: 0.5936 (mtt) REVERT: AY 33 GLN cc_start: 0.8049 (mp10) cc_final: 0.7475 (pm20) REVERT: AY 45 ILE cc_start: 0.8522 (pt) cc_final: 0.7840 (pt) REVERT: AY 48 LEU cc_start: 0.8402 (mp) cc_final: 0.7985 (mt) REVERT: AY 52 ILE cc_start: 0.9266 (pt) cc_final: 0.9017 (pt) REVERT: AZ 9 VAL cc_start: 0.8798 (p) cc_final: 0.8533 (m) REVERT: AZ 26 LEU cc_start: 0.9134 (tt) cc_final: 0.8928 (tp) REVERT: AZ 39 ASP cc_start: 0.8799 (t0) cc_final: 0.8574 (t0) REVERT: AZ 48 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8515 (mt-10) REVERT: AZ 49 LYS cc_start: 0.9006 (tppt) cc_final: 0.8523 (ttpt) REVERT: Aa 6 HIS cc_start: 0.8466 (m90) cc_final: 0.7936 (m90) REVERT: Aa 8 LYS cc_start: 0.7901 (tttm) cc_final: 0.7457 (mtmm) REVERT: Aa 32 TYR cc_start: 0.7100 (p90) cc_final: 0.6718 (p90) REVERT: Aa 42 PHE cc_start: 0.8685 (t80) cc_final: 0.8333 (t80) REVERT: Aa 47 GLN cc_start: 0.8029 (tt0) cc_final: 0.7551 (mm-40) REVERT: Aa 57 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7615 (mm-30) REVERT: Ab 15 ARG cc_start: 0.9013 (mmm-85) cc_final: 0.8758 (mtp85) REVERT: Ac 37 ARG cc_start: 0.8610 (mtt180) cc_final: 0.6130 (mmt90) REVERT: Ad 11 LYS cc_start: 0.9258 (tptt) cc_final: 0.8395 (tptp) REVERT: Ad 15 THR cc_start: 0.8794 (p) cc_final: 0.8128 (p) REVERT: Ad 47 ARG cc_start: 0.7149 (ptt180) cc_final: 0.6694 (ptm160) REVERT: Af 1 MET cc_start: 0.5233 (tpt) cc_final: 0.5006 (tpt) REVERT: Af 15 LYS cc_start: 0.8796 (mmmm) cc_final: 0.8325 (tttt) REVERT: Af 22 ARG cc_start: 0.6969 (mmm-85) cc_final: 0.5987 (mtp180) REVERT: Af 34 GLN cc_start: 0.8358 (mm-40) cc_final: 0.8082 (mm110) REVERT: BF 28 PHE cc_start: 0.7263 (t80) cc_final: 0.6294 (t80) REVERT: BF 47 THR cc_start: 0.9186 (m) cc_final: 0.8873 (m) REVERT: BF 59 GLU cc_start: 0.8734 (tt0) cc_final: 0.8373 (tp30) REVERT: BF 83 MET cc_start: 0.8638 (mtt) cc_final: 0.8418 (mtp) REVERT: BF 92 TYR cc_start: 0.7595 (p90) cc_final: 0.7086 (p90) REVERT: BF 176 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8252 (mt-10) REVERT: BG 8 ILE cc_start: 0.9180 (mm) cc_final: 0.8889 (mm) REVERT: BG 11 ARG cc_start: 0.7316 (mmp80) cc_final: 0.6662 (mmp80) REVERT: BG 15 THR cc_start: 0.9064 (p) cc_final: 0.8556 (p) REVERT: BG 142 MET cc_start: 0.9174 (tmm) cc_final: 0.8939 (tpt) REVERT: BG 175 LEU cc_start: 0.9143 (mp) cc_final: 0.8933 (mp) REVERT: BG 176 HIS cc_start: 0.8078 (m170) cc_final: 0.7782 (m170) REVERT: BG 190 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7081 (tpm170) REVERT: BG 204 LEU cc_start: 0.8856 (mt) cc_final: 0.8584 (mp) REVERT: BH 53 ASP cc_start: 0.9407 (p0) cc_final: 0.9008 (t0) REVERT: BH 54 TYR cc_start: 0.8886 (t80) cc_final: 0.8048 (t80) REVERT: BH 58 LEU cc_start: 0.9580 (tt) cc_final: 0.9125 (mt) REVERT: BH 74 GLN cc_start: 0.9118 (mp10) cc_final: 0.8771 (mp10) REVERT: BH 76 ARG cc_start: 0.9294 (ppt170) cc_final: 0.8738 (ptp-110) REVERT: BH 81 GLU cc_start: 0.9400 (tm-30) cc_final: 0.9151 (tm-30) REVERT: BH 106 TYR cc_start: 0.9033 (t80) cc_final: 0.8478 (t80) REVERT: BH 144 ASP cc_start: 0.6264 (m-30) cc_final: 0.5979 (m-30) REVERT: BH 146 ILE cc_start: 0.8419 (mm) cc_final: 0.7877 (tp) REVERT: BH 165 MET cc_start: 0.7978 (mmp) cc_final: 0.7736 (tpp) REVERT: BH 207 TYR cc_start: 0.6695 (m-10) cc_final: 0.6495 (m-10) REVERT: BI 7 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6720 (pm20) REVERT: BI 10 MET cc_start: 0.9565 (ppp) cc_final: 0.9253 (ppp) REVERT: BI 47 LYS cc_start: 0.7379 (mptt) cc_final: 0.6986 (mmtm) REVERT: BI 64 ARG cc_start: 0.9213 (mmp80) cc_final: 0.8863 (mmp80) REVERT: BI 111 GLU cc_start: 0.9193 (tt0) cc_final: 0.8747 (tt0) REVERT: BI 129 ILE cc_start: 0.9222 (pt) cc_final: 0.8494 (tp) REVERT: BI 133 TYR cc_start: 0.8536 (m-80) cc_final: 0.7872 (m-80) REVERT: BI 136 MET cc_start: 0.9058 (tmm) cc_final: 0.8858 (tmm) REVERT: BJ 15 ASP cc_start: 0.7369 (m-30) cc_final: 0.6808 (m-30) REVERT: BJ 43 LEU cc_start: 0.6690 (pt) cc_final: 0.6246 (tp) REVERT: BJ 62 TRP cc_start: 0.6971 (t60) cc_final: 0.6495 (t60) REVERT: BJ 63 TYR cc_start: 0.8142 (m-80) cc_final: 0.7607 (m-80) REVERT: BJ 67 MET cc_start: 0.6678 (pmm) cc_final: 0.5990 (pmm) REVERT: BJ 75 LEU cc_start: 0.9068 (mt) cc_final: 0.8243 (mt) REVERT: BJ 78 GLU cc_start: 0.9016 (tt0) cc_final: 0.8490 (pp20) REVERT: BK 73 MET cc_start: 0.6927 (mmm) cc_final: 0.6301 (ppp) REVERT: BK 89 MET cc_start: 0.8223 (ppp) cc_final: 0.7455 (ppp) REVERT: BK 90 GLU cc_start: 0.8143 (pp20) cc_final: 0.7334 (pp20) REVERT: BK 139 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8286 (tm-30) REVERT: BL 15 ASN cc_start: 0.8743 (m-40) cc_final: 0.8455 (m-40) REVERT: BL 25 ASP cc_start: 0.6594 (m-30) cc_final: 0.6357 (m-30) REVERT: BL 44 PHE cc_start: 0.8945 (m-80) cc_final: 0.8412 (m-80) REVERT: BL 50 ARG cc_start: 0.8345 (tpt170) cc_final: 0.8020 (tpt170) REVERT: BL 82 HIS cc_start: 0.9457 (t-90) cc_final: 0.9042 (t-170) REVERT: BL 88 LYS cc_start: 0.9368 (pttt) cc_final: 0.9099 (ptpp) REVERT: BO 11 LYS cc_start: 0.7011 (mptt) cc_final: 0.6440 (mptt) REVERT: BO 18 ARG cc_start: 0.6999 (tpt-90) cc_final: 0.6540 (mmt180) REVERT: BO 73 MET cc_start: 0.7503 (mmt) cc_final: 0.7102 (mmt) REVERT: BP 16 GLU cc_start: 0.7941 (mp0) cc_final: 0.7292 (mp0) REVERT: BP 27 LEU cc_start: 0.7822 (tp) cc_final: 0.7615 (tp) REVERT: BP 76 ASN cc_start: 0.8978 (m-40) cc_final: 0.8769 (m-40) REVERT: BQ 36 LYS cc_start: 0.4898 (tptp) cc_final: 0.4562 (mtmm) REVERT: BQ 59 TYR cc_start: 0.6749 (t80) cc_final: 0.6460 (t80) REVERT: BQ 66 LEU cc_start: 0.5651 (mm) cc_final: 0.5403 (mm) REVERT: BS 57 LEU cc_start: 0.9422 (mt) cc_final: 0.9217 (mt) REVERT: BS 58 MET cc_start: 0.9084 (mtt) cc_final: 0.8025 (mtt) REVERT: BS 59 MET cc_start: 0.9332 (tpp) cc_final: 0.8809 (tpt) REVERT: BT 1 MET cc_start: 0.7133 (mmp) cc_final: 0.6764 (mmp) REVERT: BT 54 GLU cc_start: 0.9247 (pt0) cc_final: 0.8751 (pp20) REVERT: BU 13 ASP cc_start: 0.9043 (p0) cc_final: 0.8833 (p0) REVERT: BU 29 HIS cc_start: 0.9442 (t-90) cc_final: 0.9098 (t-90) REVERT: BU 34 LYS cc_start: 0.9482 (tmmt) cc_final: 0.9109 (tttt) REVERT: BU 89 LEU cc_start: 0.8712 (mt) cc_final: 0.8484 (mt) REVERT: BV 32 ARG cc_start: 0.7628 (mtt-85) cc_final: 0.7282 (mmp80) REVERT: BV 39 VAL cc_start: 0.8253 (t) cc_final: 0.8023 (t) REVERT: BV 56 THR cc_start: 0.8346 (p) cc_final: 0.8024 (p) REVERT: BW 7 LYS cc_start: 0.7816 (tmtt) cc_final: 0.7517 (mttp) REVERT: BW 28 LYS cc_start: 0.8085 (tmmt) cc_final: 0.7773 (mmtt) REVERT: BW 73 GLU cc_start: 0.7138 (pt0) cc_final: 0.6867 (mt-10) REVERT: BW 79 THR cc_start: 0.7333 (m) cc_final: 0.7002 (p) REVERT: BX 36 LEU cc_start: 0.8790 (mp) cc_final: 0.8568 (mt) REVERT: BX 64 ASP cc_start: 0.7969 (m-30) cc_final: 0.7589 (m-30) REVERT: CA 13 HIS cc_start: 0.6220 (p-80) cc_final: 0.5920 (p-80) REVERT: CA 91 MET cc_start: 0.7955 (pmm) cc_final: 0.7196 (pmm) REVERT: CA 106 MET cc_start: 0.8441 (tpp) cc_final: 0.8194 (tpp) REVERT: CA 147 LEU cc_start: 0.8748 (tp) cc_final: 0.8516 (tp) REVERT: CA 207 MET cc_start: 0.8227 (tpt) cc_final: 0.7418 (tpt) REVERT: CA 214 TYR cc_start: 0.8460 (t80) cc_final: 0.8171 (t80) REVERT: CA 248 ASN cc_start: 0.8452 (t0) cc_final: 0.8107 (t0) REVERT: CA 293 ASN cc_start: 0.8927 (m-40) cc_final: 0.8686 (m-40) REVERT: CA 300 LEU cc_start: 0.7339 (mp) cc_final: 0.6804 (tt) REVERT: CA 326 VAL cc_start: 0.9286 (m) cc_final: 0.9037 (m) REVERT: CA 349 GLU cc_start: 0.7780 (tp30) cc_final: 0.7542 (tp30) REVERT: CA 373 MET cc_start: 0.8773 (mmp) cc_final: 0.8572 (mmm) REVERT: CA 416 MET cc_start: 0.8234 (mtm) cc_final: 0.7966 (mtp) REVERT: CA 429 MET cc_start: 0.8712 (ppp) cc_final: 0.8496 (ppp) REVERT: CA 487 VAL cc_start: 0.9004 (m) cc_final: 0.8438 (p) REVERT: CA 488 LEU cc_start: 0.8715 (mt) cc_final: 0.8410 (mt) REVERT: CA 495 LYS cc_start: 0.8675 (tptp) cc_final: 0.8326 (tmmt) REVERT: CA 505 GLN cc_start: 0.8764 (pt0) cc_final: 0.8464 (pt0) REVERT: CA 519 TYR cc_start: 0.8784 (p90) cc_final: 0.7983 (p90) REVERT: CA 579 GLU cc_start: 0.8242 (tt0) cc_final: 0.7742 (tp30) outliers start: 17 outliers final: 12 residues processed: 1673 average time/residue: 1.4077 time to fit residues: 3980.3261 Evaluate side-chains 1345 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1331 time to evaluate : 7.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 359 optimal weight: 0.4980 chunk 962 optimal weight: 3.9990 chunk 211 optimal weight: 50.0000 chunk 627 optimal weight: 30.0000 chunk 263 optimal weight: 20.0000 chunk 1070 optimal weight: 20.0000 chunk 888 optimal weight: 10.0000 chunk 495 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 353 optimal weight: 10.0000 chunk 561 optimal weight: 10.0000 overall best weight: 6.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 129 HIS ** AE 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 40 GLN ** AF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AJ 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AS 87 HIS ** AS 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AV 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AV 68 HIS ** AW 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 121 HIS ** AW 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY 60 ASN Aa 47 GLN ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 43 GLN ** Af 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Af 34 GLN ** BF 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BG 63 ASN ** BG 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 73 ASN ** BI 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 9 GLN ** BQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 101 GLN ** BR 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 411 HIS ** CA 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 1.0527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.521 163075 Z= 0.346 Angle : 0.947 37.280 242863 Z= 0.468 Chirality : 0.046 0.476 30675 Planarity : 0.008 0.141 13938 Dihedral : 26.773 179.759 79709 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 36.91 Ramachandran Plot: Outliers : 3.06 % Allowed : 20.44 % Favored : 76.50 % Rotamer: Outliers : 0.19 % Allowed : 4.31 % Favored : 95.50 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.97 % Twisted Proline : 0.90 % Twisted General : 0.43 % 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: -4.52 (0.09), residues: 6565 helix: -1.48 (0.11), residues: 1905 sheet: -2.10 (0.17), residues: 869 loop : -4.30 (0.08), residues: 3791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRPAG 29 HIS 0.014 0.002 HISBR 49 PHE 0.061 0.003 PHEAd 18 TYR 0.047 0.003 TYRAD 84 ARG 0.023 0.001 ARGAE 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1684 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1674 time to evaluate : 7.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AC 6 ARG cc_start: 0.4952 (ppt170) cc_final: 0.2326 (ttp-170) REVERT: AC 217 THR cc_start: 0.6871 (m) cc_final: 0.6585 (m) REVERT: AC 218 MET cc_start: -0.2866 (ttp) cc_final: -0.3659 (ttp) REVERT: AD 25 THR cc_start: 0.7281 (p) cc_final: 0.7056 (p) REVERT: AD 58 HIS cc_start: 0.8033 (m90) cc_final: 0.7459 (m90) REVERT: AD 87 ASN cc_start: 0.9317 (m110) cc_final: 0.8965 (m110) REVERT: AD 99 ASP cc_start: 0.8886 (p0) cc_final: 0.8604 (p0) REVERT: AD 105 ILE cc_start: 0.9375 (tp) cc_final: 0.9126 (tp) REVERT: AD 115 GLN cc_start: 0.8035 (pp30) cc_final: 0.7173 (pp30) REVERT: AD 133 LEU cc_start: 0.9383 (mm) cc_final: 0.9163 (mm) REVERT: AD 164 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8104 (tm-30) REVERT: AD 176 ARG cc_start: 0.7923 (tpp-160) cc_final: 0.7625 (tpp80) REVERT: AD 177 LEU cc_start: 0.8457 (pt) cc_final: 0.8214 (pt) REVERT: AD 217 ARG cc_start: 0.8372 (ptp-170) cc_final: 0.7776 (ptp-170) REVERT: AD 220 HIS cc_start: 0.5291 (m-70) cc_final: 0.5064 (m90) REVERT: AD 268 ARG cc_start: 0.8108 (tmt170) cc_final: 0.7164 (tmt170) REVERT: AD 271 ILE cc_start: 0.7318 (tp) cc_final: 0.6500 (tp) REVERT: AE 14 ILE cc_start: 0.8600 (mt) cc_final: 0.7778 (mt) REVERT: AE 26 ILE cc_start: 0.8189 (pt) cc_final: 0.7590 (pt) REVERT: AE 51 PHE cc_start: 0.8079 (p90) cc_final: 0.7100 (p90) REVERT: AE 120 TRP cc_start: 0.7742 (p-90) cc_final: 0.7019 (p-90) REVERT: AE 127 ASP cc_start: 0.8591 (t0) cc_final: 0.8147 (t0) REVERT: AE 160 TYR cc_start: 0.7650 (m-80) cc_final: 0.6980 (m-80) REVERT: AE 168 MET cc_start: 0.9021 (mmp) cc_final: 0.8130 (mtt) REVERT: AE 180 ASN cc_start: 0.7687 (p0) cc_final: 0.6954 (p0) REVERT: AE 185 LYS cc_start: 0.8104 (pttp) cc_final: 0.7650 (ptmm) REVERT: AF 43 LYS cc_start: 0.8596 (tttt) cc_final: 0.8314 (tmmt) REVERT: AF 88 VAL cc_start: 0.8652 (t) cc_final: 0.8341 (m) REVERT: AF 93 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8437 (mmtp) REVERT: AF 112 MET cc_start: 0.9103 (ptm) cc_final: 0.8828 (ptp) REVERT: AF 116 ASP cc_start: 0.9054 (p0) cc_final: 0.8849 (p0) REVERT: AF 122 LYS cc_start: 0.8065 (tppt) cc_final: 0.7853 (tptt) REVERT: AF 145 GLU cc_start: 0.9576 (mm-30) cc_final: 0.9058 (tm-30) REVERT: AF 160 ASN cc_start: 0.9305 (t0) cc_final: 0.9042 (t0) REVERT: AF 169 ASN cc_start: 0.7614 (t0) cc_final: 0.7204 (t0) REVERT: AF 192 LEU cc_start: 0.7997 (tp) cc_final: 0.7663 (tp) REVERT: AG 155 MET cc_start: 0.8862 (mtt) cc_final: 0.8515 (mpp) REVERT: AH 30 LYS cc_start: 0.8540 (tmtt) cc_final: 0.7859 (pttm) REVERT: AH 38 SER cc_start: 0.6261 (p) cc_final: 0.5785 (p) REVERT: AH 83 TYR cc_start: 0.8376 (t80) cc_final: 0.8060 (t80) REVERT: AH 129 THR cc_start: 0.8360 (m) cc_final: 0.8066 (m) REVERT: AJ 10 LEU cc_start: 0.7370 (pt) cc_final: 0.6905 (tp) REVERT: AJ 70 LYS cc_start: 0.7291 (pptt) cc_final: 0.6718 (pptt) REVERT: AJ 126 MET cc_start: 0.0278 (mmm) cc_final: 0.0040 (mmm) REVERT: AK 17 ASP cc_start: 0.8697 (t70) cc_final: 0.8439 (t0) REVERT: AK 84 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8522 (mmmt) REVERT: AK 106 MET cc_start: 0.8863 (mtt) cc_final: 0.8443 (mtp) REVERT: AK 121 LYS cc_start: 0.8360 (mmmt) cc_final: 0.8092 (mmmt) REVERT: AK 123 TYR cc_start: 0.8574 (m-80) cc_final: 0.8223 (m-10) REVERT: AK 134 ARG cc_start: 0.8303 (mmp80) cc_final: 0.7860 (mmm160) REVERT: AL 9 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7980 (mm-30) REVERT: AL 20 MET cc_start: 0.8297 (tpt) cc_final: 0.7967 (tmm) REVERT: AL 31 LYS cc_start: 0.9140 (mttt) cc_final: 0.8459 (ttmt) REVERT: AL 32 TYR cc_start: 0.8156 (m-80) cc_final: 0.6654 (m-80) REVERT: AL 35 VAL cc_start: 0.8913 (m) cc_final: 0.8359 (m) REVERT: AL 68 GLU cc_start: 0.6720 (mp0) cc_final: 0.3841 (mp0) REVERT: AL 114 ILE cc_start: 0.9076 (mt) cc_final: 0.8819 (mt) REVERT: AM 70 GLN cc_start: 0.6462 (pt0) cc_final: 0.5953 (mm-40) REVERT: AM 90 ARG cc_start: 0.8908 (tmm160) cc_final: 0.8668 (tpp80) REVERT: AN 6 ARG cc_start: 0.7966 (tmm160) cc_final: 0.7625 (tmt-80) REVERT: AN 37 LEU cc_start: 0.8419 (mt) cc_final: 0.8055 (mt) REVERT: AN 45 GLN cc_start: 0.9149 (mp10) cc_final: 0.8845 (mp10) REVERT: AN 80 GLU cc_start: 0.8627 (pp20) cc_final: 0.8280 (pp20) REVERT: AN 89 ASN cc_start: 0.8850 (m-40) cc_final: 0.8592 (m-40) REVERT: AN 113 GLN cc_start: 0.8619 (tt0) cc_final: 0.7618 (tm-30) REVERT: AN 115 MET cc_start: 0.9185 (mmm) cc_final: 0.8947 (mmt) REVERT: AN 128 LYS cc_start: 0.6870 (mmmt) cc_final: 0.6426 (mmtm) REVERT: AO 54 LEU cc_start: 0.9754 (mp) cc_final: 0.9493 (tt) REVERT: AO 74 LYS cc_start: 0.9369 (mmtm) cc_final: 0.9070 (tptt) REVERT: AP 46 VAL cc_start: 0.8055 (p) cc_final: 0.7759 (p) REVERT: AP 98 VAL cc_start: 0.8968 (p) cc_final: 0.8746 (p) REVERT: AQ 1 MET cc_start: 0.7728 (ppp) cc_final: 0.7251 (ppp) REVERT: AQ 38 ASN cc_start: 0.8090 (p0) cc_final: 0.6696 (p0) REVERT: AQ 70 VAL cc_start: 0.7952 (t) cc_final: 0.6751 (t) REVERT: AQ 75 ILE cc_start: 0.7674 (mt) cc_final: 0.7223 (mt) REVERT: AQ 76 PHE cc_start: 0.8336 (t80) cc_final: 0.7974 (t80) REVERT: AR 25 TRP cc_start: 0.6776 (t-100) cc_final: 0.6338 (t-100) REVERT: AR 28 ARG cc_start: 0.7723 (mtt180) cc_final: 0.7353 (mtt180) REVERT: AR 32 PHE cc_start: 0.7931 (m-10) cc_final: 0.7631 (m-10) REVERT: AR 40 PHE cc_start: 0.8810 (m-80) cc_final: 0.8561 (m-80) REVERT: AR 91 ASP cc_start: 0.7910 (m-30) cc_final: 0.7048 (m-30) REVERT: AS 22 VAL cc_start: 0.8284 (t) cc_final: 0.7492 (t) REVERT: AS 40 LEU cc_start: 0.8279 (tp) cc_final: 0.7660 (tp) REVERT: AT 29 LEU cc_start: 0.9418 (tp) cc_final: 0.9179 (tp) REVERT: AT 34 ASN cc_start: 0.8987 (m-40) cc_final: 0.8581 (m110) REVERT: AT 37 ARG cc_start: 0.8393 (ttm170) cc_final: 0.7719 (ptm160) REVERT: AT 38 TYR cc_start: 0.8310 (m-10) cc_final: 0.7812 (m-10) REVERT: AT 52 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8199 (tt0) REVERT: AT 64 MET cc_start: 0.8738 (pmm) cc_final: 0.8493 (pmm) REVERT: AU 5 TYR cc_start: 0.7552 (p90) cc_final: 0.7091 (p90) REVERT: AU 8 ILE cc_start: 0.8295 (mm) cc_final: 0.7974 (tp) REVERT: AU 64 LYS cc_start: 0.7645 (tttt) cc_final: 0.7310 (mttt) REVERT: AU 75 ASP cc_start: 0.8071 (m-30) cc_final: 0.7587 (m-30) REVERT: AV 11 ASP cc_start: 0.8617 (m-30) cc_final: 0.8323 (t0) REVERT: AV 91 GLU cc_start: 0.7264 (tp30) cc_final: 0.6860 (tm-30) REVERT: AW 28 MET cc_start: 0.7792 (ppp) cc_final: 0.7580 (ppp) REVERT: AW 75 ASN cc_start: 0.8227 (m-40) cc_final: 0.7764 (m-40) REVERT: AW 84 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6688 (pt0) REVERT: AW 125 LEU cc_start: 0.9037 (mt) cc_final: 0.8826 (mt) REVERT: AX 17 GLN cc_start: 0.8304 (tp40) cc_final: 0.7785 (tp40) REVERT: AX 21 LEU cc_start: 0.7844 (tp) cc_final: 0.7585 (tp) REVERT: AX 36 ILE cc_start: 0.8726 (mt) cc_final: 0.8410 (mt) REVERT: AX 57 PHE cc_start: 0.8530 (m-10) cc_final: 0.8086 (m-10) REVERT: AY 32 PHE cc_start: 0.7843 (m-10) cc_final: 0.7427 (m-80) REVERT: AY 36 ILE cc_start: 0.9032 (pt) cc_final: 0.8821 (pt) REVERT: AY 48 LEU cc_start: 0.8281 (mp) cc_final: 0.7747 (mt) REVERT: AZ 24 LYS cc_start: 0.7512 (tttm) cc_final: 0.7077 (tmtt) REVERT: AZ 26 LEU cc_start: 0.9106 (tt) cc_final: 0.8806 (tp) REVERT: AZ 49 LYS cc_start: 0.8932 (tppt) cc_final: 0.8478 (ttpt) REVERT: Aa 32 TYR cc_start: 0.7043 (p90) cc_final: 0.6806 (p90) REVERT: Aa 33 VAL cc_start: 0.5981 (t) cc_final: 0.5686 (t) REVERT: Aa 38 LYS cc_start: 0.7305 (tmtt) cc_final: 0.7058 (tmtt) REVERT: Aa 42 PHE cc_start: 0.8616 (t80) cc_final: 0.8375 (t80) REVERT: Ac 50 ARG cc_start: 0.8447 (ttt180) cc_final: 0.7697 (ttp80) REVERT: Ad 11 LYS cc_start: 0.9303 (tptt) cc_final: 0.8652 (tptm) REVERT: Ad 15 THR cc_start: 0.9163 (p) cc_final: 0.8781 (p) REVERT: Ae 32 LEU cc_start: 0.7723 (mt) cc_final: 0.7268 (mt) REVERT: Af 15 LYS cc_start: 0.8736 (mmmm) cc_final: 0.8338 (mttt) REVERT: Af 22 ARG cc_start: 0.7086 (mmm-85) cc_final: 0.6257 (mtp180) REVERT: BF 25 ASN cc_start: 0.9098 (m110) cc_final: 0.8809 (m110) REVERT: BF 28 PHE cc_start: 0.7215 (t80) cc_final: 0.6313 (t80) REVERT: BF 59 GLU cc_start: 0.9060 (tt0) cc_final: 0.8522 (mm-30) REVERT: BF 176 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8211 (tt0) REVERT: BF 220 ASP cc_start: 0.9009 (t0) cc_final: 0.8791 (t0) REVERT: BG 142 MET cc_start: 0.9197 (tmm) cc_final: 0.8875 (tpt) REVERT: BG 190 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7166 (tpm170) REVERT: BG 204 LEU cc_start: 0.8874 (mt) cc_final: 0.8500 (mp) REVERT: BH 54 TYR cc_start: 0.8888 (t80) cc_final: 0.8043 (t80) REVERT: BH 58 LEU cc_start: 0.9617 (tt) cc_final: 0.9119 (mt) REVERT: BH 66 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7915 (mtt90) REVERT: BH 74 GLN cc_start: 0.9112 (mp10) cc_final: 0.8778 (mp10) REVERT: BH 75 PHE cc_start: 0.9272 (t80) cc_final: 0.9012 (t80) REVERT: BH 76 ARG cc_start: 0.9180 (ppt170) cc_final: 0.8751 (ptp-110) REVERT: BH 81 GLU cc_start: 0.9370 (tm-30) cc_final: 0.9147 (tm-30) REVERT: BH 102 ASP cc_start: 0.8087 (t70) cc_final: 0.7729 (t0) REVERT: BH 106 TYR cc_start: 0.9005 (t80) cc_final: 0.8426 (t80) REVERT: BH 161 ASN cc_start: 0.8768 (m-40) cc_final: 0.8532 (m-40) REVERT: BH 165 MET cc_start: 0.8270 (mmp) cc_final: 0.7996 (tpp) REVERT: BH 190 ASP cc_start: 0.7609 (m-30) cc_final: 0.7381 (m-30) REVERT: BH 207 TYR cc_start: 0.7024 (m-10) cc_final: 0.6620 (m-10) REVERT: BI 7 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6973 (pm20) REVERT: BI 10 MET cc_start: 0.9540 (ppp) cc_final: 0.9261 (ppp) REVERT: BI 64 ARG cc_start: 0.9254 (mmp80) cc_final: 0.9035 (mmm160) REVERT: BI 79 GLU cc_start: 0.8514 (pm20) cc_final: 0.7893 (pm20) REVERT: BI 111 GLU cc_start: 0.9205 (tt0) cc_final: 0.8589 (mt-10) REVERT: BI 112 LEU cc_start: 0.9093 (tt) cc_final: 0.8580 (tt) REVERT: BI 129 ILE cc_start: 0.9221 (pt) cc_final: 0.8934 (tp) REVERT: BI 136 MET cc_start: 0.9109 (tmm) cc_final: 0.8900 (tmm) REVERT: BJ 43 LEU cc_start: 0.7024 (pt) cc_final: 0.6421 (tp) REVERT: BJ 75 LEU cc_start: 0.9105 (mt) cc_final: 0.8546 (tp) REVERT: BJ 78 GLU cc_start: 0.9011 (tt0) cc_final: 0.8497 (pp20) REVERT: BK 31 MET cc_start: 0.6181 (tmm) cc_final: 0.5704 (tmm) REVERT: BK 73 MET cc_start: 0.7336 (mmm) cc_final: 0.6394 (ppp) REVERT: BK 89 MET cc_start: 0.8338 (ppp) cc_final: 0.7761 (pmm) REVERT: BK 90 GLU cc_start: 0.8139 (pp20) cc_final: 0.7577 (pp20) REVERT: BK 142 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6380 (tp30) REVERT: BL 15 ASN cc_start: 0.8718 (m-40) cc_final: 0.8392 (m-40) REVERT: BL 42 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8708 (tm-30) REVERT: BL 44 PHE cc_start: 0.8913 (m-80) cc_final: 0.8356 (m-10) REVERT: BL 50 ARG cc_start: 0.8435 (tpt170) cc_final: 0.8064 (tpt170) REVERT: BL 82 HIS cc_start: 0.9444 (t-90) cc_final: 0.9019 (t-170) REVERT: BL 88 LYS cc_start: 0.9400 (pttt) cc_final: 0.9038 (ptpp) REVERT: BL 111 ILE cc_start: 0.9607 (mp) cc_final: 0.9367 (pt) REVERT: BM 92 TYR cc_start: 0.6293 (m-10) cc_final: 0.5737 (m-80) REVERT: BN 22 LYS cc_start: 0.8341 (mmmt) cc_final: 0.7618 (mmtm) REVERT: BO 11 LYS cc_start: 0.7003 (mptt) cc_final: 0.6367 (mptt) REVERT: BO 38 ASN cc_start: 0.8689 (m-40) cc_final: 0.8372 (t0) REVERT: BO 41 THR cc_start: 0.5769 (t) cc_final: 0.5229 (t) REVERT: BP 16 GLU cc_start: 0.8141 (mp0) cc_final: 0.7502 (mp0) REVERT: BP 77 LEU cc_start: 0.7572 (mm) cc_final: 0.7067 (mm) REVERT: BP 78 GLN cc_start: 0.8749 (mp10) cc_final: 0.8455 (pm20) REVERT: BQ 3 ARG cc_start: 0.8314 (ttm170) cc_final: 0.7380 (mmt180) REVERT: BR 37 PHE cc_start: 0.8154 (m-80) cc_final: 0.7801 (m-80) REVERT: BS 43 LEU cc_start: 0.8151 (tp) cc_final: 0.7785 (mt) REVERT: BS 53 HIS cc_start: 0.8964 (t-90) cc_final: 0.8617 (t-90) REVERT: BS 58 MET cc_start: 0.8879 (mtt) cc_final: 0.8568 (mtt) REVERT: BS 62 GLN cc_start: 0.8896 (mt0) cc_final: 0.8667 (mp10) REVERT: BT 1 MET cc_start: 0.7193 (mmp) cc_final: 0.6943 (mmp) REVERT: BT 34 GLU cc_start: 0.7885 (pm20) cc_final: 0.7574 (pm20) REVERT: BT 36 ILE cc_start: 0.9141 (mm) cc_final: 0.8905 (mm) REVERT: BT 38 TYR cc_start: 0.7164 (p90) cc_final: 0.6819 (p90) REVERT: BT 54 GLU cc_start: 0.9205 (pt0) cc_final: 0.8710 (pp20) REVERT: BT 59 TRP cc_start: 0.9161 (m100) cc_final: 0.8055 (m100) REVERT: BU 29 HIS cc_start: 0.9451 (t-90) cc_final: 0.9156 (t-90) REVERT: BU 34 LYS cc_start: 0.9470 (tmmt) cc_final: 0.9104 (tttt) REVERT: BV 32 ARG cc_start: 0.7824 (mtt-85) cc_final: 0.7079 (mmp80) REVERT: BV 39 VAL cc_start: 0.7987 (t) cc_final: 0.7726 (t) REVERT: BV 56 THR cc_start: 0.8201 (p) cc_final: 0.7729 (p) REVERT: BW 7 LYS cc_start: 0.7833 (tmtt) cc_final: 0.7562 (ptpp) REVERT: BW 28 LYS cc_start: 0.7994 (tmmt) cc_final: 0.7760 (mmtt) REVERT: BW 79 THR cc_start: 0.7335 (m) cc_final: 0.6976 (p) REVERT: BX 36 LEU cc_start: 0.8865 (mp) cc_final: 0.8600 (mp) REVERT: BY 18 TYR cc_start: 0.5834 (m-80) cc_final: 0.5598 (m-80) REVERT: CA 41 ARG cc_start: 0.4194 (ptm-80) cc_final: 0.3902 (ptm-80) REVERT: CA 70 ILE cc_start: 0.7821 (mt) cc_final: 0.7599 (mt) REVERT: CA 147 LEU cc_start: 0.8795 (tp) cc_final: 0.8560 (tp) REVERT: CA 207 MET cc_start: 0.7936 (tpt) cc_final: 0.7216 (tpt) REVERT: CA 248 ASN cc_start: 0.8392 (t0) cc_final: 0.8139 (t0) REVERT: CA 293 ASN cc_start: 0.8994 (m-40) cc_final: 0.8751 (m-40) REVERT: CA 300 LEU cc_start: 0.7460 (mp) cc_final: 0.7022 (tt) REVERT: CA 326 VAL cc_start: 0.9186 (m) cc_final: 0.8925 (m) REVERT: CA 505 GLN cc_start: 0.8762 (pt0) cc_final: 0.8461 (pt0) REVERT: CA 519 TYR cc_start: 0.8899 (p90) cc_final: 0.8231 (p90) outliers start: 10 outliers final: 9 residues processed: 1680 average time/residue: 1.4137 time to fit residues: 4026.6804 Evaluate side-chains 1372 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1363 time to evaluate : 6.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 1031 optimal weight: 0.9990 chunk 120 optimal weight: 20.0000 chunk 609 optimal weight: 30.0000 chunk 781 optimal weight: 30.0000 chunk 605 optimal weight: 9.9990 chunk 900 optimal weight: 0.0470 chunk 597 optimal weight: 2.9990 chunk 1066 optimal weight: 0.9990 chunk 667 optimal weight: 20.0000 chunk 649 optimal weight: 10.0000 chunk 492 optimal weight: 9.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AD 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 201 HIS AD 227 ASN AE 135 HIS ** AE 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 40 GLN AG 27 ASN ** AG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 89 HIS ** AN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AR 66 ASN AS 87 HIS ** AS 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AV 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AV 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 75 ASN AW 121 HIS AW 132 ASN ** AY 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 38 GLN ** AY 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 60 ASN ** AY 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 7 HIS ** Ae 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 104 ASN ** BF 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 73 ASN ** BI 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 7 ASN ** BJ 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 70 GLN BO 78 GLN BO 116 HIS BP 9 GLN ** BP 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 69 HIS ** CA 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 527 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 1.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.530 163075 Z= 0.297 Angle : 0.873 36.841 242863 Z= 0.433 Chirality : 0.043 0.478 30675 Planarity : 0.007 0.118 13938 Dihedral : 26.586 179.590 79709 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 31.64 Ramachandran Plot: Outliers : 2.73 % Allowed : 19.97 % Favored : 77.30 % Rotamer: Outliers : 0.24 % Allowed : 3.12 % Favored : 96.64 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.95 % Twisted Proline : 1.20 % Twisted General : 0.40 % 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: -4.31 (0.09), residues: 6565 helix: -1.25 (0.11), residues: 1911 sheet: -1.91 (0.17), residues: 855 loop : -4.22 (0.08), residues: 3799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRPAG 29 HIS 0.017 0.002 HISBS 53 PHE 0.044 0.003 PHEAQ 76 TYR 0.043 0.002 TYRAW 99 ARG 0.022 0.001 ARGAb 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1675 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1662 time to evaluate : 6.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AC 6 ARG cc_start: 0.4535 (ppt170) cc_final: 0.2062 (ttp-170) REVERT: AC 120 MET cc_start: 0.3410 (tpt) cc_final: 0.3030 (tpt) REVERT: AC 217 THR cc_start: 0.6755 (m) cc_final: 0.6473 (m) REVERT: AC 218 MET cc_start: -0.2743 (ttp) cc_final: -0.3518 (ttp) REVERT: AD 52 ARG cc_start: 0.7716 (tpm170) cc_final: 0.7439 (tpp-160) REVERT: AD 58 HIS cc_start: 0.7990 (m90) cc_final: 0.7472 (m90) REVERT: AD 87 ASN cc_start: 0.9387 (m110) cc_final: 0.9106 (m110) REVERT: AD 99 ASP cc_start: 0.8888 (p0) cc_final: 0.8532 (p0) REVERT: AD 115 GLN cc_start: 0.7927 (pp30) cc_final: 0.7151 (pp30) REVERT: AD 133 LEU cc_start: 0.9357 (mm) cc_final: 0.9117 (mm) REVERT: AD 164 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8108 (tm-30) REVERT: AD 217 ARG cc_start: 0.8289 (ptp-170) cc_final: 0.7728 (ptp-170) REVERT: AD 268 ARG cc_start: 0.8131 (tmt170) cc_final: 0.6962 (tmt170) REVERT: AE 26 ILE cc_start: 0.8351 (pt) cc_final: 0.7786 (pt) REVERT: AE 27 LEU cc_start: 0.7553 (tp) cc_final: 0.7321 (tp) REVERT: AE 120 TRP cc_start: 0.7731 (p-90) cc_final: 0.7019 (p-90) REVERT: AE 127 ASP cc_start: 0.8357 (t0) cc_final: 0.7845 (t0) REVERT: AE 160 TYR cc_start: 0.7541 (m-80) cc_final: 0.6968 (m-80) REVERT: AE 168 MET cc_start: 0.8987 (mmp) cc_final: 0.7070 (mtp) REVERT: AE 180 ASN cc_start: 0.7474 (p0) cc_final: 0.6896 (p0) REVERT: AE 183 LEU cc_start: 0.9174 (mm) cc_final: 0.8958 (mm) REVERT: AE 185 LYS cc_start: 0.8090 (pttp) cc_final: 0.7680 (ptmm) REVERT: AF 43 LYS cc_start: 0.8705 (tttt) cc_final: 0.8371 (tmmt) REVERT: AF 88 VAL cc_start: 0.8555 (t) cc_final: 0.8191 (m) REVERT: AF 93 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8388 (mmtp) REVERT: AF 112 MET cc_start: 0.9108 (ptm) cc_final: 0.8844 (ptp) REVERT: AF 145 GLU cc_start: 0.9566 (mm-30) cc_final: 0.9062 (tm-30) REVERT: AF 155 LEU cc_start: 0.8807 (mm) cc_final: 0.8456 (mt) REVERT: AF 160 ASN cc_start: 0.9334 (t0) cc_final: 0.9074 (t0) REVERT: AF 169 ASN cc_start: 0.7711 (t0) cc_final: 0.7221 (t0) REVERT: AF 192 LEU cc_start: 0.8212 (tp) cc_final: 0.7867 (tp) REVERT: AG 155 MET cc_start: 0.8841 (mtt) cc_final: 0.8467 (mpp) REVERT: AH 30 LYS cc_start: 0.8527 (tmtt) cc_final: 0.7834 (pttm) REVERT: AH 41 MET cc_start: 0.8256 (mtt) cc_final: 0.7940 (mtp) REVERT: AJ 10 LEU cc_start: 0.7275 (pt) cc_final: 0.6810 (tp) REVERT: AJ 70 LYS cc_start: 0.7997 (pptt) cc_final: 0.7499 (pptt) REVERT: AK 68 GLU cc_start: 0.6763 (pt0) cc_final: 0.6395 (pt0) REVERT: AK 84 LYS cc_start: 0.8878 (mtmm) cc_final: 0.8456 (mmmt) REVERT: AK 106 MET cc_start: 0.8897 (mtt) cc_final: 0.8652 (mtp) REVERT: AK 121 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7717 (mtmt) REVERT: AK 123 TYR cc_start: 0.8668 (m-80) cc_final: 0.7835 (m-80) REVERT: AL 7 TYR cc_start: 0.9346 (m-10) cc_final: 0.9037 (m-10) REVERT: AL 9 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7804 (mm-30) REVERT: AL 31 LYS cc_start: 0.9140 (mttt) cc_final: 0.8644 (ttmt) REVERT: AL 114 ILE cc_start: 0.8983 (mt) cc_final: 0.8743 (mt) REVERT: AN 25 ASP cc_start: 0.5106 (m-30) cc_final: 0.4890 (m-30) REVERT: AN 37 LEU cc_start: 0.8427 (mt) cc_final: 0.8009 (mt) REVERT: AN 74 TYR cc_start: 0.4986 (m-10) cc_final: 0.4623 (m-10) REVERT: AN 80 GLU cc_start: 0.8764 (pp20) cc_final: 0.8385 (pp20) REVERT: AN 89 ASN cc_start: 0.8696 (m-40) cc_final: 0.8448 (m-40) REVERT: AN 91 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8588 (tm-30) REVERT: AN 113 GLN cc_start: 0.8551 (tt0) cc_final: 0.7532 (tm-30) REVERT: AN 115 MET cc_start: 0.9193 (mmm) cc_final: 0.8961 (mmt) REVERT: AN 128 LYS cc_start: 0.7005 (mmmt) cc_final: 0.6694 (mmmt) REVERT: AO 42 LYS cc_start: 0.8976 (mtmm) cc_final: 0.8465 (pttt) REVERT: AO 54 LEU cc_start: 0.9747 (mp) cc_final: 0.9517 (tt) REVERT: AO 74 LYS cc_start: 0.9422 (mmtm) cc_final: 0.9151 (tptt) REVERT: AO 107 ASP cc_start: 0.8625 (p0) cc_final: 0.8357 (p0) REVERT: AO 113 LEU cc_start: 0.8458 (tp) cc_final: 0.7803 (tp) REVERT: AO 115 GLU cc_start: 0.7245 (mp0) cc_final: 0.6893 (mp0) REVERT: AP 20 ARG cc_start: 0.8352 (mtt-85) cc_final: 0.5924 (mmt-90) REVERT: AP 46 VAL cc_start: 0.7857 (p) cc_final: 0.7583 (p) REVERT: AQ 1 MET cc_start: 0.7663 (ppp) cc_final: 0.7303 (ppp) REVERT: AQ 70 VAL cc_start: 0.7510 (t) cc_final: 0.6167 (t) REVERT: AQ 75 ILE cc_start: 0.7698 (mt) cc_final: 0.7293 (mt) REVERT: AQ 76 PHE cc_start: 0.8377 (t80) cc_final: 0.8092 (t80) REVERT: AR 25 TRP cc_start: 0.6748 (t-100) cc_final: 0.6295 (t-100) REVERT: AR 28 ARG cc_start: 0.7674 (mtt180) cc_final: 0.7349 (mtt90) REVERT: AR 32 PHE cc_start: 0.7821 (m-10) cc_final: 0.7538 (m-10) REVERT: AR 91 ASP cc_start: 0.7719 (m-30) cc_final: 0.7120 (m-30) REVERT: AS 40 LEU cc_start: 0.8275 (tp) cc_final: 0.7593 (tp) REVERT: AS 89 GLN cc_start: 0.7581 (pp30) cc_final: 0.7228 (pp30) REVERT: AT 29 LEU cc_start: 0.9374 (tp) cc_final: 0.8936 (pp) REVERT: AT 30 GLU cc_start: 0.8631 (mm-30) cc_final: 0.7855 (tp30) REVERT: AT 31 GLU cc_start: 0.9003 (pm20) cc_final: 0.8543 (pm20) REVERT: AT 34 ASN cc_start: 0.9085 (m-40) cc_final: 0.8028 (m110) REVERT: AT 37 ARG cc_start: 0.8312 (ttm170) cc_final: 0.8059 (ptm160) REVERT: AT 52 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8189 (tt0) REVERT: AT 64 MET cc_start: 0.8799 (pmm) cc_final: 0.8541 (pmm) REVERT: AU 5 TYR cc_start: 0.7583 (p90) cc_final: 0.7374 (p90) REVERT: AU 33 LYS cc_start: 0.8968 (mppt) cc_final: 0.8667 (mppt) REVERT: AU 75 ASP cc_start: 0.8110 (m-30) cc_final: 0.7566 (m-30) REVERT: AV 1 MET cc_start: 0.3928 (mmt) cc_final: 0.3683 (mmp) REVERT: AV 11 ASP cc_start: 0.8764 (m-30) cc_final: 0.8531 (t0) REVERT: AV 39 VAL cc_start: 0.7948 (t) cc_final: 0.7676 (t) REVERT: AV 67 LEU cc_start: 0.9250 (pt) cc_final: 0.9027 (pt) REVERT: AV 91 GLU cc_start: 0.7375 (tp30) cc_final: 0.7064 (tm-30) REVERT: AW 75 ASN cc_start: 0.8255 (m110) cc_final: 0.7817 (m-40) REVERT: AX 17 GLN cc_start: 0.8434 (tp40) cc_final: 0.7922 (tp40) REVERT: AX 24 LYS cc_start: 0.8119 (mtmm) cc_final: 0.7609 (mttt) REVERT: AX 36 ILE cc_start: 0.8882 (mt) cc_final: 0.8599 (mt) REVERT: AX 57 PHE cc_start: 0.8629 (m-10) cc_final: 0.8174 (m-10) REVERT: AX 60 PHE cc_start: 0.8610 (p90) cc_final: 0.8348 (p90) REVERT: AY 28 MET cc_start: 0.5648 (mtt) cc_final: 0.5106 (mtt) REVERT: AY 32 PHE cc_start: 0.7726 (m-10) cc_final: 0.7204 (m-80) REVERT: AY 33 GLN cc_start: 0.8366 (mp-120) cc_final: 0.8101 (mm-40) REVERT: AZ 24 LYS cc_start: 0.7654 (tttm) cc_final: 0.7226 (tmtt) REVERT: AZ 37 LEU cc_start: 0.8924 (mt) cc_final: 0.8376 (tp) REVERT: AZ 49 LYS cc_start: 0.8939 (tppt) cc_final: 0.8434 (ttpt) REVERT: Aa 13 ARG cc_start: 0.7563 (tmm-80) cc_final: 0.7340 (tmm-80) REVERT: Aa 15 ILE cc_start: 0.7885 (mm) cc_final: 0.7402 (mm) REVERT: Aa 38 LYS cc_start: 0.7071 (tmtt) cc_final: 0.6862 (tmtt) REVERT: Aa 57 GLU cc_start: 0.7586 (mp0) cc_final: 0.7278 (mp0) REVERT: Aa 62 ARG cc_start: 0.8352 (mtt180) cc_final: 0.7559 (tpm170) REVERT: Ac 37 ARG cc_start: 0.8353 (mmt180) cc_final: 0.5501 (mmt90) REVERT: Ac 50 ARG cc_start: 0.8445 (ttt180) cc_final: 0.7761 (ttp80) REVERT: Ad 11 LYS cc_start: 0.9308 (tptt) cc_final: 0.8577 (tptm) REVERT: Ad 15 THR cc_start: 0.9123 (p) cc_final: 0.8699 (p) REVERT: Ad 41 ARG cc_start: 0.9075 (ttp-110) cc_final: 0.8400 (mpt90) REVERT: Ad 47 ARG cc_start: 0.7092 (ptt180) cc_final: 0.6796 (ptm160) REVERT: Ae 1 MET cc_start: 0.7787 (tpp) cc_final: 0.7235 (tpp) REVERT: Ae 32 LEU cc_start: 0.7822 (mt) cc_final: 0.7553 (mt) REVERT: Af 15 LYS cc_start: 0.8614 (mmmm) cc_final: 0.8177 (tttt) REVERT: Af 17 ILE cc_start: 0.8846 (mt) cc_final: 0.8636 (mt) REVERT: Af 19 ARG cc_start: 0.7725 (ttm170) cc_final: 0.7146 (mtp180) REVERT: Af 22 ARG cc_start: 0.7295 (mmm-85) cc_final: 0.6349 (mtp180) REVERT: BF 16 HIS cc_start: 0.7433 (m90) cc_final: 0.7069 (m-70) REVERT: BF 21 ARG cc_start: 0.8060 (mpp-170) cc_final: 0.7827 (ptm160) REVERT: BF 25 ASN cc_start: 0.9149 (m110) cc_final: 0.8845 (m110) REVERT: BF 28 PHE cc_start: 0.7376 (t80) cc_final: 0.6538 (t80) REVERT: BF 59 GLU cc_start: 0.8855 (tt0) cc_final: 0.8480 (tp30) REVERT: BF 92 TYR cc_start: 0.7480 (p90) cc_final: 0.7024 (p90) REVERT: BF 110 GLN cc_start: 0.9030 (pm20) cc_final: 0.8759 (pm20) REVERT: BF 148 TYR cc_start: 0.6993 (p90) cc_final: 0.6741 (p90) REVERT: BF 176 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8204 (tt0) REVERT: BG 8 ILE cc_start: 0.9078 (mm) cc_final: 0.8847 (mm) REVERT: BG 123 GLN cc_start: 0.8573 (mt0) cc_final: 0.8347 (mt0) REVERT: BG 142 MET cc_start: 0.9591 (tmm) cc_final: 0.9106 (tpt) REVERT: BG 175 LEU cc_start: 0.9040 (mp) cc_final: 0.8823 (mp) REVERT: BG 190 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7051 (tpm170) REVERT: BG 204 LEU cc_start: 0.8899 (mt) cc_final: 0.8635 (mp) REVERT: BH 53 ASP cc_start: 0.9414 (p0) cc_final: 0.9181 (t0) REVERT: BH 54 TYR cc_start: 0.8780 (t80) cc_final: 0.7748 (t80) REVERT: BH 58 LEU cc_start: 0.9568 (tt) cc_final: 0.9188 (mt) REVERT: BH 70 ILE cc_start: 0.9147 (mm) cc_final: 0.8754 (mm) REVERT: BH 74 GLN cc_start: 0.9109 (mp10) cc_final: 0.8603 (mp10) REVERT: BH 75 PHE cc_start: 0.9242 (t80) cc_final: 0.8964 (t80) REVERT: BH 76 ARG cc_start: 0.9142 (ppt170) cc_final: 0.8563 (ttm-80) REVERT: BH 81 GLU cc_start: 0.9382 (tm-30) cc_final: 0.9158 (tm-30) REVERT: BH 102 ASP cc_start: 0.8054 (t70) cc_final: 0.7752 (t0) REVERT: BH 106 TYR cc_start: 0.8951 (t80) cc_final: 0.8394 (t80) REVERT: BH 146 ILE cc_start: 0.8282 (tp) cc_final: 0.8005 (mp) REVERT: BH 190 ASP cc_start: 0.7521 (m-30) cc_final: 0.7226 (m-30) REVERT: BI 10 MET cc_start: 0.9554 (ppp) cc_final: 0.9274 (ppp) REVERT: BI 79 GLU cc_start: 0.8315 (pm20) cc_final: 0.7874 (pm20) REVERT: BI 111 GLU cc_start: 0.9175 (tt0) cc_final: 0.8684 (tt0) REVERT: BI 133 TYR cc_start: 0.8509 (m-80) cc_final: 0.8204 (m-10) REVERT: BI 137 GLU cc_start: 0.9644 (tp30) cc_final: 0.9118 (tm-30) REVERT: BJ 33 TYR cc_start: 0.6515 (m-80) cc_final: 0.5951 (m-80) REVERT: BJ 43 LEU cc_start: 0.6994 (pt) cc_final: 0.6430 (tp) REVERT: BJ 62 TRP cc_start: 0.7562 (t60) cc_final: 0.7333 (t60) REVERT: BJ 67 MET cc_start: 0.6915 (pmm) cc_final: 0.6353 (pmm) REVERT: BJ 75 LEU cc_start: 0.9268 (mt) cc_final: 0.8665 (tp) REVERT: BJ 78 GLU cc_start: 0.9153 (tt0) cc_final: 0.8590 (mm-30) REVERT: BK 73 MET cc_start: 0.7180 (mmm) cc_final: 0.6623 (ttp) REVERT: BK 89 MET cc_start: 0.8602 (ppp) cc_final: 0.8006 (ppp) REVERT: BK 90 GLU cc_start: 0.8177 (pp20) cc_final: 0.7503 (pp20) REVERT: BK 139 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8075 (tm-30) REVERT: BK 142 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7062 (tp30) REVERT: BK 149 ARG cc_start: 0.7556 (mmm160) cc_final: 0.7123 (tpt170) REVERT: BL 44 PHE cc_start: 0.8811 (m-80) cc_final: 0.8574 (m-10) REVERT: BL 52 ASP cc_start: 0.8857 (p0) cc_final: 0.8412 (t0) REVERT: BL 79 VAL cc_start: 0.9019 (t) cc_final: 0.8464 (m) REVERT: BL 82 HIS cc_start: 0.9494 (t-90) cc_final: 0.9127 (t-170) REVERT: BL 83 ILE cc_start: 0.8692 (tt) cc_final: 0.8486 (tt) REVERT: BL 111 ILE cc_start: 0.9609 (mp) cc_final: 0.9381 (pt) REVERT: BL 121 ASP cc_start: 0.8958 (p0) cc_final: 0.8717 (p0) REVERT: BM 18 PHE cc_start: 0.5283 (m-80) cc_final: 0.4703 (m-80) REVERT: BM 42 ARG cc_start: 0.5800 (mmp80) cc_final: 0.5210 (tpp-160) REVERT: BM 92 TYR cc_start: 0.6282 (m-10) cc_final: 0.5828 (m-80) REVERT: BN 56 HIS cc_start: 0.5628 (m90) cc_final: 0.5293 (m90) REVERT: BO 11 LYS cc_start: 0.6839 (mptt) cc_final: 0.6217 (mptt) REVERT: BO 38 ASN cc_start: 0.8740 (m-40) cc_final: 0.8431 (t0) REVERT: BO 123 LYS cc_start: 0.7497 (mmtm) cc_final: 0.7288 (mmtm) REVERT: BP 16 GLU cc_start: 0.8240 (mp0) cc_final: 0.7610 (mp0) REVERT: BP 77 LEU cc_start: 0.7457 (mm) cc_final: 0.7143 (mm) REVERT: BP 78 GLN cc_start: 0.8747 (mp10) cc_final: 0.8400 (mp10) REVERT: BQ 66 LEU cc_start: 0.5476 (mm) cc_final: 0.5232 (mm) REVERT: BR 37 PHE cc_start: 0.8143 (m-80) cc_final: 0.7892 (m-80) REVERT: BS 43 LEU cc_start: 0.8075 (tp) cc_final: 0.7732 (mt) REVERT: BS 53 HIS cc_start: 0.8759 (t-90) cc_final: 0.8449 (t-90) REVERT: BS 58 MET cc_start: 0.8690 (mtt) cc_final: 0.7863 (mtt) REVERT: BS 59 MET cc_start: 0.9211 (tpt) cc_final: 0.8792 (tpt) REVERT: BS 62 GLN cc_start: 0.9040 (mp10) cc_final: 0.8632 (mp10) REVERT: BT 34 GLU cc_start: 0.7999 (pm20) cc_final: 0.7497 (pm20) REVERT: BT 38 TYR cc_start: 0.6778 (p90) cc_final: 0.6532 (p90) REVERT: BT 52 ASP cc_start: 0.8921 (t0) cc_final: 0.8665 (t0) REVERT: BT 54 GLU cc_start: 0.9131 (pt0) cc_final: 0.8679 (pp20) REVERT: BT 59 TRP cc_start: 0.9156 (m100) cc_final: 0.7674 (m100) REVERT: BU 15 MET cc_start: 0.8345 (pmm) cc_final: 0.8108 (pmm) REVERT: BU 29 HIS cc_start: 0.9500 (t-90) cc_final: 0.9173 (t-90) REVERT: BU 34 LYS cc_start: 0.9436 (tmmt) cc_final: 0.9008 (tttt) REVERT: BV 39 VAL cc_start: 0.8330 (t) cc_final: 0.8062 (t) REVERT: BV 56 THR cc_start: 0.8355 (p) cc_final: 0.8098 (t) REVERT: BW 70 LYS cc_start: 0.4334 (ptpt) cc_final: 0.4098 (tttt) REVERT: BW 79 THR cc_start: 0.7402 (m) cc_final: 0.7044 (p) REVERT: CA 207 MET cc_start: 0.7569 (tpt) cc_final: 0.7211 (tpt) REVERT: CA 248 ASN cc_start: 0.8572 (t0) cc_final: 0.8269 (t0) REVERT: CA 293 ASN cc_start: 0.8889 (m-40) cc_final: 0.8671 (m-40) REVERT: CA 300 LEU cc_start: 0.7569 (mp) cc_final: 0.7216 (tt) REVERT: CA 324 LYS cc_start: 0.8854 (pttm) cc_final: 0.8294 (pttm) REVERT: CA 325 PHE cc_start: 0.8163 (m-10) cc_final: 0.7865 (m-80) REVERT: CA 416 MET cc_start: 0.8045 (mtm) cc_final: 0.7614 (ttm) REVERT: CA 487 VAL cc_start: 0.8983 (m) cc_final: 0.8594 (p) REVERT: CA 488 LEU cc_start: 0.8819 (mt) cc_final: 0.8481 (mt) REVERT: CA 505 GLN cc_start: 0.8721 (pt0) cc_final: 0.8419 (pt0) REVERT: CA 518 VAL cc_start: 0.9253 (t) cc_final: 0.8975 (t) REVERT: CA 519 TYR cc_start: 0.8856 (p90) cc_final: 0.8098 (p90) outliers start: 13 outliers final: 11 residues processed: 1670 average time/residue: 1.5493 time to fit residues: 4446.1753 Evaluate side-chains 1352 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1341 time to evaluate : 6.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 659 optimal weight: 50.0000 chunk 425 optimal weight: 0.0010 chunk 636 optimal weight: 0.0770 chunk 321 optimal weight: 9.9990 chunk 209 optimal weight: 20.0000 chunk 206 optimal weight: 20.0000 chunk 677 optimal weight: 20.0000 chunk 726 optimal weight: 20.0000 chunk 527 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 837 optimal weight: 0.3980 overall best weight: 3.6948 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 87 ASN ** AD 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 201 HIS ** AE 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 29 GLN ** AK 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 57 HIS ** AO 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 87 HIS AT 34 ASN ** AV 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AW 50 GLN ** AW 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY 60 ASN ** AY 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 7 HIS Af 34 GLN ** BF 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 68 HIS ** BP 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 106 ASN ** BR 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 69 HIS ** BX 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 108 GLN ** CA 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 527 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 1.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.519 163075 Z= 0.299 Angle : 0.861 37.216 242863 Z= 0.426 Chirality : 0.042 0.474 30675 Planarity : 0.007 0.146 13938 Dihedral : 26.486 179.979 79709 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 31.97 Ramachandran Plot: Outliers : 2.62 % Allowed : 19.88 % Favored : 77.50 % Rotamer: Outliers : 0.19 % Allowed : 2.32 % Favored : 97.49 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.95 % Twisted Proline : 1.20 % Twisted General : 0.41 % 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: -4.26 (0.09), residues: 6565 helix: -1.18 (0.11), residues: 1914 sheet: -2.01 (0.17), residues: 872 loop : -4.18 (0.08), residues: 3779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRPAG 29 HIS 0.014 0.002 HISAS 64 PHE 0.044 0.003 PHEAP 87 TYR 0.056 0.002 TYRAW 99 ARG 0.030 0.001 ARGAW 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1665 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1655 time to evaluate : 6.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AC 120 MET cc_start: 0.2909 (tpt) cc_final: 0.2484 (tpt) REVERT: AC 217 THR cc_start: 0.6418 (m) cc_final: 0.6116 (m) REVERT: AC 218 MET cc_start: -0.2819 (ttp) cc_final: -0.3371 (ttp) REVERT: AD 79 VAL cc_start: 0.8940 (t) cc_final: 0.8630 (m) REVERT: AD 87 ASN cc_start: 0.9235 (m-40) cc_final: 0.9029 (m110) REVERT: AD 99 ASP cc_start: 0.8883 (p0) cc_final: 0.8436 (p0) REVERT: AD 115 GLN cc_start: 0.7910 (pp30) cc_final: 0.6940 (pp30) REVERT: AD 164 GLN cc_start: 0.8644 (tm-30) cc_final: 0.7798 (tm-30) REVERT: AD 166 GLN cc_start: 0.8377 (tt0) cc_final: 0.8149 (mt0) REVERT: AD 176 ARG cc_start: 0.7852 (tpp-160) cc_final: 0.7531 (tpp80) REVERT: AD 177 LEU cc_start: 0.8338 (pt) cc_final: 0.8083 (pt) REVERT: AD 217 ARG cc_start: 0.8331 (ptp-170) cc_final: 0.7827 (ptp-170) REVERT: AD 268 ARG cc_start: 0.8071 (tmt170) cc_final: 0.6886 (tmt170) REVERT: AE 26 ILE cc_start: 0.8428 (pt) cc_final: 0.7721 (pt) REVERT: AE 27 LEU cc_start: 0.7560 (tp) cc_final: 0.7260 (tp) REVERT: AE 120 TRP cc_start: 0.7728 (p-90) cc_final: 0.7258 (p-90) REVERT: AE 127 ASP cc_start: 0.8420 (t0) cc_final: 0.7940 (t0) REVERT: AE 159 HIS cc_start: 0.7917 (t-90) cc_final: 0.7698 (t70) REVERT: AE 160 TYR cc_start: 0.7466 (m-80) cc_final: 0.6745 (m-80) REVERT: AE 168 MET cc_start: 0.8911 (mmp) cc_final: 0.7615 (mtt) REVERT: AE 180 ASN cc_start: 0.7535 (p0) cc_final: 0.6809 (p0) REVERT: AE 185 LYS cc_start: 0.8045 (pttp) cc_final: 0.7613 (ptmm) REVERT: AF 53 THR cc_start: 0.5936 (m) cc_final: 0.5680 (m) REVERT: AF 112 MET cc_start: 0.9208 (ptm) cc_final: 0.8962 (ptp) REVERT: AF 125 LEU cc_start: 0.6694 (mt) cc_final: 0.6211 (mt) REVERT: AF 145 GLU cc_start: 0.9518 (mm-30) cc_final: 0.9001 (tm-30) REVERT: AF 160 ASN cc_start: 0.9305 (t0) cc_final: 0.9010 (t0) REVERT: AF 169 ASN cc_start: 0.7724 (t0) cc_final: 0.7380 (t0) REVERT: AG 155 MET cc_start: 0.8945 (mtt) cc_final: 0.8635 (mpp) REVERT: AH 30 LYS cc_start: 0.8439 (tmtt) cc_final: 0.7692 (pttm) REVERT: AH 83 TYR cc_start: 0.8353 (t80) cc_final: 0.8049 (t80) REVERT: AH 86 GLU cc_start: 0.8637 (pp20) cc_final: 0.8431 (tm-30) REVERT: AH 163 TYR cc_start: 0.7635 (m-80) cc_final: 0.7062 (m-10) REVERT: AJ 70 LYS cc_start: 0.8207 (pptt) cc_final: 0.7740 (pptt) REVERT: AJ 125 ARG cc_start: 0.7614 (mpt180) cc_final: 0.7406 (mpt180) REVERT: AJ 126 MET cc_start: -0.0481 (mmm) cc_final: -0.0719 (mmm) REVERT: AK 84 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8465 (mmmt) REVERT: AK 106 MET cc_start: 0.8867 (mtt) cc_final: 0.8613 (mtp) REVERT: AK 121 LYS cc_start: 0.8351 (mmmt) cc_final: 0.7583 (ptmt) REVERT: AK 126 PRO cc_start: 0.8316 (Cg_exo) cc_final: 0.8001 (Cg_endo) REVERT: AK 134 ARG cc_start: 0.8416 (mmp80) cc_final: 0.8005 (mmp-170) REVERT: AL 7 TYR cc_start: 0.9287 (m-10) cc_final: 0.9076 (m-10) REVERT: AL 31 LYS cc_start: 0.9124 (mttt) cc_final: 0.8678 (ttmt) REVERT: AL 114 ILE cc_start: 0.9079 (mt) cc_final: 0.8838 (mt) REVERT: AN 6 ARG cc_start: 0.7138 (tmt170) cc_final: 0.6502 (ttp80) REVERT: AN 25 ASP cc_start: 0.5139 (m-30) cc_final: 0.4893 (m-30) REVERT: AN 38 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7943 (tt0) REVERT: AN 74 TYR cc_start: 0.5000 (m-10) cc_final: 0.4509 (m-10) REVERT: AN 80 GLU cc_start: 0.8808 (pp20) cc_final: 0.7842 (pp20) REVERT: AN 83 MET cc_start: 0.7945 (pmm) cc_final: 0.7708 (pmm) REVERT: AN 89 ASN cc_start: 0.8540 (m-40) cc_final: 0.8260 (m-40) REVERT: AN 113 GLN cc_start: 0.8177 (tt0) cc_final: 0.7547 (tm-30) REVERT: AN 115 MET cc_start: 0.9198 (mmm) cc_final: 0.8914 (mmt) REVERT: AN 133 ARG cc_start: 0.9103 (pmt170) cc_final: 0.8567 (mmm160) REVERT: AO 40 LYS cc_start: 0.9002 (mptt) cc_final: 0.8505 (mptt) REVERT: AO 42 LYS cc_start: 0.8984 (mtmm) cc_final: 0.8444 (pttt) REVERT: AO 54 LEU cc_start: 0.9706 (mp) cc_final: 0.9443 (tt) REVERT: AO 74 LYS cc_start: 0.9435 (mmtm) cc_final: 0.9141 (tptt) REVERT: AO 107 ASP cc_start: 0.8603 (p0) cc_final: 0.8385 (p0) REVERT: AO 113 LEU cc_start: 0.8455 (tp) cc_final: 0.8116 (tp) REVERT: AP 20 ARG cc_start: 0.8487 (mtt-85) cc_final: 0.6064 (mmt-90) REVERT: AP 23 ARG cc_start: 0.7878 (mmp80) cc_final: 0.7283 (mmp80) REVERT: AP 46 VAL cc_start: 0.7863 (p) cc_final: 0.7583 (p) REVERT: AP 56 LEU cc_start: 0.7604 (mt) cc_final: 0.7256 (tt) REVERT: AQ 1 MET cc_start: 0.7358 (ppp) cc_final: 0.6891 (ppp) REVERT: AQ 38 ASN cc_start: 0.7884 (p0) cc_final: 0.6827 (p0) REVERT: AQ 70 VAL cc_start: 0.7680 (t) cc_final: 0.6356 (t) REVERT: AQ 75 ILE cc_start: 0.7776 (mt) cc_final: 0.7361 (mt) REVERT: AQ 76 PHE cc_start: 0.8657 (t80) cc_final: 0.8365 (t80) REVERT: AR 25 TRP cc_start: 0.6873 (t-100) cc_final: 0.6204 (t-100) REVERT: AR 32 PHE cc_start: 0.7830 (m-10) cc_final: 0.7569 (m-10) REVERT: AR 91 ASP cc_start: 0.7542 (m-30) cc_final: 0.6795 (m-30) REVERT: AS 5 VAL cc_start: 0.8378 (t) cc_final: 0.8092 (t) REVERT: AS 12 TYR cc_start: 0.8408 (t80) cc_final: 0.7853 (t80) REVERT: AS 22 VAL cc_start: 0.7885 (t) cc_final: 0.7190 (t) REVERT: AS 24 LYS cc_start: 0.8304 (mmmt) cc_final: 0.7765 (mptt) REVERT: AS 40 LEU cc_start: 0.8407 (tp) cc_final: 0.7632 (tp) REVERT: AS 51 VAL cc_start: 0.5927 (t) cc_final: 0.5519 (t) REVERT: AT 29 LEU cc_start: 0.9379 (tp) cc_final: 0.9118 (tp) REVERT: AT 34 ASN cc_start: 0.9110 (m110) cc_final: 0.8765 (m110) REVERT: AT 37 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7930 (ptm160) REVERT: AT 52 GLU cc_start: 0.8801 (mm-30) cc_final: 0.7992 (tt0) REVERT: AT 88 ARG cc_start: 0.7833 (mmp80) cc_final: 0.7611 (mmp80) REVERT: AT 97 LYS cc_start: 0.7056 (ttmt) cc_final: 0.6750 (tptm) REVERT: AU 5 TYR cc_start: 0.7739 (p90) cc_final: 0.7477 (p90) REVERT: AU 8 ILE cc_start: 0.8474 (mm) cc_final: 0.8021 (mm) REVERT: AU 9 LEU cc_start: 0.7706 (mm) cc_final: 0.7486 (mm) REVERT: AU 33 LYS cc_start: 0.9032 (mppt) cc_final: 0.8752 (mppt) REVERT: AU 75 ASP cc_start: 0.7926 (m-30) cc_final: 0.7379 (m-30) REVERT: AV 11 ASP cc_start: 0.8838 (m-30) cc_final: 0.8566 (t0) REVERT: AV 67 LEU cc_start: 0.9133 (pt) cc_final: 0.8890 (pt) REVERT: AV 91 GLU cc_start: 0.7517 (tp30) cc_final: 0.7254 (tm-30) REVERT: AW 75 ASN cc_start: 0.8344 (m110) cc_final: 0.7881 (m-40) REVERT: AW 84 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6569 (pt0) REVERT: AW 118 GLN cc_start: 0.8335 (pp30) cc_final: 0.8116 (pp30) REVERT: AX 17 GLN cc_start: 0.8665 (tp40) cc_final: 0.8229 (tp40) REVERT: AX 24 LYS cc_start: 0.8366 (mtmm) cc_final: 0.7887 (mttt) REVERT: AX 36 ILE cc_start: 0.8854 (mt) cc_final: 0.8564 (mt) REVERT: AX 57 PHE cc_start: 0.8645 (m-10) cc_final: 0.8226 (m-10) REVERT: AX 60 PHE cc_start: 0.8624 (p90) cc_final: 0.8276 (p90) REVERT: AY 28 MET cc_start: 0.6039 (mtt) cc_final: 0.5537 (mtt) REVERT: AY 32 PHE cc_start: 0.7515 (m-10) cc_final: 0.7159 (m-10) REVERT: AY 33 GLN cc_start: 0.8462 (mp-120) cc_final: 0.8132 (mm-40) REVERT: AY 48 LEU cc_start: 0.8499 (pp) cc_final: 0.8176 (pp) REVERT: AY 58 VAL cc_start: 0.9464 (t) cc_final: 0.9186 (t) REVERT: AZ 24 LYS cc_start: 0.7850 (tttm) cc_final: 0.7426 (tmtt) REVERT: AZ 26 LEU cc_start: 0.9195 (tp) cc_final: 0.8842 (tp) REVERT: AZ 37 LEU cc_start: 0.9006 (mt) cc_final: 0.8391 (tp) REVERT: AZ 49 LYS cc_start: 0.9048 (tppt) cc_final: 0.8525 (ttpt) REVERT: Aa 15 ILE cc_start: 0.7882 (mm) cc_final: 0.7536 (mm) REVERT: Aa 31 ILE cc_start: 0.8227 (tp) cc_final: 0.7864 (mm) REVERT: Aa 33 VAL cc_start: 0.5888 (t) cc_final: 0.5443 (t) REVERT: Aa 38 LYS cc_start: 0.6958 (tmtt) cc_final: 0.6758 (tmtt) REVERT: Aa 57 GLU cc_start: 0.7595 (mp0) cc_final: 0.7258 (mp0) REVERT: Aa 62 ARG cc_start: 0.8374 (mtt180) cc_final: 0.7662 (tpm170) REVERT: Ab 15 ARG cc_start: 0.8896 (mtp85) cc_final: 0.8358 (ptp90) REVERT: Ab 37 LYS cc_start: 0.9121 (tppt) cc_final: 0.8847 (tppt) REVERT: Ab 51 TYR cc_start: 0.8599 (p90) cc_final: 0.8311 (p90) REVERT: Ac 18 ARG cc_start: 0.7880 (mmt-90) cc_final: 0.7264 (mmp80) REVERT: Ac 37 ARG cc_start: 0.8448 (mmt180) cc_final: 0.5243 (mmt90) REVERT: Ac 50 ARG cc_start: 0.8445 (ttt180) cc_final: 0.7934 (ttp-170) REVERT: Ad 11 LYS cc_start: 0.9244 (tptt) cc_final: 0.8349 (tptm) REVERT: Ad 15 THR cc_start: 0.9059 (p) cc_final: 0.8640 (p) REVERT: Ad 41 ARG cc_start: 0.9056 (ttp-110) cc_final: 0.8483 (mpt90) REVERT: Ad 47 ARG cc_start: 0.7015 (ptt180) cc_final: 0.6743 (ptm160) REVERT: Ae 1 MET cc_start: 0.7610 (tpp) cc_final: 0.6832 (tpp) REVERT: Ae 52 LYS cc_start: 0.9144 (pptt) cc_final: 0.8918 (pptt) REVERT: Af 15 LYS cc_start: 0.8721 (mmmm) cc_final: 0.8294 (mttt) REVERT: Af 17 ILE cc_start: 0.8780 (mt) cc_final: 0.8511 (mt) REVERT: Af 19 ARG cc_start: 0.7752 (ttm170) cc_final: 0.7253 (mtt-85) REVERT: Af 22 ARG cc_start: 0.7278 (mmm-85) cc_final: 0.6493 (mtp180) REVERT: Af 34 GLN cc_start: 0.8498 (mm-40) cc_final: 0.7928 (mm110) REVERT: BF 25 ASN cc_start: 0.9156 (m110) cc_final: 0.8858 (m110) REVERT: BF 28 PHE cc_start: 0.7598 (t80) cc_final: 0.6862 (t80) REVERT: BF 48 MET cc_start: 0.7788 (mmt) cc_final: 0.7512 (mmt) REVERT: BF 63 MET cc_start: 0.8551 (mpp) cc_final: 0.7746 (ppp) REVERT: BF 92 TYR cc_start: 0.7595 (p90) cc_final: 0.7098 (p90) REVERT: BF 95 GLN cc_start: 0.8430 (mp10) cc_final: 0.8172 (mp10) REVERT: BF 148 TYR cc_start: 0.6847 (p90) cc_final: 0.6482 (p90) REVERT: BF 176 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8339 (tt0) REVERT: BG 136 GLN cc_start: 0.9323 (tt0) cc_final: 0.8790 (tm-30) REVERT: BG 142 MET cc_start: 0.9506 (tmm) cc_final: 0.9162 (tpt) REVERT: BG 190 ARG cc_start: 0.8097 (ttm-80) cc_final: 0.7033 (tpm170) REVERT: BG 191 THR cc_start: 0.8788 (p) cc_final: 0.8562 (p) REVERT: BG 204 LEU cc_start: 0.9023 (mt) cc_final: 0.8703 (mp) REVERT: BH 33 MET cc_start: 0.8112 (mtt) cc_final: 0.7776 (mmm) REVERT: BH 53 ASP cc_start: 0.9403 (p0) cc_final: 0.9132 (t0) REVERT: BH 54 TYR cc_start: 0.8709 (t80) cc_final: 0.8162 (t80) REVERT: BH 66 ARG cc_start: 0.8294 (mtt180) cc_final: 0.7778 (mtt90) REVERT: BH 74 GLN cc_start: 0.9106 (mp10) cc_final: 0.8612 (mp10) REVERT: BH 75 PHE cc_start: 0.9156 (t80) cc_final: 0.8909 (t80) REVERT: BH 76 ARG cc_start: 0.9211 (ppt170) cc_final: 0.8969 (ptp-110) REVERT: BH 81 GLU cc_start: 0.9376 (tm-30) cc_final: 0.9154 (tm-30) REVERT: BH 102 ASP cc_start: 0.8113 (t70) cc_final: 0.7779 (t0) REVERT: BH 106 TYR cc_start: 0.8877 (t80) cc_final: 0.8610 (t80) REVERT: BH 190 ASP cc_start: 0.7263 (m-30) cc_final: 0.7045 (m-30) REVERT: BH 205 GLU cc_start: 0.8496 (pt0) cc_final: 0.7917 (pt0) REVERT: BI 79 GLU cc_start: 0.8061 (pm20) cc_final: 0.7727 (pm20) REVERT: BI 111 GLU cc_start: 0.9177 (tt0) cc_final: 0.8651 (mt-10) REVERT: BI 126 ARG cc_start: 0.8534 (ptp-110) cc_final: 0.8147 (mtp180) REVERT: BJ 33 TYR cc_start: 0.6506 (m-80) cc_final: 0.5886 (m-80) REVERT: BJ 43 LEU cc_start: 0.7229 (pt) cc_final: 0.6607 (tp) REVERT: BJ 62 TRP cc_start: 0.7624 (t60) cc_final: 0.7187 (t60) REVERT: BJ 67 MET cc_start: 0.7012 (pmm) cc_final: 0.6529 (pmm) REVERT: BJ 75 LEU cc_start: 0.9327 (mt) cc_final: 0.8802 (tp) REVERT: BJ 78 GLU cc_start: 0.9158 (tt0) cc_final: 0.8524 (mm-30) REVERT: BK 73 MET cc_start: 0.7235 (mmm) cc_final: 0.6761 (ttp) REVERT: BK 89 MET cc_start: 0.8644 (ppp) cc_final: 0.8193 (pmm) REVERT: BK 90 GLU cc_start: 0.8149 (pp20) cc_final: 0.7243 (pp20) REVERT: BK 122 HIS cc_start: 0.8660 (m-70) cc_final: 0.8303 (m-70) REVERT: BL 78 GLN cc_start: 0.9063 (pm20) cc_final: 0.8419 (pm20) REVERT: BL 79 VAL cc_start: 0.9186 (t) cc_final: 0.8724 (p) REVERT: BL 82 HIS cc_start: 0.9511 (t-90) cc_final: 0.9136 (t-170) REVERT: BL 83 ILE cc_start: 0.8742 (tt) cc_final: 0.8536 (tt) REVERT: BL 111 ILE cc_start: 0.9576 (mp) cc_final: 0.9340 (tp) REVERT: BL 119 LEU cc_start: 0.8896 (mm) cc_final: 0.8658 (mp) REVERT: BL 132 GLU cc_start: 0.8493 (tt0) cc_final: 0.8067 (tm-30) REVERT: BL 133 LEU cc_start: 0.9248 (tp) cc_final: 0.8986 (tt) REVERT: BL 134 ILE cc_start: 0.9349 (mt) cc_final: 0.9105 (mt) REVERT: BM 42 ARG cc_start: 0.5933 (mmp80) cc_final: 0.5233 (tpt170) REVERT: BM 92 TYR cc_start: 0.6428 (m-10) cc_final: 0.5830 (m-80) REVERT: BN 56 HIS cc_start: 0.5656 (m90) cc_final: 0.5331 (m90) REVERT: BO 11 LYS cc_start: 0.6876 (mptt) cc_final: 0.6261 (mptt) REVERT: BO 38 ASN cc_start: 0.8771 (m-40) cc_final: 0.8489 (t0) REVERT: BP 9 GLN cc_start: 0.9482 (tt0) cc_final: 0.9168 (tt0) REVERT: BP 16 GLU cc_start: 0.8166 (mp0) cc_final: 0.7542 (mp0) REVERT: BP 77 LEU cc_start: 0.7612 (mm) cc_final: 0.7321 (mm) REVERT: BP 78 GLN cc_start: 0.8682 (mp10) cc_final: 0.8303 (mp10) REVERT: BR 37 PHE cc_start: 0.8242 (m-80) cc_final: 0.7871 (m-80) REVERT: BR 57 ARG cc_start: 0.8406 (ttt180) cc_final: 0.7759 (ttp-170) REVERT: BS 27 VAL cc_start: 0.9047 (t) cc_final: 0.8832 (t) REVERT: BS 43 LEU cc_start: 0.8119 (tp) cc_final: 0.7841 (mt) REVERT: BS 53 HIS cc_start: 0.8833 (t-90) cc_final: 0.8572 (t70) REVERT: BS 58 MET cc_start: 0.8618 (mtt) cc_final: 0.8065 (mtt) REVERT: BT 34 GLU cc_start: 0.8161 (pm20) cc_final: 0.7539 (pm20) REVERT: BT 36 ILE cc_start: 0.9246 (mm) cc_final: 0.8800 (mm) REVERT: BT 52 ASP cc_start: 0.8993 (t0) cc_final: 0.8734 (t0) REVERT: BT 54 GLU cc_start: 0.9132 (pt0) cc_final: 0.8682 (pp20) REVERT: BT 59 TRP cc_start: 0.9169 (m100) cc_final: 0.8016 (m100) REVERT: BU 29 HIS cc_start: 0.9472 (t-90) cc_final: 0.9241 (t-90) REVERT: BU 34 LYS cc_start: 0.9444 (tmmt) cc_final: 0.8974 (tttt) REVERT: BU 59 ILE cc_start: 0.9405 (tp) cc_final: 0.9073 (tp) REVERT: BU 71 PHE cc_start: 0.8644 (m-80) cc_final: 0.8198 (m-80) REVERT: BV 39 VAL cc_start: 0.8514 (t) cc_final: 0.8271 (t) REVERT: BV 56 THR cc_start: 0.8295 (p) cc_final: 0.7940 (p) REVERT: BW 70 LYS cc_start: 0.4222 (ptpt) cc_final: 0.3898 (ttmm) REVERT: BW 79 THR cc_start: 0.7496 (m) cc_final: 0.7137 (p) REVERT: BX 33 ILE cc_start: 0.8734 (pt) cc_final: 0.8411 (mt) REVERT: BY 14 TRP cc_start: 0.5198 (t-100) cc_final: 0.4956 (t60) REVERT: CA 106 MET cc_start: 0.7544 (ttt) cc_final: 0.6911 (tmm) REVERT: CA 248 ASN cc_start: 0.8657 (t0) cc_final: 0.8287 (t0) REVERT: CA 293 ASN cc_start: 0.8629 (m-40) cc_final: 0.8288 (m-40) REVERT: CA 300 LEU cc_start: 0.7672 (mp) cc_final: 0.7254 (tt) REVERT: CA 309 MET cc_start: 0.8394 (mmt) cc_final: 0.8134 (mmp) REVERT: CA 324 LYS cc_start: 0.8951 (pttm) cc_final: 0.8361 (pttm) REVERT: CA 325 PHE cc_start: 0.8308 (m-10) cc_final: 0.8041 (m-80) REVERT: CA 416 MET cc_start: 0.8039 (mtm) cc_final: 0.7685 (ttm) REVERT: CA 488 LEU cc_start: 0.8857 (mt) cc_final: 0.8634 (mt) REVERT: CA 501 LEU cc_start: 0.8847 (mm) cc_final: 0.8641 (mt) REVERT: CA 505 GLN cc_start: 0.8721 (pt0) cc_final: 0.8419 (pt0) REVERT: CA 518 VAL cc_start: 0.9262 (t) cc_final: 0.9009 (t) REVERT: CA 519 TYR cc_start: 0.8921 (p90) cc_final: 0.8125 (p90) REVERT: CA 527 HIS cc_start: 0.9298 (t-90) cc_final: 0.8966 (t-170) outliers start: 10 outliers final: 10 residues processed: 1661 average time/residue: 1.4803 time to fit residues: 4210.2237 Evaluate side-chains 1359 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1349 time to evaluate : 6.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 969 optimal weight: 20.0000 chunk 1021 optimal weight: 10.0000 chunk 931 optimal weight: 0.2980 chunk 993 optimal weight: 7.9990 chunk 1020 optimal weight: 5.9990 chunk 597 optimal weight: 0.0030 chunk 432 optimal weight: 20.0000 chunk 780 optimal weight: 30.0000 chunk 304 optimal weight: 40.0000 chunk 897 optimal weight: 5.9990 chunk 939 optimal weight: 30.0000 overall best weight: 4.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 201 HIS ** AD 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 38 HIS ** AK 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 57 HIS ** AP 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 87 HIS ** AV 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AV 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 75 ASN AW 121 HIS AW 132 ASN ** AY 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 41 GLN ** AY 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 60 ASN ** Ac 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 7 HIS ** BF 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 139 GLN ** BH 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 73 ASN ** BJ 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 116 HIS ** BP 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 101 GLN BQ 106 ASN ** BR 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 14 HIS ** BW 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BW 69 HIS ** BX 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 234 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 1.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.513 163075 Z= 0.301 Angle : 0.851 37.301 242863 Z= 0.420 Chirality : 0.042 0.397 30675 Planarity : 0.007 0.145 13938 Dihedral : 26.435 179.927 79709 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 31.78 Ramachandran Plot: Outliers : 2.36 % Allowed : 19.80 % Favored : 77.84 % Rotamer: Outliers : 0.22 % Allowed : 1.24 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.95 % Twisted Proline : 0.90 % Twisted General : 0.43 % 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: -4.17 (0.09), residues: 6565 helix: -1.06 (0.11), residues: 1921 sheet: -1.89 (0.17), residues: 828 loop : -4.16 (0.08), residues: 3816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRPAG 29 HIS 0.017 0.002 HISAS 64 PHE 0.049 0.003 PHEAK 51 TYR 0.050 0.002 TYRAW 99 ARG 0.017 0.001 ARGAK 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1640 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1628 time to evaluate : 6.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AC 120 MET cc_start: 0.3616 (tpt) cc_final: 0.3239 (tpt) REVERT: AC 217 THR cc_start: 0.6352 (m) cc_final: 0.6087 (m) REVERT: AC 218 MET cc_start: -0.2836 (ttp) cc_final: -0.3097 (ttp) REVERT: AD 52 ARG cc_start: 0.7668 (tpm170) cc_final: 0.7306 (tpp-160) REVERT: AD 79 VAL cc_start: 0.8988 (t) cc_final: 0.8684 (m) REVERT: AD 99 ASP cc_start: 0.8949 (p0) cc_final: 0.8515 (p0) REVERT: AD 101 GLU cc_start: 0.8268 (tp30) cc_final: 0.7844 (tm-30) REVERT: AD 115 GLN cc_start: 0.7866 (pp30) cc_final: 0.6926 (pp30) REVERT: AD 164 GLN cc_start: 0.8673 (tm-30) cc_final: 0.7862 (tm-30) REVERT: AD 166 GLN cc_start: 0.8433 (tt0) cc_final: 0.8210 (mt0) REVERT: AD 174 ILE cc_start: 0.8627 (mp) cc_final: 0.8367 (mp) REVERT: AD 176 ARG cc_start: 0.7796 (tpp-160) cc_final: 0.7468 (tpp80) REVERT: AD 177 LEU cc_start: 0.8321 (pt) cc_final: 0.8090 (pt) REVERT: AD 200 ASP cc_start: 0.8727 (p0) cc_final: 0.8439 (p0) REVERT: AD 217 ARG cc_start: 0.8486 (ptp-170) cc_final: 0.7874 (ptp-170) REVERT: AD 249 PRO cc_start: 0.8472 (Cg_exo) cc_final: 0.8179 (Cg_endo) REVERT: AD 268 ARG cc_start: 0.8027 (tmt170) cc_final: 0.6965 (tmt170) REVERT: AE 120 TRP cc_start: 0.7709 (p-90) cc_final: 0.7384 (p-90) REVERT: AE 127 ASP cc_start: 0.8460 (t0) cc_final: 0.8002 (t0) REVERT: AE 160 TYR cc_start: 0.7364 (m-80) cc_final: 0.6825 (m-80) REVERT: AE 168 MET cc_start: 0.8914 (mmp) cc_final: 0.7730 (mtp) REVERT: AE 185 LYS cc_start: 0.8146 (pttp) cc_final: 0.7749 (ptmm) REVERT: AF 53 THR cc_start: 0.6187 (m) cc_final: 0.5946 (m) REVERT: AF 125 LEU cc_start: 0.6628 (mt) cc_final: 0.6065 (mt) REVERT: AF 145 GLU cc_start: 0.9523 (mm-30) cc_final: 0.9029 (tm-30) REVERT: AF 155 LEU cc_start: 0.8879 (mm) cc_final: 0.8449 (mt) REVERT: AF 160 ASN cc_start: 0.9343 (t0) cc_final: 0.9067 (t0) REVERT: AF 169 ASN cc_start: 0.7643 (t0) cc_final: 0.7235 (t0) REVERT: AG 22 ARG cc_start: 0.8853 (tpp-160) cc_final: 0.8392 (ttp-110) REVERT: AG 148 MET cc_start: 0.0192 (ptt) cc_final: -0.0020 (ptt) REVERT: AG 155 MET cc_start: 0.8904 (mtt) cc_final: 0.8537 (mpp) REVERT: AH 67 LEU cc_start: 0.8080 (tp) cc_final: 0.7859 (tp) REVERT: AH 68 THR cc_start: 0.7551 (p) cc_final: 0.7286 (p) REVERT: AH 86 GLU cc_start: 0.8497 (pp20) cc_final: 0.8201 (tm-30) REVERT: AH 143 GLN cc_start: 0.8839 (tp40) cc_final: 0.8127 (tp40) REVERT: AH 163 TYR cc_start: 0.7808 (m-80) cc_final: 0.7339 (m-10) REVERT: AH 171 LEU cc_start: 0.9084 (mt) cc_final: 0.8853 (mt) REVERT: AH 172 LYS cc_start: 0.8921 (mppt) cc_final: 0.8546 (pttm) REVERT: AJ 125 ARG cc_start: 0.7567 (mpt180) cc_final: 0.7366 (mpt180) REVERT: AJ 126 MET cc_start: -0.0435 (mmm) cc_final: -0.0697 (mmm) REVERT: AK 43 THR cc_start: 0.8663 (t) cc_final: 0.8372 (p) REVERT: AK 84 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8446 (mmmt) REVERT: AK 106 MET cc_start: 0.8929 (mtt) cc_final: 0.8688 (mtp) REVERT: AK 119 ARG cc_start: 0.7807 (ptt180) cc_final: 0.7325 (ptm160) REVERT: AK 123 TYR cc_start: 0.8781 (m-80) cc_final: 0.8538 (m-80) REVERT: AK 126 PRO cc_start: 0.8322 (Cg_exo) cc_final: 0.7991 (Cg_endo) REVERT: AK 134 ARG cc_start: 0.8442 (mmp80) cc_final: 0.8039 (mmp-170) REVERT: AL 7 TYR cc_start: 0.9230 (m-10) cc_final: 0.9019 (m-10) REVERT: AL 31 LYS cc_start: 0.9209 (mttt) cc_final: 0.8774 (ttmt) REVERT: AL 108 GLU cc_start: 0.6767 (tp30) cc_final: 0.6402 (tp30) REVERT: AL 114 ILE cc_start: 0.9015 (mt) cc_final: 0.8762 (mt) REVERT: AN 54 MET cc_start: 0.8409 (mmt) cc_final: 0.8207 (mmm) REVERT: AN 74 TYR cc_start: 0.4604 (m-10) cc_final: 0.4110 (m-10) REVERT: AN 80 GLU cc_start: 0.8708 (pp20) cc_final: 0.8261 (pp20) REVERT: AN 83 MET cc_start: 0.7955 (pmm) cc_final: 0.7642 (pmm) REVERT: AN 103 MET cc_start: 0.5871 (mpp) cc_final: 0.5624 (mpp) REVERT: AN 113 GLN cc_start: 0.8214 (tt0) cc_final: 0.7321 (tm-30) REVERT: AN 115 MET cc_start: 0.9210 (mmm) cc_final: 0.8923 (mmt) REVERT: AN 133 ARG cc_start: 0.9120 (pmt170) cc_final: 0.8537 (mmm160) REVERT: AO 26 LYS cc_start: 0.9126 (mttm) cc_final: 0.8646 (mmtt) REVERT: AO 42 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8450 (pttt) REVERT: AO 54 LEU cc_start: 0.9696 (mp) cc_final: 0.9450 (tt) REVERT: AO 74 LYS cc_start: 0.9438 (mmtm) cc_final: 0.9141 (tptt) REVERT: AO 76 VAL cc_start: 0.8792 (t) cc_final: 0.8589 (t) REVERT: AO 78 LYS cc_start: 0.9288 (tptt) cc_final: 0.8429 (tptp) REVERT: AO 107 ASP cc_start: 0.8634 (p0) cc_final: 0.8402 (p0) REVERT: AO 113 LEU cc_start: 0.8134 (tp) cc_final: 0.7821 (tp) REVERT: AP 20 ARG cc_start: 0.8385 (mtt-85) cc_final: 0.5922 (mmt-90) REVERT: AQ 1 MET cc_start: 0.7276 (ppp) cc_final: 0.6867 (ppp) REVERT: AQ 70 VAL cc_start: 0.7605 (t) cc_final: 0.6202 (t) REVERT: AQ 75 ILE cc_start: 0.7768 (mt) cc_final: 0.7374 (mt) REVERT: AQ 76 PHE cc_start: 0.8664 (t80) cc_final: 0.8379 (t80) REVERT: AQ 82 LEU cc_start: 0.8975 (tt) cc_final: 0.8240 (tt) REVERT: AR 32 PHE cc_start: 0.7817 (m-10) cc_final: 0.7580 (m-10) REVERT: AR 65 ILE cc_start: 0.9499 (mt) cc_final: 0.9273 (mt) REVERT: AR 91 ASP cc_start: 0.7550 (m-30) cc_final: 0.6935 (m-30) REVERT: AS 5 VAL cc_start: 0.8622 (t) cc_final: 0.8077 (t) REVERT: AS 12 TYR cc_start: 0.8302 (t80) cc_final: 0.7777 (t80) REVERT: AS 22 VAL cc_start: 0.7880 (t) cc_final: 0.7217 (t) REVERT: AS 24 LYS cc_start: 0.8404 (mmmt) cc_final: 0.7819 (mptt) REVERT: AS 40 LEU cc_start: 0.8733 (tp) cc_final: 0.8008 (tp) REVERT: AS 51 VAL cc_start: 0.6688 (t) cc_final: 0.6291 (t) REVERT: AT 25 ARG cc_start: 0.8645 (tmt170) cc_final: 0.8413 (ttp80) REVERT: AT 29 LEU cc_start: 0.9381 (tp) cc_final: 0.9105 (tp) REVERT: AT 34 ASN cc_start: 0.9110 (m110) cc_final: 0.8790 (m110) REVERT: AT 37 ARG cc_start: 0.7975 (ttm170) cc_final: 0.7766 (ptm160) REVERT: AT 52 GLU cc_start: 0.8798 (mm-30) cc_final: 0.7971 (tt0) REVERT: AT 88 ARG cc_start: 0.7862 (mmp80) cc_final: 0.7653 (mmp80) REVERT: AT 97 LYS cc_start: 0.6968 (ttmt) cc_final: 0.6522 (tptm) REVERT: AU 5 TYR cc_start: 0.7847 (p90) cc_final: 0.7580 (p90) REVERT: AU 7 VAL cc_start: 0.8446 (p) cc_final: 0.8017 (m) REVERT: AU 8 ILE cc_start: 0.8464 (mm) cc_final: 0.7898 (mm) REVERT: AU 28 PHE cc_start: 0.8843 (m-80) cc_final: 0.8562 (m-80) REVERT: AU 33 LYS cc_start: 0.9130 (mppt) cc_final: 0.8848 (mppt) REVERT: AU 40 LYS cc_start: 0.9249 (mtmt) cc_final: 0.8987 (mmtt) REVERT: AU 64 LYS cc_start: 0.7693 (tttt) cc_final: 0.7348 (mttt) REVERT: AU 75 ASP cc_start: 0.8056 (m-30) cc_final: 0.7528 (m-30) REVERT: AV 11 ASP cc_start: 0.8884 (m-30) cc_final: 0.8604 (t0) REVERT: AV 67 LEU cc_start: 0.9019 (pt) cc_final: 0.8792 (pp) REVERT: AW 38 TYR cc_start: 0.7118 (m-10) cc_final: 0.6902 (m-80) REVERT: AW 75 ASN cc_start: 0.8326 (m-40) cc_final: 0.8007 (m-40) REVERT: AW 118 GLN cc_start: 0.8385 (pp30) cc_final: 0.8178 (pp30) REVERT: AX 1 MET cc_start: 0.0466 (mmm) cc_final: -0.0013 (mtt) REVERT: AX 17 GLN cc_start: 0.8969 (tp40) cc_final: 0.8568 (tp40) REVERT: AX 24 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7965 (mttt) REVERT: AX 36 ILE cc_start: 0.8866 (mt) cc_final: 0.8642 (mt) REVERT: AX 57 PHE cc_start: 0.8612 (m-10) cc_final: 0.8138 (m-10) REVERT: AY 15 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8473 (mt-10) REVERT: AY 32 PHE cc_start: 0.7306 (m-10) cc_final: 0.7069 (m-10) REVERT: AY 48 LEU cc_start: 0.8413 (pp) cc_final: 0.8107 (pp) REVERT: AY 52 ILE cc_start: 0.9204 (pt) cc_final: 0.8780 (pt) REVERT: AY 58 VAL cc_start: 0.9494 (t) cc_final: 0.9279 (m) REVERT: AZ 24 LYS cc_start: 0.7706 (tttm) cc_final: 0.7318 (tmtt) REVERT: AZ 37 LEU cc_start: 0.8981 (mt) cc_final: 0.8319 (tp) REVERT: AZ 49 LYS cc_start: 0.9039 (tppt) cc_final: 0.8500 (ttpt) REVERT: Aa 13 ARG cc_start: 0.7523 (tmm-80) cc_final: 0.7181 (tmm-80) REVERT: Aa 15 ILE cc_start: 0.7816 (mm) cc_final: 0.7418 (mm) REVERT: Aa 31 ILE cc_start: 0.7947 (tp) cc_final: 0.7565 (mm) REVERT: Aa 62 ARG cc_start: 0.8428 (mtt180) cc_final: 0.7686 (tpm170) REVERT: Ac 37 ARG cc_start: 0.8433 (mmt180) cc_final: 0.5298 (mmt90) REVERT: Ac 50 ARG cc_start: 0.8521 (ttt180) cc_final: 0.7930 (ttp-170) REVERT: Ad 32 LYS cc_start: 0.8998 (tttp) cc_final: 0.8797 (ttmt) REVERT: Ad 41 ARG cc_start: 0.9037 (ttp-110) cc_final: 0.8557 (mpt90) REVERT: Ad 42 LEU cc_start: 0.6337 (mt) cc_final: 0.5864 (mp) REVERT: Ad 47 ARG cc_start: 0.6994 (ptt180) cc_final: 0.6633 (ptm160) REVERT: Ae 1 MET cc_start: 0.7602 (tpp) cc_final: 0.6834 (tpp) REVERT: Ae 37 SER cc_start: 0.5520 (m) cc_final: 0.5119 (t) REVERT: Af 15 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8290 (mttt) REVERT: Af 17 ILE cc_start: 0.8771 (mt) cc_final: 0.8566 (mt) REVERT: Af 19 ARG cc_start: 0.7696 (ttm170) cc_final: 0.7194 (mtt-85) REVERT: Af 22 ARG cc_start: 0.7742 (mmm-85) cc_final: 0.6985 (mtp180) REVERT: Af 33 LYS cc_start: 0.7978 (tppt) cc_final: 0.7078 (tmtt) REVERT: Af 34 GLN cc_start: 0.8467 (mm-40) cc_final: 0.7862 (mm110) REVERT: Af 36 GLN cc_start: 0.6235 (tm-30) cc_final: 0.4768 (tm-30) REVERT: BF 25 ASN cc_start: 0.9187 (m110) cc_final: 0.8864 (m110) REVERT: BF 28 PHE cc_start: 0.7728 (t80) cc_final: 0.6963 (t80) REVERT: BF 48 MET cc_start: 0.7798 (mmt) cc_final: 0.7545 (mmt) REVERT: BF 63 MET cc_start: 0.8488 (mpp) cc_final: 0.7606 (ppp) REVERT: BF 92 TYR cc_start: 0.7523 (p90) cc_final: 0.7162 (p90) REVERT: BF 95 GLN cc_start: 0.8366 (mp10) cc_final: 0.8116 (mp10) REVERT: BF 176 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8339 (mt-10) REVERT: BG 136 GLN cc_start: 0.9339 (tt0) cc_final: 0.8779 (tm-30) REVERT: BG 142 MET cc_start: 0.9500 (tmm) cc_final: 0.9220 (tpt) REVERT: BG 190 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.7092 (tpm170) REVERT: BG 204 LEU cc_start: 0.8913 (mt) cc_final: 0.8664 (mp) REVERT: BH 33 MET cc_start: 0.8131 (mtt) cc_final: 0.7836 (mmm) REVERT: BH 53 ASP cc_start: 0.9428 (p0) cc_final: 0.9130 (t0) REVERT: BH 54 TYR cc_start: 0.8709 (t80) cc_final: 0.8098 (t80) REVERT: BH 70 ILE cc_start: 0.8713 (mt) cc_final: 0.8371 (mm) REVERT: BH 74 GLN cc_start: 0.9151 (mp10) cc_final: 0.8546 (mp10) REVERT: BH 75 PHE cc_start: 0.9225 (t80) cc_final: 0.8962 (t80) REVERT: BH 76 ARG cc_start: 0.9121 (ppt170) cc_final: 0.8801 (ttm-80) REVERT: BH 81 GLU cc_start: 0.9380 (tm-30) cc_final: 0.9167 (tm-30) REVERT: BH 102 ASP cc_start: 0.8185 (t70) cc_final: 0.7858 (t0) REVERT: BH 165 MET cc_start: 0.7900 (tpp) cc_final: 0.7491 (tpp) REVERT: BI 10 MET cc_start: 0.9522 (ppp) cc_final: 0.9311 (ppp) REVERT: BI 79 GLU cc_start: 0.8147 (pm20) cc_final: 0.7790 (pm20) REVERT: BI 111 GLU cc_start: 0.9204 (tt0) cc_final: 0.8700 (tp30) REVERT: BI 126 ARG cc_start: 0.8416 (ptp-110) cc_final: 0.7967 (mtm180) REVERT: BJ 11 ASN cc_start: 0.7940 (t0) cc_final: 0.7567 (t0) REVERT: BJ 33 TYR cc_start: 0.6415 (m-80) cc_final: 0.6012 (m-80) REVERT: BJ 60 PHE cc_start: 0.6686 (m-80) cc_final: 0.6452 (m-10) REVERT: BJ 61 LEU cc_start: 0.8800 (tp) cc_final: 0.8534 (tp) REVERT: BJ 62 TRP cc_start: 0.7517 (t60) cc_final: 0.6637 (t60) REVERT: BJ 67 MET cc_start: 0.7119 (pmm) cc_final: 0.6666 (pmm) REVERT: BJ 75 LEU cc_start: 0.9325 (mt) cc_final: 0.8926 (tp) REVERT: BJ 78 GLU cc_start: 0.9137 (tt0) cc_final: 0.8747 (mt-10) REVERT: BJ 92 LYS cc_start: 0.8889 (pttm) cc_final: 0.8346 (pttp) REVERT: BK 73 MET cc_start: 0.7421 (mmm) cc_final: 0.6753 (ttp) REVERT: BK 139 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8461 (tm-30) REVERT: BK 141 VAL cc_start: 0.8723 (t) cc_final: 0.8409 (t) REVERT: BK 149 ARG cc_start: 0.7519 (mmm160) cc_final: 0.7068 (tpt170) REVERT: BL 64 LYS cc_start: 0.7776 (tttt) cc_final: 0.7464 (tttt) REVERT: BL 78 GLN cc_start: 0.9072 (pm20) cc_final: 0.8549 (pm20) REVERT: BL 79 VAL cc_start: 0.9196 (t) cc_final: 0.8513 (t) REVERT: BL 82 HIS cc_start: 0.9390 (t-90) cc_final: 0.9020 (t-170) REVERT: BL 83 ILE cc_start: 0.8859 (tt) cc_final: 0.8658 (tt) REVERT: BL 111 ILE cc_start: 0.9549 (mp) cc_final: 0.9276 (tp) REVERT: BL 119 LEU cc_start: 0.8905 (mm) cc_final: 0.8663 (mp) REVERT: BL 132 GLU cc_start: 0.8474 (tt0) cc_final: 0.8021 (tm-30) REVERT: BL 133 LEU cc_start: 0.9230 (tp) cc_final: 0.8928 (tp) REVERT: BL 134 ILE cc_start: 0.9338 (mt) cc_final: 0.9084 (mt) REVERT: BM 18 PHE cc_start: 0.5417 (m-80) cc_final: 0.4355 (m-80) REVERT: BM 42 ARG cc_start: 0.5876 (mmp80) cc_final: 0.5179 (tpp-160) REVERT: BN 56 HIS cc_start: 0.5713 (m90) cc_final: 0.5356 (m90) REVERT: BO 11 LYS cc_start: 0.6934 (mptt) cc_final: 0.6564 (mptt) REVERT: BO 38 ASN cc_start: 0.8792 (m-40) cc_final: 0.8510 (t0) REVERT: BO 50 TYR cc_start: 0.7885 (m-80) cc_final: 0.7131 (m-80) REVERT: BO 123 LYS cc_start: 0.7702 (mmpt) cc_final: 0.7366 (mmmm) REVERT: BP 16 GLU cc_start: 0.8176 (mp0) cc_final: 0.7546 (mp0) REVERT: BP 59 ARG cc_start: 0.8854 (tpp-160) cc_final: 0.8482 (tpp80) REVERT: BR 37 PHE cc_start: 0.8230 (m-80) cc_final: 0.7955 (m-80) REVERT: BR 57 ARG cc_start: 0.8898 (ttt180) cc_final: 0.8448 (ttp-170) REVERT: BS 28 GLN cc_start: 0.8951 (mm110) cc_final: 0.8558 (mm110) REVERT: BS 37 ASN cc_start: 0.9071 (t0) cc_final: 0.8814 (m-40) REVERT: BS 43 LEU cc_start: 0.8122 (tp) cc_final: 0.7802 (mt) REVERT: BS 58 MET cc_start: 0.8599 (mtt) cc_final: 0.8083 (mtt) REVERT: BT 34 GLU cc_start: 0.8290 (pm20) cc_final: 0.7700 (pm20) REVERT: BT 36 ILE cc_start: 0.9292 (mm) cc_final: 0.8850 (mm) REVERT: BT 52 ASP cc_start: 0.8987 (t0) cc_final: 0.8721 (t0) REVERT: BT 54 GLU cc_start: 0.9160 (pt0) cc_final: 0.8619 (pp20) REVERT: BT 59 TRP cc_start: 0.9278 (m100) cc_final: 0.8351 (m100) REVERT: BT 62 VAL cc_start: 0.9132 (m) cc_final: 0.8849 (p) REVERT: BU 15 MET cc_start: 0.8645 (pmm) cc_final: 0.8272 (pmm) REVERT: BU 29 HIS cc_start: 0.9438 (t-90) cc_final: 0.9187 (t-90) REVERT: BU 32 TYR cc_start: 0.8848 (m-10) cc_final: 0.8549 (m-10) REVERT: BU 34 LYS cc_start: 0.9488 (tmmt) cc_final: 0.8855 (ttmt) REVERT: BU 49 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7924 (mm-30) REVERT: BU 59 ILE cc_start: 0.9402 (tp) cc_final: 0.9069 (tp) REVERT: BU 71 PHE cc_start: 0.8776 (m-80) cc_final: 0.8229 (m-80) REVERT: BV 39 VAL cc_start: 0.8741 (t) cc_final: 0.8496 (t) REVERT: BV 56 THR cc_start: 0.7975 (p) cc_final: 0.7690 (p) REVERT: BW 79 THR cc_start: 0.7638 (m) cc_final: 0.7328 (p) REVERT: BX 33 ILE cc_start: 0.8785 (pt) cc_final: 0.8440 (mt) REVERT: BX 104 LEU cc_start: 0.8830 (mt) cc_final: 0.8457 (pt) REVERT: CA 248 ASN cc_start: 0.8593 (t0) cc_final: 0.8023 (t0) REVERT: CA 293 ASN cc_start: 0.8668 (m-40) cc_final: 0.8381 (m-40) REVERT: CA 300 LEU cc_start: 0.7791 (mp) cc_final: 0.7393 (tt) REVERT: CA 309 MET cc_start: 0.8429 (mmt) cc_final: 0.8188 (mmp) REVERT: CA 324 LYS cc_start: 0.9028 (pttm) cc_final: 0.8524 (pttm) REVERT: CA 373 MET cc_start: 0.8948 (mmp) cc_final: 0.8716 (mmm) REVERT: CA 416 MET cc_start: 0.8271 (mtm) cc_final: 0.7796 (ttm) REVERT: CA 456 MET cc_start: 0.7195 (mtt) cc_final: 0.6791 (mpp) REVERT: CA 488 LEU cc_start: 0.8958 (mt) cc_final: 0.8738 (mt) REVERT: CA 501 LEU cc_start: 0.8827 (mm) cc_final: 0.8607 (mt) REVERT: CA 505 GLN cc_start: 0.8714 (pt0) cc_final: 0.8446 (pt0) REVERT: CA 518 VAL cc_start: 0.9200 (t) cc_final: 0.8990 (t) REVERT: CA 519 TYR cc_start: 0.8933 (p90) cc_final: 0.8094 (p90) outliers start: 12 outliers final: 11 residues processed: 1636 average time/residue: 1.3981 time to fit residues: 3880.6500 Evaluate side-chains 1354 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1343 time to evaluate : 6.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 989 optimal weight: 40.0000 chunk 652 optimal weight: 8.9990 chunk 1050 optimal weight: 20.0000 chunk 641 optimal weight: 9.9990 chunk 498 optimal weight: 1.9990 chunk 730 optimal weight: 20.0000 chunk 1101 optimal weight: 2.9990 chunk 1014 optimal weight: 6.9990 chunk 877 optimal weight: 4.9990 chunk 91 optimal weight: 40.0000 chunk 677 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 87 ASN ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 201 HIS ** AE 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 29 GLN ** AK 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AP 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AS 87 HIS ** AV 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AW 73 GLN AW 75 ASN AW 121 HIS AY 33 GLN ** AY 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 7 HIS ** Ae 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 63 ASN ** BG 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 139 GLN ** BH 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 73 ASN ** BJ 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 122 HIS BO 78 GLN ** BP 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BR 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BS 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 69 HIS BX 18 GLN ** BX 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CA 108 GLN ** CA 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 234 ASN CA 527 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 1.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.505 163075 Z= 0.325 Angle : 0.885 37.340 242863 Z= 0.437 Chirality : 0.043 0.688 30675 Planarity : 0.007 0.130 13938 Dihedral : 26.447 179.968 79709 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 34.70 Ramachandran Plot: Outliers : 2.39 % Allowed : 20.29 % Favored : 77.32 % Rotamer: Outliers : 0.22 % Allowed : 0.87 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.97 % Twisted Proline : 1.80 % Twisted General : 0.40 % 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: -4.22 (0.09), residues: 6565 helix: -1.20 (0.11), residues: 1918 sheet: -1.85 (0.18), residues: 819 loop : -4.14 (0.08), residues: 3828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRPAG 29 HIS 0.018 0.002 HISAS 64 PHE 0.050 0.003 PHEAd 18 TYR 0.049 0.003 TYRAW 99 ARG 0.024 0.001 ARGAY 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13130 Ramachandran restraints generated. 6565 Oldfield, 0 Emsley, 6565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1626 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1614 time to evaluate : 6.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AC 217 THR cc_start: 0.6086 (m) cc_final: 0.5859 (m) REVERT: AC 218 MET cc_start: -0.2841 (ttp) cc_final: -0.3114 (ttp) REVERT: AD 32 SER cc_start: 0.7938 (t) cc_final: 0.7720 (t) REVERT: AD 52 ARG cc_start: 0.7762 (tpm170) cc_final: 0.7454 (tpp-160) REVERT: AD 87 ASN cc_start: 0.9142 (m-40) cc_final: 0.8900 (m110) REVERT: AD 99 ASP cc_start: 0.8871 (p0) cc_final: 0.8450 (p0) REVERT: AD 101 GLU cc_start: 0.8273 (tp30) cc_final: 0.7472 (tm-30) REVERT: AD 115 GLN cc_start: 0.7849 (pp30) cc_final: 0.6853 (pp30) REVERT: AD 166 GLN cc_start: 0.8430 (tt0) cc_final: 0.8228 (tt0) REVERT: AD 217 ARG cc_start: 0.8465 (ptp-170) cc_final: 0.7780 (ptp-170) REVERT: AD 268 ARG cc_start: 0.7991 (tmt170) cc_final: 0.6999 (tmt170) REVERT: AE 103 ASP cc_start: 0.7953 (p0) cc_final: 0.7725 (p0) REVERT: AE 117 MET cc_start: 0.6528 (mtt) cc_final: 0.6083 (mpp) REVERT: AE 120 TRP cc_start: 0.7656 (p-90) cc_final: 0.7343 (p-90) REVERT: AE 127 ASP cc_start: 0.8423 (t0) cc_final: 0.7959 (t0) REVERT: AE 160 TYR cc_start: 0.7550 (m-80) cc_final: 0.6867 (m-80) REVERT: AE 168 MET cc_start: 0.8974 (mmp) cc_final: 0.7785 (mtp) REVERT: AE 185 LYS cc_start: 0.8151 (pttp) cc_final: 0.7465 (ptmm) REVERT: AF 7 TYR cc_start: 0.7962 (m-10) cc_final: 0.7515 (m-80) REVERT: AF 53 THR cc_start: 0.6152 (m) cc_final: 0.5912 (m) REVERT: AF 125 LEU cc_start: 0.6971 (mt) cc_final: 0.6422 (mt) REVERT: AF 145 GLU cc_start: 0.9538 (mm-30) cc_final: 0.9094 (tm-30) REVERT: AF 160 ASN cc_start: 0.9325 (t0) cc_final: 0.9014 (t0) REVERT: AG 155 MET cc_start: 0.8929 (mtt) cc_final: 0.8618 (mpp) REVERT: AH 68 THR cc_start: 0.7713 (p) cc_final: 0.7428 (p) REVERT: AH 86 GLU cc_start: 0.8591 (pp20) cc_final: 0.8189 (tm-30) REVERT: AH 130 ARG cc_start: 0.8905 (tpt90) cc_final: 0.8589 (tpp-160) REVERT: AH 132 ARG cc_start: 0.8094 (ptt-90) cc_final: 0.7679 (ptt-90) REVERT: AH 136 ILE cc_start: 0.7373 (tp) cc_final: 0.6825 (tp) REVERT: AH 143 GLN cc_start: 0.8857 (tp40) cc_final: 0.8279 (tp40) REVERT: AH 163 TYR cc_start: 0.8168 (m-80) cc_final: 0.7792 (m-10) REVERT: AH 171 LEU cc_start: 0.9291 (mt) cc_final: 0.9041 (mt) REVERT: AH 172 LYS cc_start: 0.8950 (mppt) cc_final: 0.8607 (pttm) REVERT: AK 23 LEU cc_start: 0.8883 (tp) cc_final: 0.8645 (tt) REVERT: AK 50 ASP cc_start: 0.7170 (m-30) cc_final: 0.5546 (m-30) REVERT: AK 84 LYS cc_start: 0.8882 (mtmm) cc_final: 0.8424 (mmmt) REVERT: AK 106 MET cc_start: 0.8899 (mtt) cc_final: 0.8670 (mtp) REVERT: AK 126 PRO cc_start: 0.8351 (Cg_exo) cc_final: 0.7995 (Cg_endo) REVERT: AK 134 ARG cc_start: 0.8487 (mmp80) cc_final: 0.8110 (mmp-170) REVERT: AL 9 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8048 (mp0) REVERT: AL 31 LYS cc_start: 0.9291 (mttt) cc_final: 0.8776 (tttt) REVERT: AL 32 TYR cc_start: 0.8122 (m-80) cc_final: 0.7913 (m-80) REVERT: AL 37 ASP cc_start: 0.7718 (m-30) cc_final: 0.7224 (m-30) REVERT: AL 108 GLU cc_start: 0.7045 (tp30) cc_final: 0.6700 (tp30) REVERT: AL 114 ILE cc_start: 0.9143 (mt) cc_final: 0.8895 (mt) REVERT: AM 61 ARG cc_start: 0.6397 (tpt170) cc_final: 0.6154 (tpt170) REVERT: AM 95 VAL cc_start: 0.8436 (t) cc_final: 0.8223 (t) REVERT: AN 54 MET cc_start: 0.8505 (mmt) cc_final: 0.8283 (mmm) REVERT: AN 68 ILE cc_start: 0.8812 (mm) cc_final: 0.8572 (mm) REVERT: AN 77 LYS cc_start: 0.8288 (ptmm) cc_final: 0.8055 (tttt) REVERT: AN 80 GLU cc_start: 0.8751 (pp20) cc_final: 0.8313 (pp20) REVERT: AN 83 MET cc_start: 0.8061 (pmm) cc_final: 0.7703 (pmm) REVERT: AN 103 MET cc_start: 0.6060 (mpp) cc_final: 0.5808 (mpp) REVERT: AN 113 GLN cc_start: 0.8341 (tt0) cc_final: 0.7319 (tm-30) REVERT: AN 115 MET cc_start: 0.9213 (mmm) cc_final: 0.8955 (mmt) REVERT: AO 40 LYS cc_start: 0.8305 (mptt) cc_final: 0.8022 (mptt) REVERT: AO 42 LYS cc_start: 0.8861 (mtmm) cc_final: 0.8246 (pttt) REVERT: AO 54 LEU cc_start: 0.9706 (mp) cc_final: 0.9430 (tt) REVERT: AO 74 LYS cc_start: 0.9482 (mmtm) cc_final: 0.9118 (tptt) REVERT: AO 78 LYS cc_start: 0.9296 (tptt) cc_final: 0.8642 (tptp) REVERT: AO 113 LEU cc_start: 0.8262 (tp) cc_final: 0.7975 (tp) REVERT: AP 95 HIS cc_start: 0.7537 (p-80) cc_final: 0.6921 (p-80) REVERT: AP 101 LEU cc_start: 0.6958 (mt) cc_final: 0.6648 (mt) REVERT: AQ 1 MET cc_start: 0.7077 (ppp) cc_final: 0.6725 (ppp) REVERT: AQ 11 GLU cc_start: 0.9454 (mp0) cc_final: 0.8506 (tt0) REVERT: AQ 39 ARG cc_start: 0.8426 (mpp80) cc_final: 0.8076 (mpp80) REVERT: AQ 53 ARG cc_start: 0.8502 (tpm170) cc_final: 0.7278 (tpm170) REVERT: AQ 70 VAL cc_start: 0.7699 (t) cc_final: 0.6203 (t) REVERT: AQ 75 ILE cc_start: 0.7721 (mt) cc_final: 0.7265 (mt) REVERT: AR 32 PHE cc_start: 0.7893 (m-10) cc_final: 0.7670 (m-10) REVERT: AR 91 ASP cc_start: 0.7349 (m-30) cc_final: 0.6905 (m-30) REVERT: AS 5 VAL cc_start: 0.8662 (t) cc_final: 0.8155 (t) REVERT: AS 12 TYR cc_start: 0.8197 (t80) cc_final: 0.7161 (t80) REVERT: AS 40 LEU cc_start: 0.8660 (tp) cc_final: 0.8044 (tp) REVERT: AS 51 VAL cc_start: 0.7205 (t) cc_final: 0.6720 (t) REVERT: AT 25 ARG cc_start: 0.8698 (tmt170) cc_final: 0.8392 (ttp80) REVERT: AT 29 LEU cc_start: 0.9490 (tp) cc_final: 0.9110 (tp) REVERT: AT 34 ASN cc_start: 0.9162 (m110) cc_final: 0.8829 (m110) REVERT: AT 37 ARG cc_start: 0.8112 (ttm170) cc_final: 0.7500 (ptm160) REVERT: AT 38 TYR cc_start: 0.8207 (m-10) cc_final: 0.7593 (m-10) REVERT: AT 40 ASN cc_start: 0.8642 (p0) cc_final: 0.8230 (t0) REVERT: AT 52 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8239 (tt0) REVERT: AT 82 LEU cc_start: 0.8244 (tt) cc_final: 0.7901 (tt) REVERT: AT 83 LYS cc_start: 0.7286 (mttt) cc_final: 0.7078 (mttt) REVERT: AT 96 ILE cc_start: 0.8521 (mp) cc_final: 0.8017 (mp) REVERT: AT 97 LYS cc_start: 0.7387 (ttmt) cc_final: 0.7156 (tptp) REVERT: AU 27 THR cc_start: 0.8311 (p) cc_final: 0.8082 (p) REVERT: AU 28 PHE cc_start: 0.8864 (m-80) cc_final: 0.8496 (m-10) REVERT: AU 38 GLU cc_start: 0.9288 (tm-30) cc_final: 0.9003 (tm-30) REVERT: AU 40 LYS cc_start: 0.9226 (mtmt) cc_final: 0.8975 (ttmm) REVERT: AU 64 LYS cc_start: 0.7690 (tttt) cc_final: 0.7307 (mttt) REVERT: AU 75 ASP cc_start: 0.8138 (m-30) cc_final: 0.7629 (m-30) REVERT: AV 11 ASP cc_start: 0.8934 (m-30) cc_final: 0.8625 (t0) REVERT: AW 38 TYR cc_start: 0.7273 (m-10) cc_final: 0.7067 (m-80) REVERT: AW 75 ASN cc_start: 0.8334 (m110) cc_final: 0.7966 (m110) REVERT: AW 84 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6612 (pt0) REVERT: AW 118 GLN cc_start: 0.8518 (pp30) cc_final: 0.8131 (pp30) REVERT: AW 119 GLU cc_start: 0.8976 (tp30) cc_final: 0.8288 (tm-30) REVERT: AW 157 LEU cc_start: 0.8294 (tt) cc_final: 0.8032 (tt) REVERT: AX 1 MET cc_start: 0.0744 (mmm) cc_final: 0.0254 (mtt) REVERT: AX 17 GLN cc_start: 0.8969 (tp40) cc_final: 0.8558 (tp40) REVERT: AX 24 LYS cc_start: 0.8379 (mtmm) cc_final: 0.8020 (mttt) REVERT: AX 36 ILE cc_start: 0.8889 (mt) cc_final: 0.8411 (mt) REVERT: AX 57 PHE cc_start: 0.8646 (m-10) cc_final: 0.8113 (m-10) REVERT: AY 15 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8581 (mt-10) REVERT: AY 28 MET cc_start: 0.5446 (mtt) cc_final: 0.4512 (mtt) REVERT: AY 32 PHE cc_start: 0.7638 (m-10) cc_final: 0.7343 (m-80) REVERT: AY 48 LEU cc_start: 0.8409 (pp) cc_final: 0.8042 (pp) REVERT: AY 58 VAL cc_start: 0.9355 (t) cc_final: 0.9086 (m) REVERT: AY 61 GLU cc_start: 0.8842 (pp20) cc_final: 0.8619 (pp20) REVERT: AZ 24 LYS cc_start: 0.7925 (tttm) cc_final: 0.7441 (tmtt) REVERT: AZ 26 LEU cc_start: 0.9199 (tp) cc_final: 0.8867 (tp) REVERT: AZ 37 LEU cc_start: 0.8932 (mt) cc_final: 0.8289 (tp) REVERT: AZ 49 LYS cc_start: 0.9055 (tppt) cc_final: 0.8545 (ttpt) REVERT: Aa 15 ILE cc_start: 0.8026 (mm) cc_final: 0.7716 (mm) REVERT: Aa 31 ILE cc_start: 0.7852 (tp) cc_final: 0.7524 (mm) REVERT: Aa 62 ARG cc_start: 0.8461 (mtt180) cc_final: 0.7671 (tpm170) REVERT: Ac 37 ARG cc_start: 0.8417 (mmt180) cc_final: 0.5191 (mmt90) REVERT: Ac 50 ARG cc_start: 0.8563 (ttt180) cc_final: 0.8326 (ttt180) REVERT: Ad 11 LYS cc_start: 0.9232 (tptt) cc_final: 0.8310 (tptm) REVERT: Ad 22 MET cc_start: 0.9272 (mmm) cc_final: 0.9045 (mmm) REVERT: Ad 41 ARG cc_start: 0.9025 (ttp-110) cc_final: 0.8471 (mpt90) REVERT: Ad 42 LEU cc_start: 0.6092 (mt) cc_final: 0.5711 (mp) REVERT: Ad 47 ARG cc_start: 0.7279 (ptt180) cc_final: 0.6696 (ptm160) REVERT: Ae 1 MET cc_start: 0.7585 (tpp) cc_final: 0.7000 (tpp) REVERT: Ae 16 ILE cc_start: 0.8847 (mt) cc_final: 0.8204 (pt) REVERT: Ae 37 SER cc_start: 0.5641 (m) cc_final: 0.5084 (t) REVERT: Af 12 ASP cc_start: 0.9254 (t0) cc_final: 0.9029 (t70) REVERT: Af 15 LYS cc_start: 0.8817 (mmmm) cc_final: 0.8428 (mttt) REVERT: Af 17 ILE cc_start: 0.8726 (mt) cc_final: 0.8483 (mt) REVERT: Af 19 ARG cc_start: 0.7739 (ttm170) cc_final: 0.7255 (mtt-85) REVERT: Af 22 ARG cc_start: 0.7847 (mmm-85) cc_final: 0.7115 (mtp180) REVERT: Af 33 LYS cc_start: 0.8107 (tppt) cc_final: 0.7158 (tmtt) REVERT: Af 34 GLN cc_start: 0.8544 (mm-40) cc_final: 0.7891 (mm110) REVERT: Af 36 GLN cc_start: 0.6625 (tm-30) cc_final: 0.5629 (tm-30) REVERT: BF 25 ASN cc_start: 0.9285 (m110) cc_final: 0.9000 (m110) REVERT: BF 28 PHE cc_start: 0.7664 (t80) cc_final: 0.6931 (t80) REVERT: BF 60 ASP cc_start: 0.8660 (t70) cc_final: 0.8417 (p0) REVERT: BF 76 GLN cc_start: 0.9003 (mt0) cc_final: 0.8718 (pp30) REVERT: BF 83 MET cc_start: 0.8751 (mtt) cc_final: 0.8537 (mtp) REVERT: BF 92 TYR cc_start: 0.7622 (p90) cc_final: 0.7145 (p90) REVERT: BF 95 GLN cc_start: 0.8459 (mp10) cc_final: 0.8185 (mp10) REVERT: BF 148 TYR cc_start: 0.7216 (p90) cc_final: 0.6888 (p90) REVERT: BF 176 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8324 (tt0) REVERT: BG 139 GLN cc_start: 0.9613 (tp-100) cc_final: 0.9295 (tm-30) REVERT: BG 184 TYR cc_start: 0.7812 (t80) cc_final: 0.7607 (t80) REVERT: BG 190 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7015 (tpm170) REVERT: BG 204 LEU cc_start: 0.8967 (mt) cc_final: 0.8727 (mp) REVERT: BH 33 MET cc_start: 0.8332 (mtt) cc_final: 0.8058 (mmm) REVERT: BH 53 ASP cc_start: 0.9447 (p0) cc_final: 0.9183 (t0) REVERT: BH 54 TYR cc_start: 0.8716 (t80) cc_final: 0.7763 (t80) REVERT: BH 70 ILE cc_start: 0.8786 (mt) cc_final: 0.8431 (mm) REVERT: BH 74 GLN cc_start: 0.9209 (mp10) cc_final: 0.8690 (mp10) REVERT: BH 75 PHE cc_start: 0.9155 (t80) cc_final: 0.8849 (t80) REVERT: BH 76 ARG cc_start: 0.9227 (ppt170) cc_final: 0.8954 (ptp-110) REVERT: BH 80 GLU cc_start: 0.8811 (pp20) cc_final: 0.8539 (pp20) REVERT: BH 146 ILE cc_start: 0.8378 (mp) cc_final: 0.7897 (mp) REVERT: BH 165 MET cc_start: 0.7982 (tpp) cc_final: 0.7233 (tpp) REVERT: BH 182 LYS cc_start: 0.8157 (tptt) cc_final: 0.7897 (mmmm) REVERT: BH 190 ASP cc_start: 0.7616 (m-30) cc_final: 0.7396 (m-30) REVERT: BI 26 PHE cc_start: 0.8567 (p90) cc_final: 0.8361 (p90) REVERT: BI 73 ASN cc_start: 0.9637 (t0) cc_final: 0.9344 (p0) REVERT: BI 126 ARG cc_start: 0.8317 (ptp-110) cc_final: 0.7975 (mtm180) REVERT: BJ 11 ASN cc_start: 0.8238 (t0) cc_final: 0.7996 (t0) REVERT: BJ 61 LEU cc_start: 0.8519 (tp) cc_final: 0.8134 (tp) REVERT: BJ 67 MET cc_start: 0.7408 (pmm) cc_final: 0.7127 (pmm) REVERT: BJ 75 LEU cc_start: 0.9363 (mt) cc_final: 0.8703 (tp) REVERT: BJ 78 GLU cc_start: 0.9137 (tt0) cc_final: 0.8551 (pp20) REVERT: BJ 92 LYS cc_start: 0.8944 (pttm) cc_final: 0.8387 (ptmm) REVERT: BK 57 GLU cc_start: 0.8270 (pt0) cc_final: 0.7702 (tm-30) REVERT: BK 73 MET cc_start: 0.7258 (mmm) cc_final: 0.6543 (ttp) REVERT: BK 74 GLU cc_start: 0.7303 (pm20) cc_final: 0.7032 (pm20) REVERT: BK 90 GLU cc_start: 0.8076 (pp20) cc_final: 0.7524 (pp20) REVERT: BL 78 GLN cc_start: 0.9120 (pm20) cc_final: 0.8671 (pm20) REVERT: BL 82 HIS cc_start: 0.9345 (t-90) cc_final: 0.9021 (t-170) REVERT: BL 83 ILE cc_start: 0.8861 (tt) cc_final: 0.8656 (tt) REVERT: BL 111 ILE cc_start: 0.9480 (mp) cc_final: 0.9279 (pt) REVERT: BL 119 LEU cc_start: 0.8951 (mm) cc_final: 0.8670 (mp) REVERT: BL 132 GLU cc_start: 0.8432 (tt0) cc_final: 0.8037 (tm-30) REVERT: BL 133 LEU cc_start: 0.9222 (tp) cc_final: 0.8891 (tp) REVERT: BM 18 PHE cc_start: 0.5534 (m-80) cc_final: 0.4576 (m-80) REVERT: BM 42 ARG cc_start: 0.6000 (mmp80) cc_final: 0.5257 (tpp-160) REVERT: BN 56 HIS cc_start: 0.5714 (m90) cc_final: 0.5327 (m90) REVERT: BO 11 LYS cc_start: 0.7218 (mptt) cc_final: 0.6717 (mptt) REVERT: BO 18 ARG cc_start: 0.7466 (mmt180) cc_final: 0.7254 (mmm-85) REVERT: BO 38 ASN cc_start: 0.8714 (m-40) cc_final: 0.8448 (t0) REVERT: BO 59 TYR cc_start: 0.7987 (t80) cc_final: 0.7438 (t80) REVERT: BP 16 GLU cc_start: 0.8386 (mp0) cc_final: 0.7724 (mp0) REVERT: BP 53 ARG cc_start: 0.7061 (mmt90) cc_final: 0.6456 (mtt-85) REVERT: BP 93 LEU cc_start: 0.8818 (pt) cc_final: 0.8593 (pt) REVERT: BP 106 ASP cc_start: 0.8334 (t0) cc_final: 0.8126 (t0) REVERT: BR 37 PHE cc_start: 0.8313 (m-80) cc_final: 0.7995 (m-80) REVERT: BS 27 VAL cc_start: 0.9128 (t) cc_final: 0.8675 (t) REVERT: BS 43 LEU cc_start: 0.8225 (tp) cc_final: 0.7854 (mt) REVERT: BS 59 MET cc_start: 0.9130 (tpt) cc_final: 0.8420 (tpt) REVERT: BT 34 GLU cc_start: 0.8397 (pm20) cc_final: 0.8132 (pm20) REVERT: BT 36 ILE cc_start: 0.9354 (mm) cc_final: 0.8743 (mp) REVERT: BT 52 ASP cc_start: 0.9027 (t0) cc_final: 0.8746 (t0) REVERT: BT 54 GLU cc_start: 0.9170 (pt0) cc_final: 0.8638 (pp20) REVERT: BU 15 MET cc_start: 0.8749 (pmm) cc_final: 0.8516 (pmm) REVERT: BU 26 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8419 (mm-40) REVERT: BU 29 HIS cc_start: 0.9585 (t-90) cc_final: 0.9234 (t-90) REVERT: BU 34 LYS cc_start: 0.9436 (tmmt) cc_final: 0.8935 (tttt) REVERT: BU 49 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8003 (mm-30) REVERT: BU 59 ILE cc_start: 0.9384 (tp) cc_final: 0.9175 (tp) REVERT: BU 71 PHE cc_start: 0.9102 (m-80) cc_final: 0.8446 (m-80) REVERT: BW 79 THR cc_start: 0.7553 (m) cc_final: 0.7169 (p) REVERT: BX 33 ILE cc_start: 0.8894 (pt) cc_final: 0.8675 (mt) REVERT: BX 39 LYS cc_start: 0.7678 (tttt) cc_final: 0.7313 (tttt) REVERT: BX 64 ASP cc_start: 0.8049 (m-30) cc_final: 0.7287 (m-30) REVERT: CA 89 MET cc_start: 0.8310 (mtp) cc_final: 0.7785 (mtp) REVERT: CA 183 MET cc_start: 0.6992 (mpp) cc_final: 0.6651 (mpp) REVERT: CA 207 MET cc_start: 0.8210 (tpt) cc_final: 0.7802 (tpt) REVERT: CA 221 ILE cc_start: 0.8518 (mp) cc_final: 0.8223 (mp) REVERT: CA 248 ASN cc_start: 0.8634 (t0) cc_final: 0.8138 (t0) REVERT: CA 349 GLU cc_start: 0.7884 (tp30) cc_final: 0.7315 (tm-30) REVERT: CA 373 MET cc_start: 0.8959 (mmp) cc_final: 0.8711 (mmm) REVERT: CA 416 MET cc_start: 0.8197 (mtm) cc_final: 0.7764 (ttm) REVERT: CA 488 LEU cc_start: 0.8989 (mt) cc_final: 0.8778 (mt) REVERT: CA 505 GLN cc_start: 0.8953 (pt0) cc_final: 0.8663 (pt0) REVERT: CA 519 TYR cc_start: 0.8983 (p90) cc_final: 0.8073 (p90) REVERT: CA 527 HIS cc_start: 0.9258 (t-90) cc_final: 0.8917 (t-170) outliers start: 12 outliers final: 10 residues processed: 1622 average time/residue: 1.3987 time to fit residues: 3852.8127 Evaluate side-chains 1343 residues out of total 5532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1333 time to evaluate : 6.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1106 random chunks: chunk 538 optimal weight: 6.9990 chunk 696 optimal weight: 20.0000 chunk 934 optimal weight: 30.0000 chunk 268 optimal weight: 20.0000 chunk 809 optimal weight: 30.0000 chunk 129 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 878 optimal weight: 0.9990 chunk 367 optimal weight: 9.9990 chunk 902 optimal weight: 3.9990 chunk 111 optimal weight: 40.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AC 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 143 HIS ** AD 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AS 87 HIS ** AU 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AV 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AW 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AW 121 HIS ** AY 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AY 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 7 HIS ** BF 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 73 ASN ** BJ 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BK 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 122 HIS ** BP 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 101 GLN ** BR 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 14 HIS ** BW 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BW 69 HIS ** BX 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CA 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 234 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.086322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.069088 restraints weight = 714885.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.071276 restraints weight = 284362.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.072542 restraints weight = 149909.385| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 1.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.504 163075 Z= 0.345 Angle : 0.892 37.153 242863 Z= 0.440 Chirality : 0.044 0.561 30675 Planarity : 0.007 0.125 13938 Dihedral : 26.486 179.960 79709 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 36.51 Ramachandran Plot: Outliers : 2.28 % Allowed : 20.55 % Favored : 77.17 % Rotamer: Outliers : 0.22 % Allowed : 0.69 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.95 % Twisted Proline : 1.20 % Twisted General : 0.45 % 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: -4.19 (0.09), residues: 6565 helix: -1.13 (0.11), residues: 1917 sheet: -1.88 (0.18), residues: 780 loop : -4.12 (0.08), residues: 3868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRPBJ 62 HIS 0.020 0.002 HISAS 64 PHE 0.051 0.003 PHEAd 18 TYR 0.049 0.003 TYRAW 99 ARG 0.017 0.001 ARGAD 176 =============================================================================== Job complete usr+sys time: 56336.40 seconds wall clock time: 978 minutes 23.49 seconds (58703.49 seconds total)